Genetics

@book{fisher1930the23,
    author = "Fisher, R. A",
    title = "The Genetical Theory of Natural Selection",
    year = "1930",
    publisher = "Oxford, Claredon Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Fisher, R. A., 1930, The Genetical Theory of Natural Selection: Oxford, Claredon Press.}"
}

Page 108, last line of text, for P/P″ read P′/P″. Page 120, last line, for δ v read δ y. Page 123, line 10, for 4Nn read 4Nu. Page 125, line 1, for q read q. Page 126, line 12, for q read q. Page 135, line 5 from bottom, for y4Nsq read e4Nsq. Page 141, lines 8

@article{doi101093genetics16297,
    author = "Wright, Sewall",
    title = "EVOLUTION IN MENDELIAN POPULATIONS",
    year = "1931",
    journal = "Genetics",
    abstract = "Page 108, last line of text, for P/P″ read P′/P″. Page 120, last line, for δ v read δ y. Page 123, line 10, for 4Nn read 4Nu. Page 125, line 1, for q read q. Page 126, line 12, for q read q. Page 135, line 5 from bottom, for y4Nsq read e4Nsq. Page 141, lines 8",
    url = "https://doi.org/10.1093/genetics/16.2.97",
    doi = "10.1093/genetics/16.2.97",
    openalex = "W2171463101",
    references = "doi101017s0080456800012163, doi101017s0305004100015644, doi101086279846, doi101086279872, doi101086280193, doi101086280260, doi101111j160152231928tb02483x, doi101126science2870649, doi1023072965538, doi105962bhltitle27468"
}

@misc{wright1931evolution47,
    author = "Wright, S",
    title = "Evolution in Mendelian populations",
    year = "1931",
    howpublished = "Genetics, v. 16, p. 97- 159",
    note = "talkorigins\_source = {true}; raw\_reference = {Wright, S., 1931, Evolution in Mendelian populations: Genetics, v. 16, p. 97- 159.}"
}

@book{dobzhansky1937genetics16,
    author = "Dobzhansky, T",
    title = "Genetics and the Origin of Species [1st ed.]",
    year = "1937",
    publisher = "New York, Columbia University Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Dobzhansky, T., 1937, Genetics and the Origin of Species [1st ed.]: New York, Columbia University Press.}"
}

@article{doi1023071435536,
    author = "Schmidt, Karl P. and Dobzhansky, Theodosius",
    title = "Genetics and the Origin of Species",
    year = "1938",
    journal = "Copeia",
    url = "https://doi.org/10.2307/1435536",
    doi = "10.2307/1435536",
    openalex = "W4230640447"
}

@misc{dobzhansky1947evolutionary18,
    author = "Dobzhansky, T. and Spassky, B",
    title = "Evolutionary changes in laboratory cultures of D. pseudoobscura",
    year = "1947",
    howpublished = "Evolution, v. 1, p. 191-216",
    note = "talkorigins\_source = {true}; raw\_reference = {Dobzhansky, T., and Spassky, B., 1947, Evolutionary changes in laboratory cultures of D. pseudoobscura: Evolution, v. 1, p. 191-216.}"
}

@book{chaney1949evolutionary10,
    author = "Chaney, R. W",
    title = "Evolutionary trends in the angiosperms, in Jepsen, G. L., Simpson, G. G., and Mayr, E., eds., Genetics, Paleontology and Evolution",
    year = "1949",
    publisher = "Princeton, New Jersey, Princeton University Press, p. 190-201; 474 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Chaney, R. W., 1949, Evolutionary trends in the angiosperms, in Jepsen, G. L., Simpson, G. G., and Mayr, E., eds., Genetics, Paleontology and Evolution: Princeton, New Jersey, Princeton University Press, p. 190-201; 474 p.}"
}

@misc{darlington1949the13,
    author = "Darlington, C. D. and Mather, K",
    title = "The Elements of Genetics",
    year = "1949",
    howpublished = "London, Allen and Unwin, 446 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Darlington, C. D., and Mather, K., 1949, The Elements of Genetics: London, Allen and Unwin, 446 p.}"
}

@book{dobzhansky1951genetics17,
    author = "Dobzhansky, T",
    title = "Genetics and the Origin of Species [3rd ed.]",
    year = "1951",
    publisher = "New York, Columbia University Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Dobzhansky, T., 1951, Genetics and the Origin of Species [3rd ed.]: New York, Columbia University Press.}"
}

Genetics and the Origin of Species Get access Genetics and the Origin of Species. (3rd Edition). Dobzhansky Th.. 364 pp. Columbia University Press, 2960 Broadway, New York 27, N. Y.$5.00. AIBS Bulletin, Volume 2, Issue 2, April 1952, Page 14, https://doi.org/10.1093/aibsbulletin/2.2.14-b Published: 01 April 1952

@article{doi101093aibsbulletin2214b,
    author = "Dobzhansky, Theodosius",
    title = "Genetics and the Origin of Species",
    year = "1952",
    journal = "AIBS Bulletin",
    abstract = "Genetics and the Origin of Species Get access Genetics and the Origin of Species. (3rd Edition). Dobzhansky Th.. 364 pp. Columbia University Press, 2960 Broadway, New York 27, N. Y.$5.00. AIBS Bulletin, Volume 2, Issue 2, April 1952, Page 14, https://doi.org/10.1093/aibsbulletin/2.2.14-b Published: 01 April 1952",
    url = "https://doi.org/10.1093/aibsbulletin/2.2.14-b",
    doi = "10.1093/aibsbulletin/2.2.14-b",
    openalex = "W1599192329"
}

@article{doi1023071439305,
    author = "Dobzhansky, Theodosius",
    title = "Genetics and the Origin of Species",
    year = "1952",
    journal = "Copeia",
    url = "https://doi.org/10.2307/1439305",
    doi = "10.2307/1439305",
    openalex = "W4297899606"
}

@misc{mayr1954change38,
    author = "Mayr, E",
    title = "Change of Genetic Environment and Evolution, in Huxley, J., Hardy, A. C., and Ford, E. B., eds., Evolution as a Process",
    year = "1954",
    howpublished = "London, Allen and Unwin, p. 157-180",
    note = "talkorigins\_source = {true}; raw\_reference = {Mayr, E., 1954, Change of Genetic Environment and Evolution, in Huxley, J., Hardy, A. C., and Ford, E. B., eds., Evolution as a Process: London, Allen and Unwin, p. 157-180.}"
}

@book{dobzhansky1955evolution19,
    author = "Dobzhansky, T",
    title = "Evolution, Genetics and Man",
    year = "1955",
    publisher = "New York, John Wiley \& Sons, 398 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Dobzhansky, T., 1955, Evolution, Genetics and Man: New York, John Wiley \& Sons, 398 p.}"
}

@incollection{doi101016b9781483227344500176,
    author = "Zuckerkandl, Emile and Pauling, Linus",
    title = "Evolutionary Divergence and Convergence in Proteins",
    year = "1965",
    booktitle = "Elsevier eBooks",
    url = "https://doi.org/10.1016/b978-1-4832-2734-4.50017-6",
    doi = "10.1016/b978-1-4832-2734-4.50017-6",
    openalex = "W1534406401",
    references = "doi1043249781315081083"
}

@misc{ayala1968genotype2,
    author = "Ayala, F. J",
    title = "Genotype, environment, and population numbers",
    year = "1968",
    howpublished = "Science, v. 162, p. 1453-1459",
    note = "talkorigins\_source = {true}; raw\_reference = {Ayala, F. J., 1968, Genotype, environment, and population numbers: Science, v. 162, p. 1453-1459.}"
}

@article{crick1968the12,
    author = "Crick, F. H. C",
    title = "The origin of the genetic code",
    year = "1968",
    journal = "Journal of Molecular Biology, v. 38, p. 367-379",
    note = "talkorigins\_source = {true}; raw\_reference = {Crick, F. H. C., 1968, The origin of the genetic code: Journal of Molecular Biology, v. 38, p. 367-379.}"
}

@article{doi101038217624a0,
    author = "KIMURA, MOTOO",
    title = "Evolutionary Rate at the Molecular Level",
    year = "1968",
    journal = "Nature",
    url = "https://doi.org/10.1038/217624a0",
    doi = "10.1038/217624a0",
    openalex = "W1993351732",
    references = "doi101001jama196603100230164053, doi101007bf02984069, doi101016b9781483227344500176, doi101093genetics16297, doi101093genetics494725, doi101093genetics542577, doi101093genetics542595, doi101098rspb19660032, doi101126science147365368, openalexw2171582839"
}

@book{wright1968197848,
    author = "Wright, S",
    title = "-1978, Evolution and the Genetics of Populations. A Treatise in Four Volumes",
    year = "1968",
    publisher = "Chicago, Illinois, University of Chicago Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Wright, S., 1968-1978, Evolution and the Genetics of Populations. A Treatise in Four Volumes: Chicago, Illinois, University of Chicago Press.}"
}

@book{dobzhanshy1970genetics15,
    author = "Dobzhanshy, T",
    title = "Genetics of the Evolutionary Process",
    year = "1970",
    publisher = "New York, Columbia University Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Dobzhanshy, T., 1970, Genetics of the Evolutionary Process: New York, Columbia University Press.}"
}

@book{doi1010079783642866593,
    author = "Ohno, Susumu",
    title = "Evolution by Gene Duplication",
    year = "1970",
    url = "https://doi.org/10.1007/978-3-642-86659-3",
    doi = "10.1007/978-3-642-86659-3",
    openalex = "W2135123683"
}

@misc{klotz1970genes32,
    author = "Klotz, J. W",
    title = "Genes, Genesis, and Evolution",
    year = "1970",
    howpublished = "St. Louis, Mo., Concordia Publishing Co",
    note = "talkorigins\_source = {true}; raw\_reference = {Klotz, J. W., 1970, Genes, Genesis, and Evolution: St. Louis, Mo., Concordia Publishing Co.}"
}

@misc{anderson1971genetic1,
    author = "Anderson, W. W",
    title = "Genetic equilibrium and population growth under density- regulated selection",
    year = "1971",
    howpublished = "American Naturalist, v. 105, p. 489-498",
    note = "talkorigins\_source = {true}; raw\_reference = {Anderson, W. W., 1971, Genetic equilibrium and population growth under density- regulated selection: American Naturalist, v. 105, p. 489-498.}"
}

@book{bajema1971natural5,
    author = "Bajema, C. J",
    title = "Natural Selection in Human Populations, the Measurement of Ongoing Genetic Evolution in Contemporary Societies",
    year = "1971",
    publisher = "New York, Wiley, 406 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Bajema, C. J., 1971, Natural Selection in Human Populations, the Measurement of Ongoing Genetic Evolution in Contemporary Societies: New York, Wiley, 406 p.}"
}

@article{kohne1972evolution33,
    author = "Kohne, D. E. and Chiscon, J. A. and Hoyer, B. H",
    title = "Evolution of primate DNA sequences",
    year = "1972",
    journal = "Journal of Human Evolution, v. 1, p. 627-644",
    note = "talkorigins\_source = {true}; raw\_reference = {Kohne, D. E., Chiscon, J. A., and Hoyer, B. H., 1972, Evolution of primate DNA sequences: Journal of Human Evolution, v. 1, p. 627-644.}"
}

@article{gottlieb1973genetic28,
    author = "Gottlieb, L. D",
    title = "Genetic differentiation, sympatric speciation, and the origin of a diploid species of Stephanomeria",
    year = "1973",
    journal = "American Journal of Botany, v. 60, p. 545-553",
    note = "talkorigins\_source = {true}; raw\_reference = {Gottlieb, L. D., 1973, Genetic differentiation, sympatric speciation, and the origin of a diploid species of Stephanomeria: American Journal of Botany, v. 60, p. 545-553.}"
}

@article{openalexw2145250129,
    author = "Valen, Leigh Van",
    title = "A NEW EVOLUTIONARY LAW.",
    year = "1973",
    journal = "Medical Entomology and Zoology",
    openalex = "W2145250129"
}

@article{berry1975ecological7,
    author = "Berry, R. J. and Jakobson, M. E",
    title = "Ecological genetics of an island population of the house mouse (Mus musculus)",
    year = "1975",
    journal = "Journal of Zoology, v. 175, p. 532-540",
    note = "talkorigins\_source = {true}; raw\_reference = {Berry, R. J., and Jakobson, M. E., 1975, Ecological genetics of an island population of the house mouse (Mus musculus): Journal of Zoology, v. 175, p. 532-540.}"
}

@article{doi101111j155856461975tb00851x,
    author = "Felsenstein, Joseph",
    title = "THE GENETIC BASIS OF EVOLUTIONARY CHANGE",
    year = "1975",
    journal = "Evolution",
    url = "https://doi.org/10.1111/j.1558-5646.1975.tb00851.x",
    doi = "10.1111/j.1558-5646.1975.tb00851.x",
    openalex = "W1547248981"
}

@article{doi1023072407274,
    author = "Felsenstein, Joseph and Lewontin, Richard C",
    title = "The Genetic Basis of Evolutionary Change.",
    year = "1975",
    journal = "Evolution",
    url = "https://doi.org/10.2307/2407274",
    doi = "10.2307/2407274",
    openalex = "W4301156742"
}

@misc{valentine1975genetic43,
    author = "Valentine, J. W. and Campbell, C. A",
    title = "Genetic Regulation and the Fossil Record",
    year = "1975",
    howpublished = "American Scientist, v. 63, p. 673",
    note = "talkorigins\_source = {true}; raw\_reference = {Valentine, J. W., and Campbell, C. A., 1975, Genetic Regulation and the Fossil Record: American Scientist, v. 63, p. 673.}"
}

@book{dawkins1976the14,
    author = "Dawkins, R",
    title = "The Selfish Gene",
    year = "1976",
    publisher = "New York, Oxford University Press, 224 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Dawkins, R., 1976, The Selfish Gene: New York, Oxford University Press, 224 p.}"
}

@misc{winchester1976heredity45,
    author = "Winchester, A. M",
    title = "Heredity, Evolution and Humankind",
    year = "1976",
    howpublished = "St. Paul, Minn., West Publishing Co",
    note = "talkorigins\_source = {true}; raw\_reference = {Winchester, A. M., 1976, Heredity, Evolution and Humankind: St. Paul, Minn., West Publishing Co.}"
}

@misc{ayala1977the3,
    author = "Ayala, F. J",
    title = "The Genetic Structure of Populations, in Dobzhansky, T., Ayala, F. J., Stebbins, G. L., and Valentine, J. W., eds., Evolution",
    year = "1977",
    howpublished = "San Francisco, California, W.H. Freeman \& Co., p. 20-56",
    note = "talkorigins\_source = {true}; raw\_reference = {Ayala, F. J., 1977, The Genetic Structure of Populations, in Dobzhansky, T., Ayala, F. J., Stebbins, G. L., and Valentine, J. W., eds., Evolution: San Francisco, California, W.H. Freeman \& Co., p. 20-56.}"
}

@misc{ayala1977the4,
    author = "Ayala, F. J",
    title = "The Origin of Heredity Variation, in Dobzhansky, T., Ayala, F. J., Stebbins, G. L., and Valentine, J. W., eds., Evolution",
    year = "1977",
    howpublished = "San Francisco, California, W.H. Freeman \& Co., p. 57-94",
    note = "talkorigins\_source = {true}; raw\_reference = {Ayala, F. J., 1977, The Origin of Heredity Variation, in Dobzhansky, T., Ayala, F. J., Stebbins, G. L., and Valentine, J. W., eds., Evolution: San Francisco, California, W.H. Freeman \& Co., p. 57-94.}"
}

@misc{berry1977inheritance6,
    author = "Berry, R. J",
    title = "Inheritance and Natural History",
    year = "1977",
    howpublished = "London, Collins",
    note = "talkorigins\_source = {true}; raw\_reference = {Berry, R. J., 1977, Inheritance and Natural History: London, Collins.}"
}

@misc{hartl1977our29,
    author = "Hartl, D. L",
    title = "Our Uncertain Heritage, Genetics and Human Diversity",
    year = "1977",
    howpublished = "Philadelphia, Pa., J.B. Lippincott Co",
    note = "talkorigins\_source = {true}; raw\_reference = {Hartl, D. L., 1977, Our Uncertain Heritage, Genetics and Human Diversity: Philadelphia, Pa., J.B. Lippincott Co.}"
}

@misc{kimura1977causes31,
    author = "Kimura, M",
    title = "Causes of Evolution and Polymorphism at the Molecular Level, in Kimura, M., ed., Molecular Evolution and Polymorphism",
    year = "1977",
    howpublished = "Mishima, Japan, National Institute of Genetics, p. 1-28",
    note = "talkorigins\_source = {true}; raw\_reference = {Kimura, M., 1977, Causes of Evolution and Polymorphism at the Molecular Level, in Kimura, M., ed., Molecular Evolution and Polymorphism: Mishima, Japan, National Institute of Genetics, p. 1-28.}"
}

@misc{winchester1977genetics46,
    author = "Winchester, A. M",
    title = "Genetics [5th ed.]",
    year = "1977",
    howpublished = "Boston, Mass., Houghton Mifflin Co",
    note = "talkorigins\_source = {true}; raw\_reference = {Winchester, A. M., 1977, Genetics [5th ed.]: Boston, Mass., Houghton Mifflin Co.}"
}

Wiley, E. O. (Division of Fishes, Museum of Natural History, University of Kansas, Lawrence, KS 66045). 1978. Syst. Zool. 27:17–26.—The concept of species (as taxa) adopted by an investigator will influence his perception of the processes by which species originate. The concept adopted should have as universal applicability as current knowledge permits. Simpson's definition of a species is modified to state: a species is a lineage of ancestral descendant populations which maintains its identity from other such lineages and which has its own evolutionary tendencies and historical fate. This definition is defended as that which has widest applicability given current knowledge of evolutionary processes. Four corollaries are deduced and discussed relative to other species concepts: (1) all organisms, past and present, belong to some evolutionary species; (2) reproductive isolation must be effective enough to permit maintenance of identity from other contemporary lineages; (3) morphological distinctiveness is not necessary; and (4) no presumed (hypothesized) single lineage may be subdivided into a series of ancestral-descendant “species.” The application of the evolutionary species concept to allopatric demes and to asexual species is discussed and it is concluded that the lack of evolutionary divergence forms the basis for grouping such populations into single species. It is suggested that some ecological species definitions lead to under-estimations of the rate of extinction due to interspecific competition because their logical framework excludes unsuccessful species from being species. Finally, the implications of accepting an evolutionary species concept to the field of phylogeny reconstruction are discussed.

@article{doi1023072412809,
    author = "Wiley, E. O.",
    title = "The Evolutionary Species Concept Reconsidered",
    year = "1978",
    journal = "Systematic Zoology",
    abstract = "Wiley, E. O. (Division of Fishes, Museum of Natural History, University of Kansas, Lawrence, KS 66045). 1978. Syst. Zool. 27:17–26.—The concept of species (as taxa) adopted by an investigator will influence his perception of the processes by which species originate. The concept adopted should have as universal applicability as current knowledge permits. Simpson's definition of a species is modified to state: a species is a lineage of ancestral descendant populations which maintains its identity from other such lineages and which has its own evolutionary tendencies and historical fate. This definition is defended as that which has widest applicability given current knowledge of evolutionary processes. Four corollaries are deduced and discussed relative to other species concepts: (1) all organisms, past and present, belong to some evolutionary species; (2) reproductive isolation must be effective enough to permit maintenance of identity from other contemporary lineages; (3) morphological distinctiveness is not necessary; and (4) no presumed (hypothesized) single lineage may be subdivided into a series of ancestral-descendant “species.” The application of the evolutionary species concept to allopatric demes and to asexual species is discussed and it is concluded that the lack of evolutionary divergence forms the basis for grouping such populations into single species. It is suggested that some ecological species definitions lead to under-estimations of the rate of extinction due to interspecific competition because their logical framework excludes unsuccessful species from being species. Finally, the implications of accepting an evolutionary species concept to the field of phylogeny reconstruction are discussed.",
    url = "https://doi.org/10.2307/2412809",
    doi = "10.2307/2412809",
    openalex = "W2003879785"
}

@misc{powers1978biochemical39,
    author = "Powers, D. A. and Place, A. R",
    title = "Biochemical genetics of Fundulus heteroclitus (L.). 1. Temporal and spatial variation in gene frequencies of Ldh-B, Mdh-A, Gpi-B and Pgm-A",
    year = "1978",
    howpublished = "Biochemical Genetics, v. 16, p. 593-607",
    note = "talkorigins\_source = {true}; raw\_reference = {Powers, D. A., and Place, A. R., 1978, Biochemical genetics of Fundulus heteroclitus (L.). 1. Temporal and spatial variation in gene frequencies of Ldh-B, Mdh-A, Gpi-B and Pgm-A: Biochemical Genetics, v. 16, p. 593-607.}"
}

@phdthesis{kollar1980tooth34,
    author = "Kollar, E. J. and Fisher, C",
    title = "Tooth induction on chick epithelium",
    year = "1980",
    publisher = "expression of quiescent genes for enamel synthesis: Science, v. 207, p. 993-995",
    note = "talkorigins\_source = {true}; raw\_reference = {Kollar, E. J., and Fisher, C., 1980, Tooth induction on chick epithelium: expression of quiescent genes for enamel synthesis: Science, v. 207, p. 993-995.}"
}

@book{wilson1981genes44,
    author = "Wilson, E. O. and Lumden, C",
    title = "Genes, Mind, and Culture",
    year = "1981",
    publisher = "The Evolutionary Process: Cambridge, Mass., Harvard University Press, 248 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Wilson, E. O., and Lumden, C., 1981, Genes, Mind, and Culture: The Evolutionary Process: Cambridge, Mass., Harvard University Press, 248 p.}"
}

@misc{crick1982life11,
    author = "Crick, F",
    title = "Life Itself",
    year = "1982",
    howpublished = "Its Origin and Nature: New York, W.W. Norton, 192 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Crick, F., 1982, Life Itself: Its Origin and Nature: New York, W.W. Norton, 192 p.}"
}

Journal Article An Evolutionary Theory of Economic Change Get access An Evolutionary Theory of Economic Change. By Richard R. Nelson and Sidney G. Winter. (Cambridge, Massachusetts & London: Harvard University Press, 1982. Pp. xi +437. £17.50.) Brian J. Loasby Brian J. Loasby University of Stirling Search for other works by this author on: Oxford Academic Google Scholar The Economic Journal, Volume 93, Issue 371, 1 September 1983, Pages 652–654, https://doi.org/10.2307/2232409 Published: 01 September 1983

@article{doi1023072232409,
    author = "Loasby, Brian J. and Nelson, Richard R. and Winter, Sidney G.",
    title = "An Evolutionary Theory of Economic Change.",
    year = "1983",
    journal = "The Economic Journal",
    abstract = "Journal Article An Evolutionary Theory of Economic Change Get access An Evolutionary Theory of Economic Change. By Richard R. Nelson and Sidney G. Winter. (Cambridge, Massachusetts \& London: Harvard University Press, 1982. Pp. xi +437. £17.50.) Brian J. Loasby Brian J. Loasby University of Stirling Search for other works by this author on: Oxford Academic Google Scholar The Economic Journal, Volume 93, Issue 371, 1 September 1983, Pages 652–654, https://doi.org/10.2307/2232409 Published: 01 September 1983",
    url = "https://doi.org/10.2307/2232409",
    doi = "10.2307/2232409",
    openalex = "W2137358449"
}

@article{doi1023074581,
    author = "Ormond, Rupert and Krebs, J. R. and Davies, Nigel",
    title = "Behavioural Ecology: An Evolutionary Approach",
    year = "1983",
    journal = "Journal of Animal Ecology",
    url = "https://doi.org/10.2307/4581",
    doi = "10.2307/4581",
    openalex = "W2315288864"
}

Journal Article Mitochondrial DNA and two perspectives on evolutionary genetics Get access ALLAN C. WILSON, ALLAN C. WILSON 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar REBECCA L. CANN, REBECCA L. CANN 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A2Howard Hughes Medical Institute, U426, University of California, San Francisco, California 94143, U.S.A Search for other works by this author on: Oxford Academic Google Scholar STEVEN M. CARR, STEVEN M. CARR 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A3Wildlife Genetics Laboraiory, Department of Wildlge and Fisheries Sciences, Texas A & M University, College Station, Texas 77843, U.S.A Search for other works by this author on: Oxford Academic Google Scholar MATTHEW GEORGE, MATTHEW GEORGE 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A4Department of Biochemistry, Howard University, Washington, DC 20059, U.S.A Search for other works by this author on: Oxford Academic Google Scholar ULF B. GYLLENSTEN, ULF B. GYLLENSTEN 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A5Department of Clinical Genetics, Karolinska Hospital, Box 60500, S-104 01 Stockholm, Sweden Search for other works by this author on: Oxford Academic Google Scholar KATHLEEN M. HELM-BYCHOWSKI, KATHLEEN M. HELM-BYCHOWSKI 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar RUSSELL G. HIGUCHI, RUSSELL G. HIGUCHI 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar STEPHEN R. PALUMBI, STEPHEN R. PALUMBI 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A6Department of Zoology, University of Hawaii, Honolulu, Hawaii 96822, U.S.A Search for other works by this author on: Oxford Academic Google Scholar ELLEN M. PRAGER, ELLEN M. PRAGER 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar RICHARD D. SAGE, RICHARD D. SAGE 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A7Museum of Vertebrate Zoology, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar... Show more MARK STONEKING MARK STONEKING 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar Biological Journal of the Linnean Society, Volume 26, Issue 4, December 1985, Pages 375–400, https://doi.org/10.1111/j.1095-8312.1985.tb02048.x Published: 28 June 2008 Article history Accepted: 01 July 1985 Published: 28 June 2008

@article{doi101111j109583121985tb02048x,
    author = "Wilson, Allan C. and Cann, Rebecca L. and Carr, Steven M. and George, Matthew and GYLLENSTEN, ULF B. and Helm‐Bychowski, Kathleen and Higuchi, Russell and Palumbi, Stephen R. and Prager, Ellen M. and Sage, Richard D. and Stoneking, Mark",
    title = "Mitochondrial DNA and two perspectives on evolutionary genetics",
    year = "1985",
    journal = "Biological Journal of the Linnean Society",
    abstract = "Journal Article Mitochondrial DNA and two perspectives on evolutionary genetics Get access ALLAN C. WILSON, ALLAN C. WILSON 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar REBECCA L. CANN, REBECCA L. CANN 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A2Howard Hughes Medical Institute, U426, University of California, San Francisco, California 94143, U.S.A Search for other works by this author on: Oxford Academic Google Scholar STEVEN M. CARR, STEVEN M. CARR 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A3Wildlife Genetics Laboraiory, Department of Wildlge and Fisheries Sciences, Texas A \& M University, College Station, Texas 77843, U.S.A Search for other works by this author on: Oxford Academic Google Scholar MATTHEW GEORGE, MATTHEW GEORGE 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A4Department of Biochemistry, Howard University, Washington, DC 20059, U.S.A Search for other works by this author on: Oxford Academic Google Scholar ULF B. GYLLENSTEN, ULF B. GYLLENSTEN 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A5Department of Clinical Genetics, Karolinska Hospital, Box 60500, S-104 01 Stockholm, Sweden Search for other works by this author on: Oxford Academic Google Scholar KATHLEEN M. HELM-BYCHOWSKI, KATHLEEN M. HELM-BYCHOWSKI 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar RUSSELL G. HIGUCHI, RUSSELL G. HIGUCHI 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar STEPHEN R. PALUMBI, STEPHEN R. PALUMBI 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A6Department of Zoology, University of Hawaii, Honolulu, Hawaii 96822, U.S.A Search for other works by this author on: Oxford Academic Google Scholar ELLEN M. PRAGER, ELLEN M. PRAGER 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar RICHARD D. SAGE, RICHARD D. SAGE 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A7Museum of Vertebrate Zoology, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar... Show more MARK STONEKING MARK STONEKING 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar Biological Journal of the Linnean Society, Volume 26, Issue 4, December 1985, Pages 375–400, https://doi.org/10.1111/j.1095-8312.1985.tb02048.x Published: 28 June 2008 Article history Accepted: 01 July 1985 Published: 28 June 2008",
    url = "https://doi.org/10.1111/j.1095-8312.1985.tb02048.x",
    doi = "10.1111/j.1095-8312.1985.tb02048.x",
    openalex = "W2065697254",
    references = "doi101038202147a0, doi101073pnas504672, doi101073pnas581142, doi101111j155856461983tb05533x, doi101126science15838051200, doi1023071438156, doi1023072407274, doi107312simp93764, openalexw788933220, sarich1967immunological"
}

The amounts of inbreeding depression upon selfing and of heterosis upon outcrossing determine the strength of selection on the selfing rate in a population when this evolves polygenically by small steps. Genetic models are constructed which allow inbreeding depression to change with the mean selfing rate in a population by incorporating both mutation to recessive and partially dominant lethal and sublethal alleles at many loci and mutation in quantitative characters under stabilizing selection. The models help to explain observations of high inbreeding depression (> 50%) upon selfing in primarily outcrossing populations, as well as considerable heterosis upon outcrossing in primarily selfing populations. Predominant selfing and predominant outcrossing are found to be alternative stable states of the mating system in most plant populations. Which of these stable states a species approaches depends on the history of its population structure and the magnitude of effect of genes influencing the selfing rate.

@article{doi101111j155856461985tb04077x,
    author = "Lande, Russell and Schemske, Douglas W.",
    title = "THE EVOLUTION OF SELF‐FERTILIZATION AND INBREEDING DEPRESSION IN PLANTS. I. GENETIC MODELS",
    year = "1985",
    journal = "Evolution",
    abstract = "The amounts of inbreeding depression upon selfing and of heterosis upon outcrossing determine the strength of selection on the selfing rate in a population when this evolves polygenically by small steps. Genetic models are constructed which allow inbreeding depression to change with the mean selfing rate in a population by incorporating both mutation to recessive and partially dominant lethal and sublethal alleles at many loci and mutation in quantitative characters under stabilizing selection. The models help to explain observations of high inbreeding depression (> 50\%) upon selfing in primarily outcrossing populations, as well as considerable heterosis upon outcrossing in primarily selfing populations. Predominant selfing and predominant outcrossing are found to be alternative stable states of the mating system in most plant populations. Which of these stable states a species approaches depends on the history of its population structure and the magnitude of effect of genes influencing the selfing rate.",
    url = "https://doi.org/10.1111/j.1558-5646.1985.tb04077.x",
    doi = "10.1111/j.1558-5646.1985.tb04077.x",
    openalex = "W2316973238",
    references = "doi101017s0016672300016037, doi101111j155856461983tb00236x, doi1023072407274"
}

@misc{britten1986rates8,
    author = "Britten, R. J",
    title = "Rates of DNA sequence evolution differ between taxonomic groups",
    year = "1986",
    howpublished = "Science, v. 231, p. 1393-1398",
    note = "talkorigins\_source = {true}; raw\_reference = {Britten, R. J., 1986, Rates of DNA sequence evolution differ between taxonomic groups: Science, v. 231, p. 1393-1398.}"
}

Culture and the evolutionary process Culture and the evolutionary process. Robert Boyd, Peter J. Richerson(ed.), 1985. The University of Chicago Press, Chicago viii + 331 pages. $29.95 Marcy F. Lawton Marcy F. Lawton Search for other works by this author on: Oxford Academic Google Scholar The Condor, Volume 88, Issue 1, 1 February 1986, Pages 123–124, https://doi.org/10.2307/1367778 Published: 01 February 1986

@article{doi1023071367778,
    author = "Griesemer, James R. and Boyd, Robert and Richerson, Peter J.",
    title = "Culture and the Evolutionary Process",
    year = "1986",
    journal = "Ornithological Applications",
    abstract = "Culture and the evolutionary process Culture and the evolutionary process. Robert Boyd, Peter J. Richerson(ed.), 1985. The University of Chicago Press, Chicago viii + 331 pages. $29.95 Marcy F. Lawton Marcy F. Lawton Search for other works by this author on: Oxford Academic Google Scholar The Condor, Volume 88, Issue 1, 1 February 1986, Pages 123–124, https://doi.org/10.2307/1367778 Published: 01 February 1986",
    url = "https://doi.org/10.2307/1367778",
    doi = "10.2307/1367778",
    openalex = "W1811781384"
}

@article{ghiselin1986we25,
    author = "Ghiselin, M. T",
    title = "We Are All Contraptions",
    year = "1986",
    journal = "New York Times Book Review, p. 18-19",
    note = "talkorigins\_source = {true}; raw\_reference = {Ghiselin, M. T., 1986, We Are All Contraptions: New York Times Book Review, p. 18-19.}"
}

@misc{gilbert1986the26,
    author = "Gilbert, W",
    title = "The RNA world",
    year = "1986",
    howpublished = "Nature, v. 319, p. 619",
    note = "talkorigins\_source = {true}; raw\_reference = {Gilbert, W., 1986, The RNA world: Nature, v. 319, p. 619.}"
}

@misc{max1986plagiarized37,
    author = "Max, E. E",
    title = "Plagiarized Errors and Molecular Genetics",
    year = "1986",
    howpublished = "Another Argument in the Evolution-Creation Controversy: Creation/Evolution, v. 19, p. 34-46",
    note = "talkorigins\_source = {true}; raw\_reference = {Max, E. E., 1986, Plagiarized Errors and Molecular Genetics: Another Argument in the Evolution-Creation Controversy: Creation/Evolution, v. 19, p. 34-46.}"
}

@misc{cann1987mitochondrial9,
    author = "Cann, R. L. and Stoncking, M. and Wilson, A. C",
    title = "Mitochondrial DNA and human evolution",
    year = "1987",
    howpublished = "Nature, v. 325, p. 31-36",
    note = "talkorigins\_source = {true}; raw\_reference = {Cann, R. L., Stoncking, M., and Wilson, A. C., 1987, Mitochondrial DNA and human evolution: Nature, v. 325, p. 31-36.}"
}

There is abundant geographic variation in both morphology and gene frequency in most species. The extent of geographic variation results from a balance of forces tending to produce local genetic differentiation and forces tending to produce genetic homogeneity. Mutation, genetic drift due to finite population size, and natural selection favoring adaptations to local environmental conditions will all lead to the genetic differentiation of local populations, and the movement of gametes, individuals, and even entire populations--collectively called gene flow--will oppose that differentiation. Gene flow may either constrain evolution by preventing adaptation to local conditions or promote evolution by spreading new genes and combinations of genes throughout a species' range. Several methods are available for estimating the amount of gene flow. Direct methods monitor ongoing gene flow, and indirect methods use spatial distributions of gene frequencies to infer past gene flow. Applications of these methods show that species differ widely in the gene flow that they experience. Of particular interest are those species for which direct methods indicate little current gene flow but indirect methods indicate much higher levels of gene flow in the recent past. Such species probably have undergone large-scale demographic changes relatively frequently.

@article{doi101126science3576198,
    author = "Slatkin, Montgomery",
    title = "Gene Flow and the Geographic Structure of Natural Populations",
    year = "1987",
    journal = "Science",
    abstract = "There is abundant geographic variation in both morphology and gene frequency in most species. The extent of geographic variation results from a balance of forces tending to produce local genetic differentiation and forces tending to produce genetic homogeneity. Mutation, genetic drift due to finite population size, and natural selection favoring adaptations to local environmental conditions will all lead to the genetic differentiation of local populations, and the movement of gametes, individuals, and even entire populations--collectively called gene flow--will oppose that differentiation. Gene flow may either constrain evolution by preventing adaptation to local conditions or promote evolution by spreading new genes and combinations of genes throughout a species' range. Several methods are available for estimating the amount of gene flow. Direct methods monitor ongoing gene flow, and indirect methods use spatial distributions of gene frequencies to infer past gene flow. Applications of these methods show that species differ widely in the gene flow that they experience. Of particular interest are those species for which direct methods indicate little current gene flow but indirect methods indicate much higher levels of gene flow in the recent past. Such species probably have undergone large-scale demographic changes relatively frequently.",
    url = "https://doi.org/10.1126/science.3576198",
    doi = "10.1126/science.3576198",
    openalex = "W2066362596",
    references = "doi1010079783642686351, doi1010160040580977900454, doi1010382011145a0, doi101086410450, doi101093genetics16297, doi101098rspb19830075, doi101111j146918091949tb02451x, doi101111j155856461981tb04864x, doi101111j155856461984tb05657x, doi101111j155856461985tb04079x, doi101146annureves16110185002141, doi101722611310, doi104159harvard9780674865327, doi105962bhltitle27468, openalexw1593551567, openalexw1606400913"
}

(Uploaded by Plazi for the Bat Literature Project) No abstract provided.

@article{doi101146annureves18110187001321,
    author = "Charlesworth, Deborah and Charlesworth, Brian",
    title = "INBREEDING DEPRESSION AND ITS EVOLUTIONARY CONSEQUENCES",
    year = "1987",
    journal = "Annual Review of Ecology and Systematics",
    abstract = "(Uploaded by Plazi for the Bat Literature Project) No abstract provided.",
    url = "https://doi.org/10.1146/annurev.es.18.110187.001321",
    doi = "10.1146/annurev.es.18.110187.001321",
    openalex = "W2167243456",
    references = "doi101017s0305004100015644, doi101073pnas4211855, doi101111j155856461975tb00851x, doi105962bhltitle122451, doi107312steb94536, openalexw2062594085"
}

@book{doi107312nei92038,
    author = "Nei, Masatoshi",
    title = "Molecular Evolutionary Genetics",
    year = "1987",
    booktitle = "Columbia University Press eBooks",
    url = "https://doi.org/10.7312/nei-92038",
    doi = "10.7312/nei-92038",
    openalex = "W93588716"
}

@book{dulbecco1987the20,
    author = "Dulbecco, R",
    title = "The Design of Life",
    year = "1987",
    publisher = "New Haven, Connecticut, Yale University Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Dulbecco, R., 1987, The Design of Life: New Haven, Connecticut, Yale University Press.}"
}

@article{doi101016016953478890033x,
    author = "Hewitt, Godfrey M.",
    title = "Hybrid zones-natural laboratories for evolutionary studies",
    year = "1988",
    journal = "Trends in Ecology \& Evolution",
    url = "https://doi.org/10.1016/0169-5347(88)90033-x",
    doi = "10.1016/0169-5347(88)90033-x",
    openalex = "W2032950375",
    references = "doi101086282975, doi101146annureves06110175002011, doi1023071439305, doi1023072412932"
}

Predicting the extinction of single populations or species requires ecological and evolutionary information. Primary demographic factors affecting population dynamics include social structure, life history variation caused by environmental fluctuation, dispersal in spatially heterogeneous environments, and local extinction and colonization. In small populations, inbreeding can greatly reduce the average individual fitness, and loss of genetic variability from random genetic drift can diminish future adaptability to a changing environment. Theory and empirical examples suggest that demography is usually of more immediate importance than population genetics in determining the minimum viable sizes of wild populations. The practical need in biological conservation for understanding the interaction of demographic and genetic factors in extinction may provide a focus for fundamental advances at the interface of ecology and evolution.

@article{doi101126science3420403,
    author = "Lande, Russell",
    title = "Genetics and Demography in Biological Conservation",
    year = "1988",
    journal = "Science",
    abstract = "Predicting the extinction of single populations or species requires ecological and evolutionary information. Primary demographic factors affecting population dynamics include social structure, life history variation caused by environmental fluctuation, dispersal in spatially heterogeneous environments, and local extinction and colonization. In small populations, inbreeding can greatly reduce the average individual fitness, and loss of genetic variability from random genetic drift can diminish future adaptability to a changing environment. Theory and empirical examples suggest that demography is usually of more immediate importance than population genetics in determining the minimum viable sizes of wild populations. The practical need in biological conservation for understanding the interaction of demographic and genetic factors in extinction may provide a focus for fundamental advances at the interface of ecology and evolution.",
    url = "https://doi.org/10.1126/science.3420403",
    doi = "10.1126/science.3420403",
    openalex = "W2094387116",
    references = "doi101016000632078690025x, doi101016c20090029523, doi101017s0016672300016037, doi101093besa153237, doi101111j146918091949tb02451x, doi101111j155856461975tb00851x, doi101126science2214609459, doi101126science2314734129, doi101146annureves18110187001321, doi1015159781400881376, doi1023071308256, doi1023072529912, openalexw1500291103, openalexw2318111898"
}

@misc{frauenfelder1988biomolecules24,
    author = "Frauenfelder, H",
    title = "Biomolecules, in Pines, D., ed., Emerging Syntheses in Science",
    year = "1988",
    howpublished = "Redwood City, California, Addison-Wesley",
    note = "talkorigins\_source = {true}; raw\_reference = {Frauenfelder, H., 1988, Biomolecules, in Pines, D., ed., Emerging Syntheses in Science: Redwood City, California, Addison-Wesley.}"
}

@misc{lewin1988conflict35,
    author = "Lewin, R",
    title = "Conflict over DNA Clock Results",
    year = "1988",
    howpublished = "Science, v. 241, p. 1598-1600",
    note = "talkorigins\_source = {true}; raw\_reference = {Lewin, R., 1988, Conflict over DNA Clock Results: Science, v. 241, p. 1598-1600.}"
}

@misc{lewin1988family36,
    author = "Lewin, R",
    title = "Family Relationships are a Biological Conundrum",
    year = "1988",
    howpublished = "Science, v. 242, p. 671",
    note = "talkorigins\_source = {true}; raw\_reference = {Lewin, R., 1988, Family Relationships are a Biological Conundrum: Science, v. 242, p. 671.}"
}

@misc{rubin1988drosophilia40,
    author = "Rubin, G. M",
    title = "Drosophilia melanogaster as an Experimental Organism",
    year = "1988",
    howpublished = "Science, v. 240, p. 1453-1459",
    note = "talkorigins\_source = {true}; raw\_reference = {Rubin, G. M., 1988, Drosophilia melanogaster as an Experimental Organism: Science, v. 240, p. 1453-1459.}"
}

Journal Article The Evolutionary Significance of Phenotypic Plasticity: Phenotypic sources of variation among organisms can be described by developmental switches and reaction norms Get access Stephen C. Stearns Stephen C. Stearns Search for other works by this author on: Oxford Academic Google Scholar BioScience, Volume 39, Issue 7, July/August 1989, Pages 436–445, https://doi.org/10.2307/1311135 Published: 01 August 1989

@article{doi1023071311135,
    author = "Stearns, Stephen C.",
    title = "The Evolutionary Significance of Phenotypic Plasticity",
    year = "1989",
    journal = "BioScience",
    abstract = "Journal Article The Evolutionary Significance of Phenotypic Plasticity: Phenotypic sources of variation among organisms can be described by developmental switches and reaction norms Get access Stephen C. Stearns Stephen C. Stearns Search for other works by this author on: Oxford Academic Google Scholar BioScience, Volume 39, Issue 7, July/August 1989, Pages 436–445, https://doi.org/10.2307/1311135 Published: 01 August 1989",
    url = "https://doi.org/10.2307/1311135",
    doi = "10.2307/1311135",
    openalex = "W2058670567",
    references = "doi101001jama195002910300087029, doi1015159780691224244, doi1023071439305, doi1023072389364, openalexw1635425035"
}

@misc{edey1989blueprints21,
    author = "Edey, M. A. and Johanson, D. C",
    title = "Blueprints",
    year = "1989",
    howpublished = "Solving the Mystery of Evolution: Boston, Mass., Little, Brown and Co",
    note = "talkorigins\_source = {true}; raw\_reference = {Edey, M. A., and Johanson, D. C., 1989, Blueprints: Solving the Mystery of Evolution: Boston, Mass., Little, Brown and Co.}"
}

@misc{elmerdewitt1989the22,
    author = "Elmer-Dewitt, P",
    title = "The Perils of Treading on Heredity",
    year = "1989",
    howpublished = "Time, v. 133, no. 12, p. 70-71",
    note = "talkorigins\_source = {true}; raw\_reference = {Elmer-Dewitt, P., 1989, The Perils of Treading on Heredity: Time, v. 133, no. 12, p. 70-71.}"
}

@book{glover1989genes27,
    author = "Glover, D. M. and Hames, B. D",
    title = "Genes and Embryos",
    year = "1989",
    publisher = "New York, Oxford University Press, 228 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Glover, D. M., and Hames, B. D., 1989, Genes and Embryos: New York, Oxford University Press, 228 p.}"
}

@misc{jaroff1989the30,
    author = "Jaroff, L",
    title = "The Gene Hunt",
    year = "1989",
    howpublished = "Time, v. 133, no. 12, p. 62-67",
    note = "talkorigins\_source = {true}; raw\_reference = {Jaroff, L., 1989, The Gene Hunt: Time, v. 133, no. 12, p. 62-67.}"
}

@book{suzuki1989genethics42,
    author = "Suzuki, D. and Knudtson, P",
    title = "Genethics",
    year = "1989",
    publisher = "The Clash Between the New Genetics and Human Values: Cambridge, Mass., Harvard University Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Suzuki, D., and Knudtson, P., 1989, Genethics: The Clash Between the New Genetics and Human Values: Cambridge, Mass., Harvard University Press.}"
}

@misc{sachs1990translational41,
    author = "Sachs, A. B. and Davis, R. W",
    title = "Translational initiation and ribosomal biogenesis",
    year = "1990",
    howpublished = "involvement of a putative rRNA helicase and RPL46: Science, v. 247, p. 1077",
    note = "talkorigins\_source = {true}; raw\_reference = {Sachs, A. B., and Davis, R. W., 1990, Translational initiation and ribosomal biogenesis: involvement of a putative rRNA helicase and RPL46: Science, v. 247, p. 1077.}"
}

@article{doi101038359826a0,
    author = "Nowak, Martin A. and May, Robert M.",
    title = "Evolutionary games and spatial chaos",
    year = "1992",
    journal = "Nature",
    url = "https://doi.org/10.1038/359826a0",
    doi = "10.1038/359826a0",
    openalex = "W2025490132",
    references = "doi101007978146847862422, doi101007bf00450633, doi101017cbo9780511806292, doi101038280445a0, doi102307257983"
}

Part 1 Natural selection and life histories: evolutionary models in behavioural ecology evolution of life histories human behavioural ecology. Part 2 Exploitation of resources: decision-making competition for resources interactions between predators and prey. Part 3 Sexual selection and reproductive strategies: sexual selection parental investment mating systems. Part 4 Co-operation and conflict: co-operative breeding in birds and mammals conflict and co-operation in insects communication.

@article{doi1023075530,
    author = "Adams, Jonathan and Krebs, J. R. and Davies, N. B.",
    title = "Behavioural Ecology: An Evolutionary Approach",
    year = "1992",
    journal = "Journal of Animal Ecology",
    abstract = "Part 1 Natural selection and life histories: evolutionary models in behavioural ecology evolution of life histories human behavioural ecology. Part 2 Exploitation of resources: decision-making competition for resources interactions between predators and prey. Part 3 Sexual selection and reproductive strategies: sexual selection parental investment mating systems. Part 4 Co-operation and conflict: co-operative breeding in birds and mammals conflict and co-operation in insects communication.",
    url = "https://doi.org/10.2307/5530",
    doi = "10.2307/5530",
    openalex = "W2136284908"
}

An accurately resolved gene tree may not be congruent with the species tree because of lineage sorting of ancestral polymorphisms. DNA sequences from the mitochondrially encoded genes (mtDNA) are attractive sources of characters for estimating the phylogenies of recently evolved taxa because mtDNA evolves rapidly, but its utility is limited because the mitochondrial genes are inherited as a single linkage group (haplotype) and provide only one independent estimate of the species tree. In contrast, a set of nuclear genes can be selected from distinct chromosomes, such that each gene tree provides an independent estimate of the species tree. Another aspect of the gene-tree versus species-tree problem, however, favors the use of mtDNA for inferring species trees. For a three-species segment of a phylogeny, the branching order of a gene tree will correspond to that of the species tree if coalescence of the alleles or haplotypes occurred in the internode between the first and second bifurcation. From neutral theory, it is apparent that the probability of coalescence increases as effective population size decreases. Because the mitochondrial genome is maternally inherited and effectively haploid, its effective population size is one-fourth that of a nuclear-autosomal gene. Thus, the mitochondrial-haplotype tree has a substantially higher probability of accurately tracking a short internode than does a nuclear-autosomal-gene tree. When an internode is sufficiently long that the probability that the mitochondrial-haplotype tree will be congruent with the species tree is 0.95, the probability that a nuclear-autosomalgene tree will be congruent is only 0.62. If each of k independently sampled nuclear-gene trees has a probability of congruence with the species tree of 0.62, then a sample of 16 such trees would be required to be as confident of the inference based on the mitochondrial-haplotype tree. A survey of mtDNA-haplotype diversity in 34 species of birds indicates that coalescence is generally very recent, which suggests that coalescence times are typically much shorter than internodal branch lengths of the species tree, and that sorting of mtDNA lineages is not likely to confound the species tree. Hybridization resulting in transfer of mtDNA haplotypes among branches could also result in a haplotype tree that is incongruent with the species tree; if undetected, this could confound the species tree. However, hybridization is usually easy to detect and should be incorporated in the historical narrative of the group, because reticulation, as well as cladistic events, contributed to the evolution of the group.

@article{doi101111j155856461995tb02308x,
    author = "Moore, William S.",
    title = "INFERRING PHYLOGENIES FROM mt DNA VARIATION: MITOCHONDRIAL-GENE TREES VERSUS NUCLEAR-GENE TREES",
    year = "1995",
    journal = "Evolution",
    abstract = "An accurately resolved gene tree may not be congruent with the species tree because of lineage sorting of ancestral polymorphisms. DNA sequences from the mitochondrially encoded genes (mtDNA) are attractive sources of characters for estimating the phylogenies of recently evolved taxa because mtDNA evolves rapidly, but its utility is limited because the mitochondrial genes are inherited as a single linkage group (haplotype) and provide only one independent estimate of the species tree. In contrast, a set of nuclear genes can be selected from distinct chromosomes, such that each gene tree provides an independent estimate of the species tree. Another aspect of the gene-tree versus species-tree problem, however, favors the use of mtDNA for inferring species trees. For a three-species segment of a phylogeny, the branching order of a gene tree will correspond to that of the species tree if coalescence of the alleles or haplotypes occurred in the internode between the first and second bifurcation. From neutral theory, it is apparent that the probability of coalescence increases as effective population size decreases. Because the mitochondrial genome is maternally inherited and effectively haploid, its effective population size is one-fourth that of a nuclear-autosomal gene. Thus, the mitochondrial-haplotype tree has a substantially higher probability of accurately tracking a short internode than does a nuclear-autosomal-gene tree. When an internode is sufficiently long that the probability that the mitochondrial-haplotype tree will be congruent with the species tree is 0.95, the probability that a nuclear-autosomalgene tree will be congruent is only 0.62. If each of k independently sampled nuclear-gene trees has a probability of congruence with the species tree of 0.62, then a sample of 16 such trees would be required to be as confident of the inference based on the mitochondrial-haplotype tree. A survey of mtDNA-haplotype diversity in 34 species of birds indicates that coalescence is generally very recent, which suggests that coalescence times are typically much shorter than internodal branch lengths of the species tree, and that sorting of mtDNA lineages is not likely to confound the species tree. Hybridization resulting in transfer of mtDNA haplotypes among branches could also result in a haplotype tree that is incongruent with the species tree; if undetected, this could confound the species tree. However, hybridization is usually easy to detect and should be incorporated in the historical narrative of the group, because reticulation, as well as cladistic events, contributed to the evolution of the group.",
    url = "https://doi.org/10.1111/j.1558-5646.1995.tb02308.x",
    doi = "10.1111/j.1558-5646.1995.tb02308.x",
    openalex = "W2088587174",
    references = "doi101038347550a0"
}

The origin of organismal complexity is generally thought to be tightly coupled to the evolution of new gene functions arising subsequent to gene duplication. Under the classical model for the evolution of duplicate genes, one member of the duplicated pair usually degenerates within a few million years by accumulating deleterious mutations, while the other duplicate retains the original function. This model further predicts that on rare occasions, one duplicate may acquire a new adaptive function, resulting in the preservation of both members of the pair, one with the new function and the other retaining the old. However, empirical data suggest that a much greater proportion of gene duplicates is preserved than predicted by the classical model. Here we present a new conceptual framework for understanding the evolution of duplicate genes that may help explain this conundrum. Focusing on the regulatory complexity of eukaryotic genes, we show how complementary degenerative mutations in different regulatory elements of duplicated genes can facilitate the preservation of both duplicates, thereby increasing long-term opportunities for the evolution of new gene functions. The duplication-degeneration-complementation (DDC) model predicts that (1) degenerative mutations in regulatory elements can increase rather than reduce the probability of duplicate gene preservation and (2) the usual mechanism of duplicate gene preservation is the partitioning of ancestral functions rather than the evolution of new functions. We present several examples (including analysis of a new engrailed gene in zebrafish) that appear to be consistent with the DDC model, and we suggest several analytical and experimental approaches for determining whether the complementary loss of gene subfunctions or the acquisition of novel functions are likely to be the primary mechanisms for the preservation of gene duplicates. For a newly duplicated paralog, survival depends on the outcome of the race between entropic decay and chance acquisition of an advantageous regulatory mutation. Sidow 1996(p. 717) On one hand, it may fix an advantageous allele giving it a slightly different, and selectable, function from its original copy. This initial fixation provides substantial protection against future fixation of null mutations, allowing additional mutations to accumulate that refine functional differentiation. Alternatively, a duplicate locus can instead first fix a null allele, becoming a pseudogene. Walsh 1995 (p. 426) Duplicated genes persist only if mutations create new and essential protein functions, an event that is predicted to occur rarely. Nadeau and Sankoff 1997 (p. 1259) Thus overall, with complex metazoans, the major mechanism for retention of ancient gene duplicates would appear to have been the acquisition of novel expression sites for developmental genes, with its accompanying opportunity for new gene roles underlying the progressive extension of development itself. Cooke et al. 1997 (p. 362)

@article{doi101093genetics15141531,
    author = "Force, Allan and Lynch, Michael and Pickett, F. Bryan and Amores, Angel and Yan, Yi‐Lin and Postlethwait, John H.",
    title = "Preservation of Duplicate Genes by Complementary, Degenerative Mutations",
    year = "1999",
    journal = "Genetics",
    abstract = "The origin of organismal complexity is generally thought to be tightly coupled to the evolution of new gene functions arising subsequent to gene duplication. Under the classical model for the evolution of duplicate genes, one member of the duplicated pair usually degenerates within a few million years by accumulating deleterious mutations, while the other duplicate retains the original function. This model further predicts that on rare occasions, one duplicate may acquire a new adaptive function, resulting in the preservation of both members of the pair, one with the new function and the other retaining the old. However, empirical data suggest that a much greater proportion of gene duplicates is preserved than predicted by the classical model. Here we present a new conceptual framework for understanding the evolution of duplicate genes that may help explain this conundrum. Focusing on the regulatory complexity of eukaryotic genes, we show how complementary degenerative mutations in different regulatory elements of duplicated genes can facilitate the preservation of both duplicates, thereby increasing long-term opportunities for the evolution of new gene functions. The duplication-degeneration-complementation (DDC) model predicts that (1) degenerative mutations in regulatory elements can increase rather than reduce the probability of duplicate gene preservation and (2) the usual mechanism of duplicate gene preservation is the partitioning of ancestral functions rather than the evolution of new functions. We present several examples (including analysis of a new engrailed gene in zebrafish) that appear to be consistent with the DDC model, and we suggest several analytical and experimental approaches for determining whether the complementary loss of gene subfunctions or the acquisition of novel functions are likely to be the primary mechanisms for the preservation of gene duplicates. For a newly duplicated paralog, survival depends on the outcome of the race between entropic decay and chance acquisition of an advantageous regulatory mutation. Sidow 1996(p. 717) On one hand, it may fix an advantageous allele giving it a slightly different, and selectable, function from its original copy. This initial fixation provides substantial protection against future fixation of null mutations, allowing additional mutations to accumulate that refine functional differentiation. Alternatively, a duplicate locus can instead first fix a null allele, becoming a pseudogene. Walsh 1995 (p. 426) Duplicated genes persist only if mutations create new and essential protein functions, an event that is predicted to occur rarely. Nadeau and Sankoff 1997 (p. 1259) Thus overall, with complex metazoans, the major mechanism for retention of ancient gene duplicates would appear to have been the acquisition of novel expression sites for developmental genes, with its accompanying opportunity for new gene roles underlying the progressive extension of development itself. Cooke et al. 1997 (p. 362)",
    url = "https://doi.org/10.1093/genetics/151.4.1531",
    doi = "10.1093/genetics/151.4.1531",
    openalex = "W2152075687",
    references = "doi101006dbio19960034, doi1010079783642866593, doi1010160092867494902909, doi101038276565a0, doi101038346035a0, doi101038353031a0, doi10103841710, doi10103842711, doi101038ng0498345, doi101038scientificamerican117998, doi101046j14390388200200356x, doi101093oxfordjournalsmolbeva040454, doi101126science28253941711, doi101242dev1994supplement125"
}

▪ Abstract Molecular chaperones, including the heat-shock proteins (Hsps), are a ubiquitous feature of cells in which these proteins cope with stress-induced denaturation of other proteins. Hsps have received the most attention in model organisms undergoing experimental stress in the laboratory, and the function of Hsps at the molecular and cellular level is becoming well understood in this context. A complementary focus is now emerging on the Hsps of both model and nonmodel organisms undergoing stress in nature, on the roles of Hsps in the stress physiology of whole multicellular eukaryotes and the tissues and organs they comprise, and on the ecological and evolutionary correlates of variation in Hsps and the genes that encode them. This focus discloses that (a) expression of Hsps can occur in nature, (b) all species have hsp genes but they vary in the patterns of their expression, (c) Hsp expression can be correlated with resistance to stress, and (d) species' thresholds for Hsp expression are correlated with levels of stress that they naturally undergo. These conclusions are now well established and may require little additional confirmation; many significant questions remain unanswered concerning both the mechanisms of Hsp-mediated stress tolerance at the organismal level and the evolutionary mechanisms that have diversified the hsp genes.

@article{doi101146annurevphysiol611243,
    author = "Feder, Martin E. and Hofmann, Gretchen E.",
    title = "HEAT-SHOCK PROTEINS, MOLECULAR CHAPERONES, AND THE STRESS RESPONSE: Evolutionary and Ecological Physiology",
    year = "1999",
    journal = "Annual Review of Physiology",
    abstract = "▪ Abstract Molecular chaperones, including the heat-shock proteins (Hsps), are a ubiquitous feature of cells in which these proteins cope with stress-induced denaturation of other proteins. Hsps have received the most attention in model organisms undergoing experimental stress in the laboratory, and the function of Hsps at the molecular and cellular level is becoming well understood in this context. A complementary focus is now emerging on the Hsps of both model and nonmodel organisms undergoing stress in nature, on the roles of Hsps in the stress physiology of whole multicellular eukaryotes and the tissues and organs they comprise, and on the ecological and evolutionary correlates of variation in Hsps and the genes that encode them. This focus discloses that (a) expression of Hsps can occur in nature, (b) all species have hsp genes but they vary in the patterns of their expression, (c) Hsp expression can be correlated with resistance to stress, and (d) species' thresholds for Hsp expression are correlated with levels of stress that they naturally undergo. These conclusions are now well established and may require little additional confirmation; many significant questions remain unanswered concerning both the mechanisms of Hsp-mediated stress tolerance at the organismal level and the evolutionary mechanisms that have diversified the hsp genes.",
    url = "https://doi.org/10.1146/annurev.physiol.61.1.243",
    doi = "10.1146/annurev.physiol.61.1.243",
    openalex = "W2141261198",
    references = "doi101086285141"
}

@article{doi10103835046017,
    author = "Kopp, Artyom and Duncan, Ian and Carroll, Sean B.",
    title = "Genetic control and evolution of sexually dimorphic characters in Drosophila",
    year = "2000",
    journal = "Nature",
    url = "https://doi.org/10.1038/35046017",
    doi = "10.1038/35046017",
    openalex = "W1588649406",
    references = "doi101038384236a0, doi101073pnas7863721, doi101093oxfordjournalsmolbeva040214, doi101111j155856461982tb05003x, doi101111j155856461998tb05132x, doi101146annurevgenet301637, doi101242dev1212333, doi1015159780691207278, doi1023072341823, doi105962bhltitle27468"
}

In 1950, G. Ledyard Stebbins devoted two chapters of his book Variation and Evolution in Plants (Columbia Univ. Press, New York) to polyploidy, one on occurrence and nature and one on distribution and significance. Fifty years later, many of the questions Stebbins posed have not been answered, and many new questions have arisen. In this paper, we review some of the genetic attributes of polyploids that have been suggested to account for the tremendous success of polyploid plants. Based on a limited number of studies, we conclude: (i) Polyploids, both individuals and populations, generally maintain higher levels of heterozygosity than do their diploid progenitors. (ii) Polyploids exhibit less inbreeding depression than do their diploid parents and can therefore tolerate higher levels of selfing; polyploid ferns indeed have higher levels of selfing than do their diploid parents, but polyploid angiosperms do not differ in outcrossing rates from their diploid parents. (iii) Most polyploid species are polyphyletic, having formed recurrently from genetically different diploid parents. This mode of formation incorporates genetic diversity from multiple progenitor populations into the polyploid "species"; thus, genetic diversity in polyploid species is much higher than expected by models of polyploid formation involving a single origin. (iv) Genome rearrangement may be a common attribute of polyploids, based on evidence from genome in situ hybridization (GISH), restriction fragment length polymorphism (RFLP) analysis, and chromosome mapping. (v) Several groups of plants may be ancient polyploids, with large regions of homologous DNA. These duplicated genes and genomes can undergo divergent evolution and evolve new functions. These genetic and genomic attributes of polyploids may have both biochemical and ecological benefits that contribute to the success of polyploids in nature.

@article{doi101073pnas97137051,
    author = "Soltis, Pamela S. and Soltis, Pamela S.",
    title = "The role of genetic and genomic attributes in the success of polyploids",
    year = "2000",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = {In 1950, G. Ledyard Stebbins devoted two chapters of his book Variation and Evolution in Plants (Columbia Univ. Press, New York) to polyploidy, one on occurrence and nature and one on distribution and significance. Fifty years later, many of the questions Stebbins posed have not been answered, and many new questions have arisen. In this paper, we review some of the genetic attributes of polyploids that have been suggested to account for the tremendous success of polyploid plants. Based on a limited number of studies, we conclude: (i) Polyploids, both individuals and populations, generally maintain higher levels of heterozygosity than do their diploid progenitors. (ii) Polyploids exhibit less inbreeding depression than do their diploid parents and can therefore tolerate higher levels of selfing; polyploid ferns indeed have higher levels of selfing than do their diploid parents, but polyploid angiosperms do not differ in outcrossing rates from their diploid parents. (iii) Most polyploid species are polyphyletic, having formed recurrently from genetically different diploid parents. This mode of formation incorporates genetic diversity from multiple progenitor populations into the polyploid "species"; thus, genetic diversity in polyploid species is much higher than expected by models of polyploid formation involving a single origin. (iv) Genome rearrangement may be a common attribute of polyploids, based on evidence from genome in situ hybridization (GISH), restriction fragment length polymorphism (RFLP) analysis, and chromosome mapping. (v) Several groups of plants may be ancient polyploids, with large regions of homologous DNA. These duplicated genes and genomes can undergo divergent evolution and evolve new functions. These genetic and genomic attributes of polyploids may have both biochemical and ecological benefits that contribute to the success of polyploids in nature.},
    url = "https://doi.org/10.1073/pnas.97.13.7051",
    doi = "10.1073/pnas.97.13.7051",
    openalex = "W2001670067",
    references = "doi1010079781489930439"
}

One of the oldest problems in evolutionary biology remains largely unsolved. Which mutations generate evolutionarily relevant phenotypic variation? What kinds of molecular changes do they entail? What are the phenotypic magnitudes, frequencies of origin, and pleiotropic effects of such mutations? How is the genome constructed to allow the observed abundance of phenotypic diversity? Historically, the neo-Darwinian synthesizers stressed the predominance of micromutations in evolution, whereas others noted the similarities between some dramatic mutations and evolutionary transitions to argue for macromutationism. Arguments on both sides have been biased by misconceptions of the developmental effects of mutations. For example, the traditional view that mutations of important developmental genes always have large pleiotropic effects can now be seen to be a conclusion drawn from observations of a small class of mutations with dramatic effects. It is possible that some mutations, for example, those in cis-regulatory DNA, have few or no pleiotropic effects and may be the predominant source of morphological evolution. In contrast, mutations causing dramatic phenotypic effects, although superficially similar to hypothesized evolutionary transitions, are unlikely to fairly represent the true path of evolution. Recent developmental studies of gene function provide a new way of conceptualizing and studying variation that contrasts with the traditional genetic view that was incorporated into neo-Darwinian theory and population genetics. This new approach in developmental biology is as important for microevolutionary studies as the actual results from recent evolutionary developmental studies. In particular, this approach will assist in the task of identifying the specific mutations generating phenotypic variation and elucidating how they alter gene function. These data will provide the current missing link between molecular and phenotypic variation in natural populations.

@article{doi101111j001438202000tb00544x,
    author = "Stern, David L.",
    title = "PERSPECTIVE: EVOLUTIONARY DEVELOPMENTAL BIOLOGY AND THE PROBLEM OF VARIATION",
    year = "2000",
    journal = "Evolution",
    abstract = "One of the oldest problems in evolutionary biology remains largely unsolved. Which mutations generate evolutionarily relevant phenotypic variation? What kinds of molecular changes do they entail? What are the phenotypic magnitudes, frequencies of origin, and pleiotropic effects of such mutations? How is the genome constructed to allow the observed abundance of phenotypic diversity? Historically, the neo-Darwinian synthesizers stressed the predominance of micromutations in evolution, whereas others noted the similarities between some dramatic mutations and evolutionary transitions to argue for macromutationism. Arguments on both sides have been biased by misconceptions of the developmental effects of mutations. For example, the traditional view that mutations of important developmental genes always have large pleiotropic effects can now be seen to be a conclusion drawn from observations of a small class of mutations with dramatic effects. It is possible that some mutations, for example, those in cis-regulatory DNA, have few or no pleiotropic effects and may be the predominant source of morphological evolution. In contrast, mutations causing dramatic phenotypic effects, although superficially similar to hypothesized evolutionary transitions, are unlikely to fairly represent the true path of evolution. Recent developmental studies of gene function provide a new way of conceptualizing and studying variation that contrasts with the traditional genetic view that was incorporated into neo-Darwinian theory and population genetics. This new approach in developmental biology is as important for microevolutionary studies as the actual results from recent evolutionary developmental studies. In particular, this approach will assist in the task of identifying the specific mutations generating phenotypic variation and elucidating how they alter gene function. These data will provide the current missing link between molecular and phenotypic variation in natural populations.",
    url = "https://doi.org/10.1111/j.0014-3820.2000.tb00544.x",
    doi = "10.1111/j.0014-3820.2000.tb00544.x",
    openalex = "W3028418616",
    references = "doi101016016895259090017z, doi101038276565a0, doi101038347550a0, doi101038386485a0, doi101111j155856461975tb00851x, doi1023071438156, doi1023071439305, doi1023072407274, doi105962bhltitle27468, openalexw1493831303"
}

Gene duplication has generally been viewed as a necessary source of material for the origin of evolutionary novelties, but it is unclear how often gene duplicates arise and how frequently they evolve new functions. Observations from the genomic databases for several eukaryotic species suggest that duplicate genes arise at a very high rate, on average 0.01 per gene per million years. Most duplicated genes experience a brief period of relaxed selection early in their history, with a moderate fraction of them evolving in an effectively neutral manner during this period. However, the vast majority of gene duplicates are silenced within a few million years, with the few survivors subsequently experiencing strong purifying selection. Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species.

@article{doi101126science29054941151,
    author = "Lynch, Michael and Conery, John S.",
    title = "The Evolutionary Fate and Consequences of Duplicate Genes",
    year = "2000",
    journal = "Science",
    abstract = "Gene duplication has generally been viewed as a necessary source of material for the origin of evolutionary novelties, but it is unclear how often gene duplicates arise and how frequently they evolve new functions. Observations from the genomic databases for several eukaryotic species suggest that duplicate genes arise at a very high rate, on average 0.01 per gene per million years. Most duplicated genes experience a brief period of relaxed selection early in their history, with a moderate fraction of them evolving in an effectively neutral manner during this period. However, the vast majority of gene duplicates are silenced within a few million years, with the few survivors subsequently experiencing strong purifying selection. Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species.",
    url = "https://doi.org/10.1126/science.290.5494.1151",
    doi = "10.1126/science.290.5494.1151",
    openalex = "W2019591778",
    references = "doi101023a1006392424384, doi101038387489a0, doi101046j14390388200200356x, doi101093genetics15141531, doi101093genetics1541459, doi101093nar25173389, doi101098rspb19940058, doi101126science28253941711, doi101126science28754612204, doi101242dev1994supplement125, doi1023072412932"
}

Introductions and Concepts 1. Why evolutionary genetics doesn't always add up 2. Beyond the average: The evolutionary importance of gene interactions and variability of epistatic effects 3. Epistasis and Complex Traits 4. Detecting epistasis among quantitative trait loci 5. The evolution of developmental interations: Epistasis, canalization, and integration 6. Epistasis and the maintenance of sex 7. Genetic partners in crime: Evolution of an ultraselfish supergene that specializes in sperm sabotage 8. Modeling gene interaction in structured populations 9. Epistasis, linkage, and balancing selection 10. Indirect genetic effects and gene interactions 11. Epistasis in morphology and mating behavior Genetic Differentiation: From Populations to Speciation 12. Gene interactions and the origin of species 13. Epistasis as a genetic constraint within populations and an accelerant of adaptive divergence among them 14. The contribution of epistasis to the evolution of natural populations: A case study of an annual plant 15. Epistasis and the evolution of genetic architectures in natural populations 16. Inferring Epistasis in wild sunflower hybrid zones Literature cited Index

@book{openalexw1554403518,
    author = "Wolf, Jason B. and Brodie, Edmund D. and Wade, Michael J.",
    title = "Epistasis and the Evolutionary Process",
    year = "2000",
    abstract = "Introductions and Concepts 1. Why evolutionary genetics doesn't always add up 2. Beyond the average: The evolutionary importance of gene interactions and variability of epistatic effects 3. Epistasis and Complex Traits 4. Detecting epistasis among quantitative trait loci 5. The evolution of developmental interations: Epistasis, canalization, and integration 6. Epistasis and the maintenance of sex 7. Genetic partners in crime: Evolution of an ultraselfish supergene that specializes in sperm sabotage 8. Modeling gene interaction in structured populations 9. Epistasis, linkage, and balancing selection 10. Indirect genetic effects and gene interactions 11. Epistasis in morphology and mating behavior Genetic Differentiation: From Populations to Speciation 12. Gene interactions and the origin of species 13. Epistasis as a genetic constraint within populations and an accelerant of adaptive divergence among them 14. The contribution of epistasis to the evolution of natural populations: A case study of an annual plant 15. Epistasis and the evolution of genetic architectures in natural populations 16. Inferring Epistasis in wild sunflower hybrid zones Literature cited Index",
    url = "https://openalex.org/W1554403518",
    openalex = "W1554403518"
}

@article{doi101023a1012294324713,
    author = "Bouchard, Thomas J. and Loehlin, John C.",
    title = "Genes, Evolution, and Personality",
    year = "2001",
    journal = "Behavior Genetics",
    url = "https://doi.org/10.1023/a:1012294324713",
    doi = "10.1023/a:1012294324713",
    openalex = "W1734767862",
    references = "doi1010160198971590900504, doi101046j14390388200200356x, doi101111j174465701991tb00688x, doi101126science27452921527, doi101537ase188722495, doi1023075403, doi1041359781446220986n8, doi105962bhltitle17416, doi107208chicago97802261495160010001, openalexw1486903121, openalexw1554403518, openalexw1556033561, openalexw1617412188, openalexw1641003075"
}

@article{doi101016s0169534702025545,
    author = "Lee, Carol Eunmi",
    title = "Evolutionary genetics of invasive species",
    year = "2002",
    journal = "Trends in Ecology \& Evolution",
    url = "https://doi.org/10.1016/s0169-5347(02)02554-5",
    doi = "10.1016/s0169-5347(02)02554-5",
    openalex = "W2155928419",
    references = "doi101038sjhdy6886170, doi101073pnas97137043, doi101073pnas97137051, doi101111j155856461951tb02788x, doi101126science2925517673, doi1016410006356820000500053eaecon23co2, doi1023072261425, doi1023072265769, doi1023072412809, doi104159harvard9780674865327, openalexw1554403518, openalexw1584633894"
}

@article{doi101038nature01025,
    author = "Enard, Wolfgang and Przeworski, Molly and Fisher, Simon E. and Lai, Cecilia and Wiebe, Victor and Kitano, Takashi and Monaco, Anthony P. and Pääbo, Svante",
    title = "Molecular evolution of FOXP2, a gene involved in speech and language",
    year = "2002",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature01025",
    doi = "10.1038/nature01025",
    openalex = "W2107934935",
    references = "doi10103831927, doi101093bioinformatics152174, doi101111j155856461991tb04425x"
}

We studied human population structure using genotypes at 377 autosomal microsatellite loci in 1056 individuals from 52 populations. Within-population differences among individuals account for 93 to 95% of genetic variation; differences among major groups constitute only 3 to 5%. Nevertheless, without using prior information about the origins of individuals, we identified six main genetic clusters, five of which correspond to major geographic regions, and subclusters that often correspond to individual populations. General agreement of genetic and predefined populations suggests that self-reported ancestry can facilitate assessments of epidemiological risks but does not obviate the need to use genetic information in genetic association studies.

@article{doi101126science1078311,
    author = "Rosenberg, Noah A. and Pritchard, Jonathan K. and Weber, James L. and Cann, Howard M. and Kídd, Kenneth K. and Zhivotovsky, Lev A. and Feldman, Marcus W.",
    title = "Genetic Structure of Human Populations",
    year = "2002",
    journal = "Science",
    abstract = "We studied human population structure using genotypes at 377 autosomal microsatellite loci in 1056 individuals from 52 populations. Within-population differences among individuals account for 93 to 95\% of genetic variation; differences among major groups constitute only 3 to 5\%. Nevertheless, without using prior information about the origins of individuals, we identified six main genetic clusters, five of which correspond to major geographic regions, and subclusters that often correspond to individual populations. General agreement of genetic and predefined populations suggests that self-reported ancestry can facilitate assessments of epidemiological risks but does not obviate the need to use genetic information in genetic association studies.",
    url = "https://doi.org/10.1126/science.1078311",
    doi = "10.1126/science.1078311",
    openalex = "W2141042406",
    references = "doi101006tpbi20011543, doi101038368455a0, doi101038ng761, doi101073pnas9494516, doi101086302825, doi101086339929, doi101093genetics1552945, doi101093genetics1592699, doi101126science2965566261b, doi101186gb200237comment2007"
}

@article{doi101016jtree200309010,
    author = "Olden, Julian D. and Poff, N. LeRoy and Douglas, Marlis R. and Douglas, Michael E. and Fausch, Kurt D.",
    title = "Ecological and evolutionary consequences of biotic homogenization",
    year = "2003",
    journal = "Trends in Ecology \& Evolution",
    url = "https://doi.org/10.1016/j.tree.2003.09.010",
    doi = "10.1016/j.tree.2003.09.010",
    openalex = "W2159330259",
    references = "doi1010079789400958517, doi101016s0169534701022832, doi101016s0169534702000447, doi101016s0169534702025545, doi101016s0169534703000089, doi101016s0169534703001009, doi101016s0169534799016791, doi101046j13652745200000473x, doi101111j155856461954tb01504x, doi101111j155856461987tb02459x, doi101126science25350241099, doi101126science27753301300, doi101126science2885467854, doi101146annurevecolsys27183, doi1015159780691209418, doi1023072257385, doi1023072409086, doi102307jctvx5wbbh"
}

Robustness is the invariance of phenotypes in the face of perturbation. The robustness of phenotypes appears at various levels of biological organization, including gene expression, protein folding, metabolic flux, physiological homeostasis, development, and even organismal fitness. The mechanisms underlying robustness are diverse, ranging from thermodynamic stability at the RNA and protein level to behavior at the organismal level. Phenotypes can be robust either against heritable perturbations (e.g., mutations) or nonheritable perturbations (e.g., the weather). Here we primarily focus on the first kind of robustness--genetic robustness--and survey three growing avenues of research: (1) measuring genetic robustness in nature and in the laboratory; (2) understanding the evolution of genetic robustness: and (3) exploring the implications of genetic robustness for future evolution.

@article{doi101111j001438202003tb00377x,
    author = "de Visser, J. Arjan G. M. and Hermisson, Joachim and Wagner, Günter P. and Meyers, Lauren Ancel and Bagheri, Homayoun C. and Blanchard, Jeffrey L. and Chao, Lin and Cheverud, James M. and Elena, Santiago F. and Fontana, Walter and Gibson, Greg and Hansen, Thomas F. and Krakauer, David C. and Lewontin, Richard C and Ofria, Charles and Rice, Sean H. and von Dassow, George and Wagner, Andreas and Whitlock, Michael C.",
    title = "PERSPECTIVE: EVOLUTION AND DETECTION OF GENETIC ROBUSTNESS",
    year = "2003",
    journal = "Evolution",
    abstract = "Robustness is the invariance of phenotypes in the face of perturbation. The robustness of phenotypes appears at various levels of biological organization, including gene expression, protein folding, metabolic flux, physiological homeostasis, development, and even organismal fitness. The mechanisms underlying robustness are diverse, ranging from thermodynamic stability at the RNA and protein level to behavior at the organismal level. Phenotypes can be robust either against heritable perturbations (e.g., mutations) or nonheritable perturbations (e.g., the weather). Here we primarily focus on the first kind of robustness--genetic robustness--and survey three growing avenues of research: (1) measuring genetic robustness in nature and in the laboratory; (2) understanding the evolution of genetic robustness: and (3) exploring the implications of genetic robustness for future evolution.",
    url = "https://doi.org/10.1111/j.0014-3820.2003.tb00377.x",
    doi = "10.1111/j.0014-3820.2003.tb00377.x",
    openalex = "W2168338628",
    references = "doi10103824550, doi10103835018085, doi101038nature749, doi101038ng881, doi101086280193, doi101086283602, doi101086414425, doi101093nar309e36, doi101111j155856461953tb00070x, doi101146annurevphysiol611243, doi1043249781315765471, openalexw1554403518, openalexw3135630760"
}

@article{doi101038nature02415,
    author = "Shapiro, Michael D. and Marks, Melissa E. and Peichel, Catherine L. and Blackman, Benjamin K. and Nereng, Kirsten S. and Jónsson, Bjarni and Schluter, Dolph and Kingsley, David M.",
    title = "Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks",
    year = "2004",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature02415",
    doi = "10.1038/nature02415",
    openalex = "W2066908868",
    references = "doi1010020471142905, doi101016s0092867400808685, doi101016s0092867401004937, doi10103820944, doi10103835046017, doi101038414901a, doi101038nature02064, doi101073pnas9794530, doi101111j001438202000tb00544x, openalexw2062594085"
}

Estimating the genetic basis of quantitative traits can be tricky for wild populations in natural environments, as environmental variation frequently obscures the underlying evolutionary patterns. I review the recent application of restricted maximum-likelihood "animal models" to multigenerational data from natural populations, and show how the estimation of variance components and prediction of breeding values using these methods offer a powerful means of tackling the potentially confounding effects of environmental variation, as well as generating a wealth of new areas of investigation.

@article{doi101098rstb20031437,
    author = "Kruuk, Loeske E. B.",
    title = "Estimating genetic parameters in natural populations using the ‘animal model’",
    year = "2004",
    journal = "Philosophical Transactions of the Royal Society B Biological Sciences",
    abstract = {Estimating the genetic basis of quantitative traits can be tricky for wild populations in natural environments, as environmental variation frequently obscures the underlying evolutionary patterns. I review the recent application of restricted maximum-likelihood "animal models" to multigenerational data from natural populations, and show how the estimation of variance components and prediction of breeding values using these methods offer a powerful means of tackling the potentially confounding effects of environmental variation, as well as generating a wealth of new areas of investigation.},
    url = "https://doi.org/10.1098/rstb.2003.1437",
    doi = "10.1098/rstb.2003.1437",
    openalex = "W2073035337",
    references = "doi101016s0169534702000447, doi101038nrg700, doi101111j155856461984tb00344x, doi105860choice355054"
}

Over 35 years ago, Susumu Ohno stated that gene duplication was the single most important factor in evolution. He reiterated this point a few years later in proposing that without duplicated genes the creation of metazoans, vertebrates, and mammals from unicellular organisms would have been impossible. Such big leaps in evolution, he argued, required the creation of new gene loci with previously nonexistent functions. Bold statements such as these, combined with his proposal that at least one whole-genome duplication event facilitated the evolution of vertebrates, have made Ohno an icon in the literature on genome evolution. However, discussion on the occurrence and consequences of gene and genome duplication events has a much longer, and often neglected, history. Here we review literature dealing with the occurrence and consequences of gene duplication, beginning in 1911. We document conceptual and technological advances in gene duplication research from this early research in comparative cytology up to recent research on whole genomes, "transcriptomes," and "interactomes."

@article{doi101146annurevgenet38072902092831,
    author = "Taylor, John S. and Raes, Jeroen",
    title = "Duplication and Divergence: The Evolution of New Genes and Old Ideas",
    year = "2004",
    journal = "Annual Review of Genetics",
    abstract = {Over 35 years ago, Susumu Ohno stated that gene duplication was the single most important factor in evolution. He reiterated this point a few years later in proposing that without duplicated genes the creation of metazoans, vertebrates, and mammals from unicellular organisms would have been impossible. Such big leaps in evolution, he argued, required the creation of new gene loci with previously nonexistent functions. Bold statements such as these, combined with his proposal that at least one whole-genome duplication event facilitated the evolution of vertebrates, have made Ohno an icon in the literature on genome evolution. However, discussion on the occurrence and consequences of gene and genome duplication events has a much longer, and often neglected, history. Here we review literature dealing with the occurrence and consequences of gene duplication, beginning in 1911. We document conceptual and technological advances in gene duplication research from this early research in comparative cytology up to recent research on whole genomes, "transcriptomes," and "interactomes."},
    url = "https://doi.org/10.1146/annurev.genet.38.072902.092831",
    doi = "10.1146/annurev.genet.38.072902.092831",
    openalex = "W2166085889",
    references = "doi101006dbio19960034, doi101016s0378111902010399, doi101038095550b0, doi10103831933, doi101038370563a0, doi1023071437764, doi1023071438156"
}

Emerging knowledge about organismal evolution suggests that changes in the regulation of gene expression have played a major role - a thesis proposed 30 years ago by King and Wilson.

@article{doi101371journalpbio0030245,
    author = "Carroll, Sean B.",
    title = "Evolution at Two Levels: On Genes and Form",
    year = "2005",
    journal = "PLoS Biology",
    abstract = "Emerging knowledge about organismal evolution suggests that changes in the regulation of gene expression have played a major role - a thesis proposed 30 years ago by King and Wilson.",
    url = "https://doi.org/10.1371/journal.pbio.0030245",
    doi = "10.1371/journal.pbio.0030245",
    openalex = "W1999027354",
    references = "doi1010079783642866593, doi101016b9781483227344500176, doi101016s0022283661800727, doi10103835046017, doi10103835097076, doi101038376479a0, doi101038nature01025, doi101038nature01262, doi101073pnas6341181, doi101073pnas7183028, doi101073pnas9794530, doi101111j001438202000tb00544x, doi101126science1090005, doi101126science1653891349, doi101126science29054941151, doi101126science860134, doi105860choice395182"
}

@article{doi101038nrc2013,
    author = "Merlo, Lauren M.F. and Pepper, John W. and Reid, Brian J. and Maley, Carlo C.",
    title = "Cancer as an evolutionary and ecological process",
    year = "2006",
    journal = "Nature reviews. Cancer",
    url = "https://doi.org/10.1038/nrc2013",
    doi = "10.1038/nrc2013",
    openalex = "W2123558100",
    references = "doi1010021521187820001222121057aidbies330co2w, doi101016s0169534701021012, doi101016s0169534702024953, doi10103842701, doi101038nrg1088, doi101146annurevgenet341401, doi1023072407274"
}

Preface 1. SELFISH GENETIC ELEMENTS Genetic Cooperation and Conflict Three Ways to Achieve Within-Individual Kinship Conflicts Rates of Spread Effects on the Host Population The Study of Selfish Genetic Elements Design of This Book 2. AUTOSOMAL KILLERS The t Haplotype Discovery Structure of the t Haplotype History and Distribution Genetics of Drive Importance of Mating System and Gamete Competition Fate of Resistant Alleles Selection for Inversions Recessive Lethals in t Complexes Enhancers and Suppressors t and the Major Histocompatability Complex Heterozygous (+/t) Fitness Effects: Sex Antagonistic? Accounting for t Frequencies in Nature Other Gamete Killers Segregation Distorter in Drosophila Spore Killers in Fungi Incidence of Gamete Killers Maternal-Effect Killers Medea in Flour Beetles HSR, scat+, and OmDDK in Mice The Evolution of Maternal-Effect Killers Gestational Drive? Gametophyte Factors in Plants 3. SELFISH SEX CHROMOSOMES Sex Chromosome Drive in the Diptera Killer X Chromosomes Killer Y Chromosomes Taxonomic Distribution of Killer Sex Chromosomes Evolutionary Cycles of Sex Determination Feminizing X (and Y) Chromosomes in Rodents The Varying Lemming The Wood Lemming Other Murids Other Conflicts: Sex Ratios and Mate Choice 4. GENOMIC IMPRINTING Imprinting and Parental Investment in Mammals Igf2 and Igf2r: Oppositely Imprinted, Oppositely Acting Growth Factors in Mice Growth Effects of Imprinted Genes in Mice and Humans Evolution of the Imprinting Apparatus The Mechanisms of Imprinting Involve Methylation and Are Complex Conflict Between Different Components of the Imprinting Machinery History of Conflict Reflected in the Imprinting Apparatus Evolutionary Turnover of the Imprinting Apparatus Intralocus Interactions, Polar Overdominance, and Paramutation Transmission Ratio Distortion at Imprinted Loci Biparental Imprinting and Other Possibilities Other Traits: Social Interactions after the Period of Parental Investment Maternal Behavior in Mice Inbreeding and Dispersal Kin Recognition Functional Interpretation of Tissue Effects in Chimeric Mice Deceit and Selves-Deception Imprinting and the Sex Chromosomes Genomic Imprinting in Other Taxa Flowering Plants Other Taxa Predicted to Have Imprinting 5. SELFISH MITOCHONDRIAL DNA Mitochondrial Genomics: A Primer Mitochondrial Selection within the Individual Petite Mutations in Yeast Within-Individual Selection and the Evolution of Uniparental Inheritance Within-Individual Selection under Uniparental Inheritance DUI: Mother-to-Daughter and Father-to-Son mtDNA Inheritance in Mussels Cytoplasmic Male Sterility Uniparental Inheritance Implies Unisexual Selection Disproportionate Role of mtDNA in Plant Male Sterility Mechanisms of Mitochondrial Action and Nuclear Reaction CMS and Restorers in Natural Populations CMS, Masculinization, and the Evolution of Separate Sexes Pollen Limitation, Frequency Dependence, and Local Extinction Resource Reallocation Versus Inbreeding Avoidance Importance of Mutational Variation CMS and Paternal Transmission Other Traces of Mito-Nuclear Conflict Mitochondria and Apoptosis Mitochondria and Germ Cell Determination Mitochondria and RNA Editing 6. GENE CONVERSION AND HOMING Biased Gene Conversion Molecular Mechanisms Effective Selection Coefficients Due to BGC in Fungi BGC and Genome Evolution BGC and Evolution of the Meiotic Machinery Homing and Retrohoming How HEGs Home HEGs Usually Associated with Self-Splicing Introns or Inteins HEGs and Host Mating System Evolutionary Cycle of Horizontal Transmission, Degeneration, and Loss HEG Domestication and Mating-Type Switching in Yeast Group II Introns Artificial HEGs As Tools for Population Genetic Engineering The Basic Construct Increasing the Load Preventing Natural Resistance and Horizontal Transmission Population Genetic Engineering Other Uses 7. TRANSPOSABLE ELEMENTS Molecular Structure and Mechanisms DNA Transposons LINEs and SINEs LTR Retroelements Population Biology and Natural Selection Transposition Rates Low But Greater Than Excision Rates Natural Selection on the Host Slows the Spread of Transposable Elements Rapid Spread of P Elements in D. melanogaster Net Reproductive Rate a Function of Transposition Rate and Effect on Host Fitness Reducing Harm to the Host Transposition Rate and Copy Number Regulation Selection for Self-Recognition Defective and Repressor Elements Extinction of Active Elements in Host Species Horizontal Transmission and Long-Term Persistence Transposable Elements in Inbred and Outcrossed Populations Beneficial Inserts Rates of Fixation Transposable Elements and Host Evolution Transposable Elements and Chromosomal Rearrangements Transposable Elements and Genome Size Co-Option of Transposable Element Functions and Host Defenses Transposable Elements As Parasites, Not Host Adaptations or Mutualists Origins Ancient, Chimeric, and Polyphyletic Origins 8. FEMALE DRIVE Selfish Centromeres and Female Meiosis Abnormal Chromosome 10 of Maize Other Knobs in Maize Deleterious Effects of Knobs in Maize Knobs, Supernumerary Segments, and Neocentromeres in Other Species Meiosis-Specific Centromeres and Holocentric Chromosomes Selfish Centromeres and Meiosis I The Importance of Centromere Number: Robertsonian Translocations in Mammals Sperm-Dependent Female Drive? Female Drive and Karyotype Evolution Polar Bodies Rejoining the Germline 9. B CHROMOSOMES Drive Types of Drive Genetics of A and B Factors Affecting B Drive Transmission Rates inWell-Studied Species Absence of Drive Degree of Outcrossing and Drive Effects on the Phenotype Effects on Genome Size, Cell Size, and Cell Cycle Effects on the External Phenotype Disappearance from Somatic Tissue B Number and the Odd-Even Effect Negative Effects of Bs More Pronounced under Harsher Conditions Is the Sex of Drive Associated with the Sex of Phenotypic Effect? B Effects on Recombination Among the As Pairing of A Chromosomes in Hybrids Neutral and Beneficial Bs Beneficial B Chromosomes B Chromosomes in Eyprepocnemis plorans: A Case of Continuous Neutralization? Structure and Content Size Polymorphism Heterochromatin Genes Tandem Repeats The Origin of Bs A Factors Associated with B Presence Genome Size Chromosome Number Ploidy Shape of A Chromosomes Bs and the Sex Ratio Paternal Sex Ratio (PSR) in Nasonia X-B Associations in Orthoptera Has the Drosophila Y Evolved from a B? Other Effects of Bs on the Sex Ratio Male Sterility in Plantago 10. GENOMIC EXCLUSION Paternal Genome Loss in Males, or Parahaplodiploidy PGL in Mites PGL in Scale Insects PGL in the Coffee Borer Beetle PGL in Springtails? Evolution of PGL PGL and Haplodiploidy Sciarid Chromosome System Notable Features of the Sciarid System An Evolutionary Hypothesis Mechanisms PGL in Gall Midges Hybridogenesis, or Hemiclonal Reproduction The Topminnow Poeciliopsis The Water Frog Rana esculenta The Stick Insect Bacillus rossius-grandii Evolution of Hybridogenesis Androgenesis, or Maternal Genome Loss The Conifer Cupressus dupreziana The Clam Corbicula The Stick Insect Bacillus rossius-grandii 11. SELFISH CELL LINEAGES Mosaics Somatic Cell Lineage Selection: Cancer and the Adaptive Immune System Cell Lineage Selection in the Germline Evolution of the Germline Selfish Genes and Germline-Limited DNA Chimeras Taxonomic Survey of Chimerism Somatic Chimerism and Polar Bodies 12. SUMMARY AND FUTURE DIRECTIONS Logic of Selfish Genetic Elements Molecular Genetics Selfish Genes and Sex Fate of a Selfish Gene within a Species Movement between Species Distribution among Species Role in Host Evolution The HiddenWorld of Selfish Genetic Elements References Glossary Index

@article{doi105860choice435875,
    title = "Genes in conflict: the biology of selfish genetic elements",
    year = "2006",
    journal = "Choice Reviews Online",
    abstract = "Preface 1. SELFISH GENETIC ELEMENTS Genetic Cooperation and Conflict Three Ways to Achieve Within-Individual Kinship Conflicts Rates of Spread Effects on the Host Population The Study of Selfish Genetic Elements Design of This Book 2. AUTOSOMAL KILLERS The t Haplotype Discovery Structure of the t Haplotype History and Distribution Genetics of Drive Importance of Mating System and Gamete Competition Fate of Resistant Alleles Selection for Inversions Recessive Lethals in t Complexes Enhancers and Suppressors t and the Major Histocompatability Complex Heterozygous (+/t) Fitness Effects: Sex Antagonistic? Accounting for t Frequencies in Nature Other Gamete Killers Segregation Distorter in Drosophila Spore Killers in Fungi Incidence of Gamete Killers Maternal-Effect Killers Medea in Flour Beetles HSR, scat+, and OmDDK in Mice The Evolution of Maternal-Effect Killers Gestational Drive? Gametophyte Factors in Plants 3. SELFISH SEX CHROMOSOMES Sex Chromosome Drive in the Diptera Killer X Chromosomes Killer Y Chromosomes Taxonomic Distribution of Killer Sex Chromosomes Evolutionary Cycles of Sex Determination Feminizing X (and Y) Chromosomes in Rodents The Varying Lemming The Wood Lemming Other Murids Other Conflicts: Sex Ratios and Mate Choice 4. GENOMIC IMPRINTING Imprinting and Parental Investment in Mammals Igf2 and Igf2r: Oppositely Imprinted, Oppositely Acting Growth Factors in Mice Growth Effects of Imprinted Genes in Mice and Humans Evolution of the Imprinting Apparatus The Mechanisms of Imprinting Involve Methylation and Are Complex Conflict Between Different Components of the Imprinting Machinery History of Conflict Reflected in the Imprinting Apparatus Evolutionary Turnover of the Imprinting Apparatus Intralocus Interactions, Polar Overdominance, and Paramutation Transmission Ratio Distortion at Imprinted Loci Biparental Imprinting and Other Possibilities Other Traits: Social Interactions after the Period of Parental Investment Maternal Behavior in Mice Inbreeding and Dispersal Kin Recognition Functional Interpretation of Tissue Effects in Chimeric Mice Deceit and Selves-Deception Imprinting and the Sex Chromosomes Genomic Imprinting in Other Taxa Flowering Plants Other Taxa Predicted to Have Imprinting 5. SELFISH MITOCHONDRIAL DNA Mitochondrial Genomics: A Primer Mitochondrial Selection within the Individual Petite Mutations in Yeast Within-Individual Selection and the Evolution of Uniparental Inheritance Within-Individual Selection under Uniparental Inheritance DUI: Mother-to-Daughter and Father-to-Son mtDNA Inheritance in Mussels Cytoplasmic Male Sterility Uniparental Inheritance Implies Unisexual Selection Disproportionate Role of mtDNA in Plant Male Sterility Mechanisms of Mitochondrial Action and Nuclear Reaction CMS and Restorers in Natural Populations CMS, Masculinization, and the Evolution of Separate Sexes Pollen Limitation, Frequency Dependence, and Local Extinction Resource Reallocation Versus Inbreeding Avoidance Importance of Mutational Variation CMS and Paternal Transmission Other Traces of Mito-Nuclear Conflict Mitochondria and Apoptosis Mitochondria and Germ Cell Determination Mitochondria and RNA Editing 6. GENE CONVERSION AND HOMING Biased Gene Conversion Molecular Mechanisms Effective Selection Coefficients Due to BGC in Fungi BGC and Genome Evolution BGC and Evolution of the Meiotic Machinery Homing and Retrohoming How HEGs Home HEGs Usually Associated with Self-Splicing Introns or Inteins HEGs and Host Mating System Evolutionary Cycle of Horizontal Transmission, Degeneration, and Loss HEG Domestication and Mating-Type Switching in Yeast Group II Introns Artificial HEGs As Tools for Population Genetic Engineering The Basic Construct Increasing the Load Preventing Natural Resistance and Horizontal Transmission Population Genetic Engineering Other Uses 7. TRANSPOSABLE ELEMENTS Molecular Structure and Mechanisms DNA Transposons LINEs and SINEs LTR Retroelements Population Biology and Natural Selection Transposition Rates Low But Greater Than Excision Rates Natural Selection on the Host Slows the Spread of Transposable Elements Rapid Spread of P Elements in D. melanogaster Net Reproductive Rate a Function of Transposition Rate and Effect on Host Fitness Reducing Harm to the Host Transposition Rate and Copy Number Regulation Selection for Self-Recognition Defective and Repressor Elements Extinction of Active Elements in Host Species Horizontal Transmission and Long-Term Persistence Transposable Elements in Inbred and Outcrossed Populations Beneficial Inserts Rates of Fixation Transposable Elements and Host Evolution Transposable Elements and Chromosomal Rearrangements Transposable Elements and Genome Size Co-Option of Transposable Element Functions and Host Defenses Transposable Elements As Parasites, Not Host Adaptations or Mutualists Origins Ancient, Chimeric, and Polyphyletic Origins 8. FEMALE DRIVE Selfish Centromeres and Female Meiosis Abnormal Chromosome 10 of Maize Other Knobs in Maize Deleterious Effects of Knobs in Maize Knobs, Supernumerary Segments, and Neocentromeres in Other Species Meiosis-Specific Centromeres and Holocentric Chromosomes Selfish Centromeres and Meiosis I The Importance of Centromere Number: Robertsonian Translocations in Mammals Sperm-Dependent Female Drive? Female Drive and Karyotype Evolution Polar Bodies Rejoining the Germline 9. B CHROMOSOMES Drive Types of Drive Genetics of A and B Factors Affecting B Drive Transmission Rates inWell-Studied Species Absence of Drive Degree of Outcrossing and Drive Effects on the Phenotype Effects on Genome Size, Cell Size, and Cell Cycle Effects on the External Phenotype Disappearance from Somatic Tissue B Number and the Odd-Even Effect Negative Effects of Bs More Pronounced under Harsher Conditions Is the Sex of Drive Associated with the Sex of Phenotypic Effect? B Effects on Recombination Among the As Pairing of A Chromosomes in Hybrids Neutral and Beneficial Bs Beneficial B Chromosomes B Chromosomes in Eyprepocnemis plorans: A Case of Continuous Neutralization? Structure and Content Size Polymorphism Heterochromatin Genes Tandem Repeats The Origin of Bs A Factors Associated with B Presence Genome Size Chromosome Number Ploidy Shape of A Chromosomes Bs and the Sex Ratio Paternal Sex Ratio (PSR) in Nasonia X-B Associations in Orthoptera Has the Drosophila Y Evolved from a B? Other Effects of Bs on the Sex Ratio Male Sterility in Plantago 10. GENOMIC EXCLUSION Paternal Genome Loss in Males, or Parahaplodiploidy PGL in Mites PGL in Scale Insects PGL in the Coffee Borer Beetle PGL in Springtails? Evolution of PGL PGL and Haplodiploidy Sciarid Chromosome System Notable Features of the Sciarid System An Evolutionary Hypothesis Mechanisms PGL in Gall Midges Hybridogenesis, or Hemiclonal Reproduction The Topminnow Poeciliopsis The Water Frog Rana esculenta The Stick Insect Bacillus rossius-grandii Evolution of Hybridogenesis Androgenesis, or Maternal Genome Loss The Conifer Cupressus dupreziana The Clam Corbicula The Stick Insect Bacillus rossius-grandii 11. SELFISH CELL LINEAGES Mosaics Somatic Cell Lineage Selection: Cancer and the Adaptive Immune System Cell Lineage Selection in the Germline Evolution of the Germline Selfish Genes and Germline-Limited DNA Chimeras Taxonomic Survey of Chimerism Somatic Chimerism and Polar Bodies 12. SUMMARY AND FUTURE DIRECTIONS Logic of Selfish Genetic Elements Molecular Genetics Selfish Genes and Sex Fate of a Selfish Gene within a Species Movement between Species Distribution among Species Role in Host Evolution The HiddenWorld of Selfish Genetic Elements References Glossary Index",
    url = "https://doi.org/10.5860/choice.43-5875",
    doi = "10.5860/choice.43-5875",
    openalex = "W1608363683"
}

CHAPTER 1 The Genome for Animal Development CHAPTER 2 cis-Regulatory Modules, and the Structure/Function Basis of Regulatory Logic CHAPTER 3 Development as a Process of Regulatory State Specification CHAPTER 4 Gene Regulatory Networks for Development: What They Are, How They Work, and What They Mean CHAPTER 5 Gene Regulatory Networks: The Roots of Causality and Diversity in Animal Evolution

@book{openalexw614012683,
    author = "Davidson, Eric H.",
    title = "The Regulatory Genome: Gene Regulatory Networks In Development And Evolution",
    year = "2006",
    abstract = "CHAPTER 1 The Genome for Animal Development CHAPTER 2 cis-Regulatory Modules, and the Structure/Function Basis of Regulatory Logic CHAPTER 3 Development as a Process of Regulatory State Specification CHAPTER 4 Gene Regulatory Networks for Development: What They Are, How They Work, and What They Mean CHAPTER 5 Gene Regulatory Networks: The Roots of Causality and Diversity in Animal Evolution",
    openalex = "W614012683"
}

@article{doi101016jcell200710022,
    author = "Otto, Sarah P.",
    title = "The Evolutionary Consequences of Polyploidy",
    year = "2007",
    journal = "Cell",
    url = "https://doi.org/10.1016/j.cell.2007.10.022",
    doi = "10.1016/j.cell.2007.10.022",
    openalex = "W2010032067",
    references = "doi101371journalpbio0030314, openalexw1493831303, openalexw2065039187"
}

@article{doi101016jcub200706004,
    author = "West, Stuart A. and Griffin, Ashleigh S. and Gardner, Andy",
    title = "Evolutionary Explanations for Cooperation",
    year = "2007",
    journal = "Current Biology",
    url = "https://doi.org/10.1016/j.cub.2007.06.004",
    doi = "10.1016/j.cub.2007.06.004",
    openalex = "W2143868963",
    references = "doi1010160022519364900384, doi101038359826a0, doi101038415137a, doi10108019390450903037302, doi101086383541, doi101086406755, doi101111j143903101963tb01161x, doi101126science1133755, doi101126science16238591243, doi101126science7466396, doi105860choice435875, openalexw2624262714"
}

@article{doi101038nature06341,
    author = "Aquadro, Charles F. and Ram, K. Ravi and Wolfner, Mariana F. and Clark, Andrew G. and Wong, Alex and Yang, Hsiao-Pei and Singh, Nadia D. and Greenberg, Anthony J. and Huntley, Melanie A. and Larracuente, Amanda M. and Sirot, Laura K. and Sackton, Timothy B. and Barbash, Daniel A. and Eisen, Michael B. and Hoskins, Roger A. and Celniker, S and Eisen, Michael B. and Brand, Adrianne and Ebling, Heather and David, Robert and Wei, Tao and Bosak, Stephanie and Garvin, Barry E. and McKernan, Kevin and Rubenfield, Marc and Tsolas, Jason M. and Parisi, Matthew J. and Gustafson, Erik and Saranga, David J. and Smith, Douglas R. and McKernan, Brendan and Griffiths‐Jones, Sam and Bergman, Casey and Sturgill, David and Oliver, Brian and Parisi, Michael and Zhang, Yu and Markow, Therese A. and Watts, Thomas D. and Machado, Carlos A. and Matzkin, Luciano M. and Kwok, Roberta and Gilbert, Don and Kaufman, Thomas C. and Hahn, Matthew W. and Kheradpour, Pouya and Rasmussen, M. D. and Stark, Alexander and Kellis, M. and Lin, Michael F. and Parts, Leopold and Dupes, Alan and Jaffe, David B. and Farina, Abderrahim and Gnerre, Sante and Nguyen, Nga Thi Thuy and Shea, Terry and Zimmer, Andrew and Mauceli, Evan and Ryan, Elizabeth and Bourzgui, Imane and Sherpa, Ngawang and Wangdi, Tsering and Dhargay, Norbu and Lara, Marcia and Liu, Jinlei and Reyes, Rebecca and Vassiliev, Helen and Anderson, Erica and Liu, Shangtao and Mihova, Tanya and Negash, Tamrat and Strader, C. and Mehta, Teena and Rise, Cecil and Brockman, Will and Azer, Marc and Norbu, Choe and Hollinger, Andrew and Degray, Stuart and Fritz, P and Patti, Christopher and Phunkhang, Pema and Brown, Adam and Meldrim, James C. and Shi, Lu and Bachantsang, Pasang and Hall, Jennifer L. and Lokyitsang, Yeshi and Lui, Annie and D'Aco, Katie and MacDonald, Pen and Costello, Maura and Abdouelleil, Amr and Thoulutsang, Dawa and Meneus, Louis and Citroen, Mieke and Wilkinson, Jane and Lindblad-Toh, Kerstin and Gearin, Christina R.",
    title = "Evolution of genes and genomes on the Drosophila phylogeny",
    year = "2007",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature06341",
    doi = "10.1038/nature06341",
    openalex = "W2099762535",
    references = "doi101016s0378111900005333, doi101038276565a0"
}

@article{doi101038nrg2063,
    author = "Wray, Gregory A.",
    title = "The evolutionary significance of cis-regulatory mutations",
    year = "2007",
    journal = "Nature Reviews Genetics",
    url = "https://doi.org/10.1038/nrg2063",
    doi = "10.1038/nrg2063",
    openalex = "W2012354488",
    references = "doi101016s0022283661800727, doi10103835046017, doi101038nature02415, doi101038ng1946, doi101038sjmp4001851, doi101056nejm197608052950602, doi101073pnas0431157100, doi101073pnas9794530, doi101086406830, doi101086421051, doi101093genetics15141531, doi101093molbevmsg140, doi101111j001438202000tb00544x, doi101126science1071829, doi101126science1072290, doi101126science1090005"
}

Abstract Even before the publication of Darwin's Origin of Species, the perception of evolutionary change has been a tree-like pattern of diversification — with divergent branches spreading further and further from the trunk. In the only illustration of Darwin's treatise, branches large and small never reconnect. However, it is now evident that this view does not adequately encompass the richness of evolutionary pattern and process. Instead, the evolution of species from microbes to mammals builds like a web that crosses and re-crosses through genetic exchange, even as it grows outward from a point of origin. Some of the avenues for genetic exchange, for example introgression through sexual recombination versus lateral gene transfer mediated by transposable elements, are based on definably different molecular mechanisms. However, even such widely different genetic processes may result in similar effects on adaptations (either new or transferred), genome evolution, population genetics, and the evolutionary/ecological trajectory of organisms. For example, the evolution of novel adaptations (resulting from lateral gene transfer) leading to the flea-borne, deadly, causative agent of plague from a rarely-fatal, orally-transmitted, bacterial species is quite similar to the adaptations accrued from natural hybridization between annual sunflower species resulting in the formation of several new species. Thus, more and more data indicate that evolution has resulted in lineages consisting of mosaics of genes derived from different ancestors. It is therefore becoming increasingly clear that the tree is an inadequate metaphor of evolutionary change. In this book, the author promotes the ‘web-of-life’ metaphor as a more appropriate representation of evolutionary change in all life-forms.

@book{doi101093acprofoso97801992290310010001,
    author = "Arnold, Michael L.",
    title = "Evolution through Genetic Exchange",
    year = "2007",
    booktitle = "Oxford University Press eBooks",
    abstract = "Abstract Even before the publication of Darwin's Origin of Species, the perception of evolutionary change has been a tree-like pattern of diversification — with divergent branches spreading further and further from the trunk. In the only illustration of Darwin's treatise, branches large and small never reconnect. However, it is now evident that this view does not adequately encompass the richness of evolutionary pattern and process. Instead, the evolution of species from microbes to mammals builds like a web that crosses and re-crosses through genetic exchange, even as it grows outward from a point of origin. Some of the avenues for genetic exchange, for example introgression through sexual recombination versus lateral gene transfer mediated by transposable elements, are based on definably different molecular mechanisms. However, even such widely different genetic processes may result in similar effects on adaptations (either new or transferred), genome evolution, population genetics, and the evolutionary/ecological trajectory of organisms. For example, the evolution of novel adaptations (resulting from lateral gene transfer) leading to the flea-borne, deadly, causative agent of plague from a rarely-fatal, orally-transmitted, bacterial species is quite similar to the adaptations accrued from natural hybridization between annual sunflower species resulting in the formation of several new species. Thus, more and more data indicate that evolution has resulted in lineages consisting of mosaics of genes derived from different ancestors. It is therefore becoming increasingly clear that the tree is an inadequate metaphor of evolutionary change. In this book, the author promotes the ‘web-of-life’ metaphor as a more appropriate representation of evolutionary change in all life-forms.",
    url = "https://doi.org/10.1093/acprof:oso/9780199229031.001.0001",
    doi = "10.1093/acprof:oso/9780199229031.001.0001",
    openalex = "W1540818229"
}

Rapid climate change is likely to impose strong selection pressures on traits important for fitness, and therefore, microevolution in response to climate-mediated selection is potentially an important mechanism mitigating negative consequences of climate change. We reviewed the empirical evidence for recent microevolutionary responses to climate change in longitudinal studies emphasizing the following three perspectives emerging from the published data. First, although signatures of climate change are clearly visible in many ecological processes, similar examples of microevolutionary responses in literature are in fact very rare. Second, the quality of evidence for microevolutionary responses to climate change is far from satisfactory as the documented responses are often - if not typically - based on nongenetic data. We reinforce the view that it is as important to make the distinction between genetic (evolutionary) and phenotypic (includes a nongenetic, plastic component) responses clear, as it is to understand the relative roles of plasticity and genetics in adaptation to climate change. Third, in order to illustrate the difficulties and their potential ubiquity in detection of microevolution in response to natural selection, we reviewed the quantitative genetic studies on microevolutionary responses to natural selection in the context of long-term studies of vertebrates. The available evidence points to the overall conclusion that many responses perceived as adaptations to changing environmental conditions could be environmentally induced plastic responses rather than microevolutionary adaptations. Hence, clear-cut evidence indicating a significant role for evolutionary adaptation to ongoing climate warming is conspicuously scarce.

@article{doi101111j1365294x200703413x,
    author = "Gienapp, Phillip and Teplitsky, Céline and Alho, Jussi and Mills, James A. and Merilä, Juha",
    title = "Climate change and evolution: disentangling environmental and genetic responses",
    year = "2007",
    journal = "Molecular Ecology",
    abstract = "Rapid climate change is likely to impose strong selection pressures on traits important for fitness, and therefore, microevolution in response to climate-mediated selection is potentially an important mechanism mitigating negative consequences of climate change. We reviewed the empirical evidence for recent microevolutionary responses to climate change in longitudinal studies emphasizing the following three perspectives emerging from the published data. First, although signatures of climate change are clearly visible in many ecological processes, similar examples of microevolutionary responses in literature are in fact very rare. Second, the quality of evidence for microevolutionary responses to climate change is far from satisfactory as the documented responses are often - if not typically - based on nongenetic data. We reinforce the view that it is as important to make the distinction between genetic (evolutionary) and phenotypic (includes a nongenetic, plastic component) responses clear, as it is to understand the relative roles of plasticity and genetics in adaptation to climate change. Third, in order to illustrate the difficulties and their potential ubiquity in detection of microevolution in response to natural selection, we reviewed the quantitative genetic studies on microevolutionary responses to natural selection in the context of long-term studies of vertebrates. The available evidence points to the overall conclusion that many responses perceived as adaptations to changing environmental conditions could be environmentally induced plastic responses rather than microevolutionary adaptations. Hence, clear-cut evidence indicating a significant role for evolutionary adaptation to ongoing climate warming is conspicuously scarce.",
    url = "https://doi.org/10.1111/j.1365-294x.2007.03413.x",
    doi = "10.1111/j.1365-294x.2007.03413.x",
    openalex = "W2153330886",
    references = "doi101007978940100585210, doi101016s0169534702000447, doi101038nature02415, doi101038nature04843, doi101126science1070315, doi101126science1098095"
}

Invasive species are predicted to suffer from reductions in genetic diversity during founding events, reducing adaptive potential. Integrating evidence from two literature reviews and two case studies, we address the following questions: How much genetic diversity is lost in invasions? Do multiple introductions ameliorate this loss? Is there evidence for loss of diversity in quantitative traits? Do invaders that have experienced strong bottlenecks show adaptive evolution? How do multiple introductions influence adaptation on a landscape scale? We reviewed studies of 80 species of animals, plants, and fungi that quantified nuclear molecular diversity within introduced and source populations. Overall, there were significant losses of both allelic richness and heterozygosity in introduced populations, and large gains in diversity were rare. Evidence for multiple introductions was associated with increased diversity, and allelic variation appeared to increase over long timescales (~100 years), suggesting a role for gene flow in augmenting diversity over the long-term. We then reviewed the literature on quantitative trait diversity and found that broad-sense variation rarely declines in introductions, but direct comparisons of additive variance were lacking. Our studies of Hypericum canariense invasions illustrate how populations with diminished diversity may still evolve rapidly. Given the prevalence of genetic bottlenecks in successful invading populations and the potential for adaptive evolution in quantitative traits, we suggest that the disadvantages associated with founding events may have been overstated. However, our work on the successful invader Verbascum thapsus illustrates how multiple introductions may take time to commingle, instead persisting as a 'mosaic of maladaptation' where traits are not distributed in a pattern consistent with adaptation. We conclude that management limiting gene flow among introduced populations may reduce adaptive potential but is unlikely to prevent expansion or the evolution of novel invasive behaviour.

@article{doi101111j1365294x200703538x,
    author = "Dlugosch, Katrina M. and Parker, Ingrid M.",
    title = "Founding events in species invasions: genetic variation, adaptive evolution, and the role of multiple introductions",
    year = "2007",
    journal = "Molecular Ecology",
    abstract = "Invasive species are predicted to suffer from reductions in genetic diversity during founding events, reducing adaptive potential. Integrating evidence from two literature reviews and two case studies, we address the following questions: How much genetic diversity is lost in invasions? Do multiple introductions ameliorate this loss? Is there evidence for loss of diversity in quantitative traits? Do invaders that have experienced strong bottlenecks show adaptive evolution? How do multiple introductions influence adaptation on a landscape scale? We reviewed studies of 80 species of animals, plants, and fungi that quantified nuclear molecular diversity within introduced and source populations. Overall, there were significant losses of both allelic richness and heterozygosity in introduced populations, and large gains in diversity were rare. Evidence for multiple introductions was associated with increased diversity, and allelic variation appeared to increase over long timescales (\textasciitilde 100 years), suggesting a role for gene flow in augmenting diversity over the long-term. We then reviewed the literature on quantitative trait diversity and found that broad-sense variation rarely declines in introductions, but direct comparisons of additive variance were lacking. Our studies of Hypericum canariense invasions illustrate how populations with diminished diversity may still evolve rapidly. Given the prevalence of genetic bottlenecks in successful invading populations and the potential for adaptive evolution in quantitative traits, we suggest that the disadvantages associated with founding events may have been overstated. However, our work on the successful invader Verbascum thapsus illustrates how multiple introductions may take time to commingle, instead persisting as a 'mosaic of maladaptation' where traits are not distributed in a pattern consistent with adaptation. We conclude that management limiting gene flow among introduced populations may reduce adaptive potential but is unlikely to prevent expansion or the evolution of novel invasive behaviour.",
    url = "https://doi.org/10.1111/j.1365-294x.2007.03538.x",
    doi = "10.1111/j.1365-294x.2007.03538.x",
    openalex = "W2168307546",
    references = "doi101007978940100585210, doi101016s0169534702000447, doi101016s0169534702025545, doi101146annurevecolsys32081501114037"
}

An important tenet of evolutionary developmental biology ("evo devo") is that adaptive mutations affecting morphology are more likely to occur in the cis-regulatory regions than in the protein-coding regions of genes. This argument rests on two claims: (1) the modular nature of cis-regulatory elements largely frees them from deleterious pleiotropic effects, and (2) a growing body of empirical evidence appears to support the predominant role of gene regulatory change in adaptation, especially morphological adaptation. Here we discuss and critique these assertions. We first show that there is no theoretical or empirical basis for the evo devo contention that adaptations involving morphology evolve by genetic mechanisms different from those involving physiology and other traits. In addition, some forms of protein evolution can avoid the negative consequences of pleiotropy, most notably via gene duplication. In light of evo devo claims, we then examine the substantial data on the genetic basis of adaptation from both genome-wide surveys and single-locus studies. Genomic studies lend little support to the cis-regulatory theory: many of these have detected adaptation in protein-coding regions, including transcription factors, whereas few have examined regulatory regions. Turning to single-locus studies, we note that the most widely cited examples of adaptive cis-regulatory mutations focus on trait loss rather than gain, and none have yet pinpointed an evolved regulatory site. In contrast, there are many studies that have both identified structural mutations and functionally verified their contribution to adaptation and speciation. Neither the theoretical arguments nor the data from nature, then, support the claim for a predominance of cis-regulatory mutations in evolution. Although this claim may be true, it is at best premature. Adaptation and speciation probably proceed through a combination of cis-regulatory and structural mutations, with a substantial contribution of the latter.

@article{doi101111j15585646200700105x,
    author = "Hoekstra, Hopi E. and Coyne, Jerry A.",
    title = "THE LOCUS OF EVOLUTION: EVO DEVO AND THE GENETICS OF ADAPTATION",
    year = "2007",
    journal = "Evolution",
    abstract = {An important tenet of evolutionary developmental biology ("evo devo") is that adaptive mutations affecting morphology are more likely to occur in the cis-regulatory regions than in the protein-coding regions of genes. This argument rests on two claims: (1) the modular nature of cis-regulatory elements largely frees them from deleterious pleiotropic effects, and (2) a growing body of empirical evidence appears to support the predominant role of gene regulatory change in adaptation, especially morphological adaptation. Here we discuss and critique these assertions. We first show that there is no theoretical or empirical basis for the evo devo contention that adaptations involving morphology evolve by genetic mechanisms different from those involving physiology and other traits. In addition, some forms of protein evolution can avoid the negative consequences of pleiotropy, most notably via gene duplication. In light of evo devo claims, we then examine the substantial data on the genetic basis of adaptation from both genome-wide surveys and single-locus studies. Genomic studies lend little support to the cis-regulatory theory: many of these have detected adaptation in protein-coding regions, including transcription factors, whereas few have examined regulatory regions. Turning to single-locus studies, we note that the most widely cited examples of adaptive cis-regulatory mutations focus on trait loss rather than gain, and none have yet pinpointed an evolved regulatory site. In contrast, there are many studies that have both identified structural mutations and functionally verified their contribution to adaptation and speciation. Neither the theoretical arguments nor the data from nature, then, support the claim for a predominance of cis-regulatory mutations in evolution. Although this claim may be true, it is at best premature. Adaptation and speciation probably proceed through a combination of cis-regulatory and structural mutations, with a substantial contribution of the latter.},
    url = "https://doi.org/10.1111/j.1558-5646.2007.00105.x",
    doi = "10.1111/j.1558-5646.2007.00105.x",
    openalex = "W2101103652",
    references = "doi1010079783642866593, doi101016s0022283661800727, doi101017s0094837300005224, doi101038366223a0, doi10103847412, doi101038nature04843, doi101038nrg2063, doi101038scientificamerican117998, doi101038sjhdy6800154, doi101073pnas0431157100, doi101073pnas7183028, doi101073pnas9794530, doi101093molbevmsg140, doi101111j001438202000tb00544x, doi101111j001438202004tb00462x, doi101126science1090005, doi101126science1098095, doi101126science1113832, doi101126science29054941151, doi101126science860134, doi101146annurevphysiol631359, doi101371journalpbio0030245, doi105860choice395182, doi105962bhltitle27468, openalexw3135630760"
}

@article{doi101016jcell200806030,
    author = "Carroll, Sean B.",
    title = "Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution",
    year = "2008",
    journal = "Cell",
    url = "https://doi.org/10.1016/j.cell.2008.06.030",
    doi = "10.1016/j.cell.2008.06.030",
    openalex = "W2171193618",
    references = "doi1010079783642866593, doi101016b9781483227344500176, doi101038276565a0, doi101038376479a0, doi10103841710, doi101038nature02415, doi101038nature03158, doi101038nrg2063, doi101086406830, doi101111j001438202000tb00544x, doi101111j15585646200700105x, doi101126science1090005, doi101126science1107239, doi101126science147365368, doi101126science7892602, doi101242dev1212333, doi101371journalpbio0030245, doi105860choice395182, openalexw591049712, openalexw614012683"
}

@article{doi101038nrg2398,
    author = "López‐Maury, Luis and Marguerat, Samuel and Bähler, Jürg",
    title = "Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation",
    year = "2008",
    journal = "Nature Reviews Genetics",
    url = "https://doi.org/10.1038/nrg2398",
    doi = "10.1038/nrg2398",
    openalex = "W2028979517",
    references = "doi101038nrg1088, doi101038nrg2063"
}

@article{doi101038nrg2452,
    author = "Phillips, Patrick C.",
    title = "Epistasis — the essential role of gene interactions in the structure and evolution of genetic systems",
    year = "2008",
    journal = "Nature Reviews Genetics",
    url = "https://doi.org/10.1038/nrg2452",
    doi = "10.1038/nrg2452",
    openalex = "W2094189284",
    references = "doi1010160020711x94901198, doi101017s0080456800012163, doi101038091009b0, doi101038nature05874, doi101038nature05911, doi101038ng1537, doi101073pnas0702207104, doi101093hmg11202463, doi101111j001438202003tb00377x, doi101126science1065810, doi101126science1091317, doi101126science1123348, doi101126science1123539, doi101126science860134, doi101159000073735, doi105962bhltitle27468, doi105962bhltitle44575, openalexw1554403518"
}

The relative proportion of additive and non-additive variation for complex traits is important in evolutionary biology, medicine, and agriculture. We address a long-standing controversy and paradox about the contribution of non-additive genetic variation, namely that knowledge about biological pathways and gene networks imply that epistasis is important. Yet empirical data across a range of traits and species imply that most genetic variance is additive. We evaluate the evidence from empirical studies of genetic variance components and find that additive variance typically accounts for over half, and often close to 100%, of the total genetic variance. We present new theoretical results, based upon the distribution of allele frequencies under neutral and other population genetic models, that show why this is the case even if there are non-additive effects at the level of gene action. We conclude that interactions at the level of genes are not likely to generate much interaction at the level of variance.

@article{doi101371journalpgen1000008,
    author = "Hill, William G. and Goddard, Michael E. and Visscher, Peter M.",
    title = "Data and Theory Point to Mainly Additive Genetic Variance for Complex Traits",
    year = "2008",
    journal = "PLoS Genetics",
    abstract = "The relative proportion of additive and non-additive variation for complex traits is important in evolutionary biology, medicine, and agriculture. We address a long-standing controversy and paradox about the contribution of non-additive genetic variation, namely that knowledge about biological pathways and gene networks imply that epistasis is important. Yet empirical data across a range of traits and species imply that most genetic variance is additive. We evaluate the evidence from empirical studies of genetic variance components and find that additive variance typically accounts for over half, and often close to 100\%, of the total genetic variance. We present new theoretical results, based upon the distribution of allele frequencies under neutral and other population genetic models, that show why this is the case even if there are non-additive effects at the level of gene action. We conclude that interactions at the level of genes are not likely to generate much interaction at the level of variance.",
    url = "https://doi.org/10.1371/journal.pgen.1000008",
    doi = "10.1371/journal.pgen.1000008",
    openalex = "W2072214908",
    references = "doi1010160169534789900372, doi101038nrg700"
}

Abstract Evolutionary dynamics shape the living world around us. At the centre of every evolutionary process is a population of reproducing individuals. The structure of that population affects evolutionary dynamics. The individuals can be molecules, cells, viruses, multicellular organisms or humans. Whenever the fitness of individuals depends on the relative abundance of phenotypes in the population, we are in the realm of evolutionary game theory. Evolutionary game theory is a general approach that can describe the competition of species in an ecosystem, the interaction between hosts and parasites, between viruses and cells, and also the spread of ideas and behaviours in the human population. In this perspective, we review the recent advances in evolutionary game dynamics with a particular emphasis on stochastic approaches in finite sized and structured populations. We give simple, fundamental laws that determine how natural selection chooses between competing strategies. We study the well-mixed population, evolutionary graph theory, games in phenotype space and evolutionary set theory. We apply these results to the evolution of cooperation. The mechanism that leads to the evolution of cooperation in these settings could be called ‘spatial selection’: cooperators prevail against defectors by clustering in physical or other spaces.

@article{doi101098rstb20090215,
    author = "Nowak, Martin A. and Tarnita, Corina E. and Antal, Tibor",
    title = "Evolutionary dynamics in structured populations",
    year = "2009",
    journal = "Philosophical Transactions of the Royal Society B Biological Sciences",
    abstract = "Abstract Evolutionary dynamics shape the living world around us. At the centre of every evolutionary process is a population of reproducing individuals. The structure of that population affects evolutionary dynamics. The individuals can be molecules, cells, viruses, multicellular organisms or humans. Whenever the fitness of individuals depends on the relative abundance of phenotypes in the population, we are in the realm of evolutionary game theory. Evolutionary game theory is a general approach that can describe the competition of species in an ecosystem, the interaction between hosts and parasites, between viruses and cells, and also the spread of ideas and behaviours in the human population. In this perspective, we review the recent advances in evolutionary game dynamics with a particular emphasis on stochastic approaches in finite sized and structured populations. We give simple, fundamental laws that determine how natural selection chooses between competing strategies. We study the well-mixed population, evolutionary graph theory, games in phenotype space and evolutionary set theory. We apply these results to the evolution of cooperation. The mechanism that leads to the evolution of cooperation in these settings could be called ‘spatial selection’: cooperators prevail against defectors by clustering in physical or other spaces.",
    url = "https://doi.org/10.1098/rstb.2009.0215",
    doi = "10.1098/rstb.2009.0215",
    openalex = "W2167637335",
    references = "doi101007bf00420631, doi101016jcub200706004, doi101023a1020504900646, doi101111j155856461977tb00991x"
}

Adaptation to a sudden extreme change in environment, beyond the usual range of background environmental fluctuations, is analysed using a quantitative genetic model of phenotypic plasticity. Generations are discrete, with time lag tau between a critical period for environmental influence on individual development and natural selection on adult phenotypes. The optimum phenotype, and genotypic norms of reaction, are linear functions of the environment. Reaction norm elevation and slope (plasticity) vary among genotypes. Initially, in the average background environment, the character is canalized with minimum genetic and phenotypic variance, and no correlation between reaction norm elevation and slope. The optimal plasticity is proportional to the predictability of environmental fluctuations over time lag tau. During the first generation in the new environment the mean fitness suddenly drops and the mean phenotype jumps towards the new optimum phenotype by plasticity. Subsequent adaptation occurs in two phases. Rapid evolution of increased plasticity allows the mean phenotype to closely approach the new optimum. The new phenotype then undergoes slow genetic assimilation, with reduction in plasticity compensated by genetic evolution of reaction norm elevation in the original environment.

@article{doi101111j14209101200901754x,
    author = "Lande, Russell",
    title = "Adaptation to an extraordinary environment by evolution of phenotypic plasticity and genetic assimilation",
    year = "2009",
    journal = "Journal of Evolutionary Biology",
    abstract = "Adaptation to a sudden extreme change in environment, beyond the usual range of background environmental fluctuations, is analysed using a quantitative genetic model of phenotypic plasticity. Generations are discrete, with time lag tau between a critical period for environmental influence on individual development and natural selection on adult phenotypes. The optimum phenotype, and genotypic norms of reaction, are linear functions of the environment. Reaction norm elevation and slope (plasticity) vary among genotypes. Initially, in the average background environment, the character is canalized with minimum genetic and phenotypic variance, and no correlation between reaction norm elevation and slope. The optimal plasticity is proportional to the predictability of environmental fluctuations over time lag tau. During the first generation in the new environment the mean fitness suddenly drops and the mean phenotype jumps towards the new optimum phenotype by plasticity. Subsequent adaptation occurs in two phases. Rapid evolution of increased plasticity allows the mean phenotype to closely approach the new optimum. The new phenotype then undergoes slow genetic assimilation, with reduction in plasticity compensated by genetic evolution of reaction norm elevation in the original environment.",
    url = "https://doi.org/10.1111/j.1420-9101.2009.01754.x",
    doi = "10.1111/j.1420-9101.2009.01754.x",
    openalex = "W2002666608",
    references = "doi101001jama195002910300087029, doi1010160168952596814582, doi101017s0016672300016037, doi101086276408, doi101111j001438202003tb00377x, doi101126science1157707, doi105962bhltitle84435, openalexw2416298343, openalexw2971318137"
}

@article{openalexw2611511275,
    author = "Maddison, Wayne P. and Maddison, David R.",
    title = "Mesquite: a modular system for evolutionary analysis. Version 2.6",
    year = "2009",
    openalex = "W2611511275"
}

Ecology Letters (2010) 13: 1459-1474 ABSTRACT: There is growing concern that rapid environmental degradation threatens mutualistic interactions. Because mutualisms can bind species to a common fate, mutualism breakdown has the potential to expand and accelerate effects of global change on biodiversity loss and ecosystem disruption. The current focus on the ecological dynamics of mutualism under global change has skirted fundamental evolutionary issues. Here, we develop an evolutionary perspective on mutualism breakdown to complement the ecological perspective, by focusing on three processes: (1) shifts from mutualism to antagonism, (2) switches to novel partners and (3) mutualism abandonment. We then identify the evolutionary factors that may make particular classes of mutualisms especially susceptible or resistant to breakdown and discuss how communities harbouring mutualisms may be affected by these evolutionary responses. We propose a template for evolutionary research on mutualism resilience and identify conservation approaches that may help conserve targeted mutualisms in the face of environmental change.

@article{doi101111j14610248201001538x,
    author = "Kiers, E. Toby and Palmer, Todd M. and Ives, Anthony R. and Bruno, John F. and Bronstein, Judith L.",
    title = "Mutualisms in a changing world: an evolutionary perspective",
    year = "2010",
    journal = "Ecology Letters",
    abstract = "Ecology Letters (2010) 13: 1459-1474 ABSTRACT: There is growing concern that rapid environmental degradation threatens mutualistic interactions. Because mutualisms can bind species to a common fate, mutualism breakdown has the potential to expand and accelerate effects of global change on biodiversity loss and ecosystem disruption. The current focus on the ecological dynamics of mutualism under global change has skirted fundamental evolutionary issues. Here, we develop an evolutionary perspective on mutualism breakdown to complement the ecological perspective, by focusing on three processes: (1) shifts from mutualism to antagonism, (2) switches to novel partners and (3) mutualism abandonment. We then identify the evolutionary factors that may make particular classes of mutualisms especially susceptible or resistant to breakdown and discuss how communities harbouring mutualisms may be affected by these evolutionary responses. We propose a template for evolutionary research on mutualism resilience and identify conservation approaches that may help conserve targeted mutualisms in the face of environmental change.",
    url = "https://doi.org/10.1111/j.1461-0248.2010.01538.x",
    doi = "10.1111/j.1461-0248.2010.01538.x",
    openalex = "W2170289272",
    references = "doi101016jcub200706004"
}

One of the most important shifts in evolutionary biology in the past 50 years is an increased recognition of sluggish evolution and failures to adapt, which seem paradoxical in view of abundant genetic variation and many instances of rapid local adaptation. I review hypotheses of evolutionary constraint (or restraint), and suggest that although constraints on individual characters or character complexes may often reside in the structure or paucity of genetic variation, organism-wide stasis, as described by paleontologists, might better be explained by a hypothesis of ephemeral divergence, according to which the spatial or temporal divergence of populations is often short-lived because of interbreeding with nondivergent populations. Among the many consequences of acknowledging evolutionary constraints, community ecology is being transformed as it takes into account phylogenetic niche conservatism and the strong imprint of deep history.

@article{doi101111j15585646201000960x,
    author = "Futuyma, Douglas J.",
    title = "EVOLUTIONARY CONSTRAINT AND ECOLOGICAL CONSEQUENCES",
    year = "2010",
    journal = "Evolution",
    abstract = "One of the most important shifts in evolutionary biology in the past 50 years is an increased recognition of sluggish evolution and failures to adapt, which seem paradoxical in view of abundant genetic variation and many instances of rapid local adaptation. I review hypotheses of evolutionary constraint (or restraint), and suggest that although constraints on individual characters or character complexes may often reside in the structure or paucity of genetic variation, organism-wide stasis, as described by paleontologists, might better be explained by a hypothesis of ephemeral divergence, according to which the spatial or temporal divergence of populations is often short-lived because of interbreeding with nondivergent populations. Among the many consequences of acknowledging evolutionary constraints, community ecology is being transformed as it takes into account phylogenetic niche conservatism and the strong imprint of deep history.",
    url = "https://doi.org/10.1111/j.1558-5646.2010.00960.x",
    doi = "10.1111/j.1558-5646.2010.00960.x",
    openalex = "W1989499709",
    references = "doi101016s003101829600096x, doi10106313050879, doi101073pnas0704088104, doi101093acprofoso97801992290310010001, doi101093genetics16297, doi101093oso97801985052350010001, doi101098rspb19790086, doi101098rstb20031393, doi101111j1365294x200803899x, doi101111j1525142x200600101x, doi101111j155856461964tb01674x, doi101111j155856461975tb00851x, doi101146annurevecolsys33010802150448, doi101146annureves10110179001335, doi104159harvard9780674865327, doi105860choice415285, openalexw295599524, openalexw3135630760"
}

@article{doi101038nrg3095,
    author = "Wittkopp, Patricia J. and Kalay, Gizem",
    title = "Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence",
    year = "2011",
    journal = "Nature Reviews Genetics",
    url = "https://doi.org/10.1038/nrg3095",
    doi = "10.1038/nrg3095",
    openalex = "W2089806726",
    references = "doi101016jcell200806030, doi101038nrg2063, doi101111j15585646200700105x, doi101111j15585646200800450x, doi101126science1208227"
}

Explaining the origins of novel traits is central to evolutionary biology. Longstanding theory suggests that developmental plasticity, the ability of an individual to modify its development in response to environmental conditions, might facilitate the evolution of novel traits. Yet whether and how such developmental flexibility promotes innovations that persist over evolutionary time remains unclear. Here, we examine three distinct ways by which developmental plasticity can promote evolutionary innovation. First, we show how the process of genetic accommodation provides a feasible and possibly common avenue by which environmentally induced phenotypes can become subject to heritable modification. Second, we posit that the developmental underpinnings of plasticity increase the degrees of freedom by which environmental and genetic factors influence ontogeny, thereby diversifying targets for evolutionary processes to act on and increasing opportunities for the construction of novel, functional and potentially adaptive phenotypes. Finally, we examine the developmental genetic architectures of environment-dependent trait expression, and highlight their specific implications for the evolutionary origin of novel traits. We critically review the empirical evidence supporting each of these processes, and propose future experiments and tests that would further illuminate the interplay between environmental factors, condition-dependent development, and the initiation and elaboration of novel phenotypes.

@article{doi101098rspb20110971,
    author = "Moczek, Armin P. and Sultan, Sonia E. and Foster, Susan A. and Ledón-Rettig, Cris C. and Dworkin, Ian and Nijhout, H. Fred and Abouheif, Ehab and Pfennig, David W.",
    title = "The role of developmental plasticity in evolutionary innovation",
    year = "2011",
    journal = "Proceedings of the Royal Society B Biological Sciences",
    abstract = "Explaining the origins of novel traits is central to evolutionary biology. Longstanding theory suggests that developmental plasticity, the ability of an individual to modify its development in response to environmental conditions, might facilitate the evolution of novel traits. Yet whether and how such developmental flexibility promotes innovations that persist over evolutionary time remains unclear. Here, we examine three distinct ways by which developmental plasticity can promote evolutionary innovation. First, we show how the process of genetic accommodation provides a feasible and possibly common avenue by which environmentally induced phenotypes can become subject to heritable modification. Second, we posit that the developmental underpinnings of plasticity increase the degrees of freedom by which environmental and genetic factors influence ontogeny, thereby diversifying targets for evolutionary processes to act on and increasing opportunities for the construction of novel, functional and potentially adaptive phenotypes. Finally, we examine the developmental genetic architectures of environment-dependent trait expression, and highlight their specific implications for the evolutionary origin of novel traits. We critically review the empirical evidence supporting each of these processes, and propose future experiments and tests that would further illuminate the interplay between environmental factors, condition-dependent development, and the initiation and elaboration of novel phenotypes.",
    url = "https://doi.org/10.1098/rspb.2011.0971",
    doi = "10.1098/rspb.2011.0971",
    openalex = "W2142774476",
    references = "doi101038sjhdy6800154, doi101098rstb20090263, doi101111j001438202003tb00377x, doi1023072411226"
}

@article{doi101038nrg3483,
    author = "Stern, David L.",
    title = "The genetic causes of convergent evolution",
    year = "2013",
    journal = "Nature Reviews Genetics",
    url = "https://doi.org/10.1038/nrg3483",
    doi = "10.1038/nrg3483",
    openalex = "W2046793790",
    references = "doi101016jcell200806030, doi101016jtree200709008, doi101038287795a0, doi101038nature10944, doi101038nature11041, doi101038ng1946, doi101038nrg2452, doi101073pnas9794530, doi101093acref97801995711230010001, doi101105tpc115949, doi101111j001438202000tb00544x, doi101111j15585646200800450x, doi101111j15585646201101289x, doi101126science1113832, doi101126science1123539, doi101126science1188021, doi101126science1208227, doi101146annurevento451371, openalexw2080618944"
}

@article{doi101038nrg3605,
    author = "Meyer, Rachel S. and Purugganan, Michael D.",
    title = "Evolution of crop species: genetics of domestication and diversification",
    year = "2013",
    journal = "Nature Reviews Genetics",
    url = "https://doi.org/10.1038/nrg3605",
    doi = "10.1038/nrg3605",
    openalex = "W2025987231",
    references = "doi101038386485a0, doi101146annureven10010165000525, doi105962bhltitle84435"
}

The transition from outcrossing to self-fertilization is one of the most common evolutionary changes in plants, yet only about 10-15% of flowering plants are predominantly selfing. To explain this phenomenon, Stebbins proposed that selfing may be an 'evolutionary dead end'. According to this hypothesis, transitions from outcrossing to selfing are irreversible, and selfing lineages suffer from an increased risk of extinction owing to a reduced potential for adaptation. Thus, although selfing can be advantageous in the short term, selfing lineages may be mostly short-lived owing to higher extinction rates. Here, we review recent results relevant to the 'dead-end hypothesis' of selfing and the maintenance of outcrossing over longer evolutionary time periods. In particular, we highlight recent results regarding diversification rates in self-incompatible and self-compatible taxa, and review evidence regarding the accumulation of deleterious mutations in selfing lineages. We conclude that while some aspects of the hypothesis of selfing as a dead end are supported by theory and empirical results, the evolutionary and ecological mechanisms remain unclear. We highlight the need for more studies on the effects of quantitative changes in outcrossing rates and on the potential for adaptation, particularly in selfing plants. In addition, there is growing evidence that transitions to selfing may themselves be drivers of speciation, and future studies of diversification and speciation should investigate this further.

@article{doi101098rspb20130133,
    author = "Wright, Stephen and Kalisz, Susan and Slotte, Tanja",
    title = "Evolutionary consequences of self-fertilization in plants",
    year = "2013",
    journal = "Proceedings of the Royal Society B Biological Sciences",
    abstract = "The transition from outcrossing to self-fertilization is one of the most common evolutionary changes in plants, yet only about 10-15\% of flowering plants are predominantly selfing. To explain this phenomenon, Stebbins proposed that selfing may be an 'evolutionary dead end'. According to this hypothesis, transitions from outcrossing to selfing are irreversible, and selfing lineages suffer from an increased risk of extinction owing to a reduced potential for adaptation. Thus, although selfing can be advantageous in the short term, selfing lineages may be mostly short-lived owing to higher extinction rates. Here, we review recent results relevant to the 'dead-end hypothesis' of selfing and the maintenance of outcrossing over longer evolutionary time periods. In particular, we highlight recent results regarding diversification rates in self-incompatible and self-compatible taxa, and review evidence regarding the accumulation of deleterious mutations in selfing lineages. We conclude that while some aspects of the hypothesis of selfing as a dead end are supported by theory and empirical results, the evolutionary and ecological mechanisms remain unclear. We highlight the need for more studies on the effects of quantitative changes in outcrossing rates and on the potential for adaptation, particularly in selfing plants. In addition, there is growing evidence that transitions to selfing may themselves be drivers of speciation, and future studies of diversification and speciation should investigate this further.",
    url = "https://doi.org/10.1098/rspb.2013.0133",
    doi = "10.1098/rspb.2013.0133",
    openalex = "W2037092474",
    references = "doi101111j15585646200700006x"
}

The development of the emerging field of 'paleovirology' allows biologists to reconstruct the evolutionary history of fossil endogenous retroviral sequences integrated within the genome of living organisms and has led to the retrieval of conserved, ancient retroviral genes 'exapted' by ancestral hosts to fulfil essential physiological roles, syncytin genes being undoubtedly among the most remarkable examples of such a phenomenon. Indeed, syncytins are 'new' genes encoding proteins derived from the envelope protein of endogenous retroviral elements that have been captured and domesticated on multiple occasions and independently in diverse mammalian species, through a process of convergent evolution. Knockout of syncytin genes in mice provided evidence for their absolute requirement for placenta development and embryo survival, via formation by cell-cell fusion of syncytial cell layers at the fetal-maternal interface. These genes of exogenous origin, acquired 'by chance' and yet still 'necessary' to carry out a basic function in placental mammals, may have been pivotal in the emergence of mammalian ancestors with a placenta from egg-laying animals via the capture of a founding retroviral env gene, subsequently replaced in the diverse mammalian lineages by new env-derived syncytin genes, each providing its host with a positive selective advantage.

@article{doi101098rstb20120507,
    author = "Lavialle, Christian and Cornelis, Guillaume and Dupressoír, Anne and Esnault, Cécile and Heidmann, Odile and Vernochet, Cécile and Heidmann, Thiérry",
    title = "Paleovirology of ‘ syncytins ’, retroviral env genes exapted for a role in placentation",
    year = "2013",
    journal = "Philosophical Transactions of the Royal Society B Biological Sciences",
    abstract = "The development of the emerging field of 'paleovirology' allows biologists to reconstruct the evolutionary history of fossil endogenous retroviral sequences integrated within the genome of living organisms and has led to the retrieval of conserved, ancient retroviral genes 'exapted' by ancestral hosts to fulfil essential physiological roles, syncytin genes being undoubtedly among the most remarkable examples of such a phenomenon. Indeed, syncytins are 'new' genes encoding proteins derived from the envelope protein of endogenous retroviral elements that have been captured and domesticated on multiple occasions and independently in diverse mammalian species, through a process of convergent evolution. Knockout of syncytin genes in mice provided evidence for their absolute requirement for placenta development and embryo survival, via formation by cell-cell fusion of syncytial cell layers at the fetal-maternal interface. These genes of exogenous origin, acquired 'by chance' and yet still 'necessary' to carry out a basic function in placental mammals, may have been pivotal in the emergence of mammalian ancestors with a placenta from egg-laying animals via the capture of a founding retroviral env gene, subsequently replaced in the diverse mammalian lineages by new env-derived syncytin genes, each providing its host with a positive selective advantage.",
    url = "https://doi.org/10.1098/rstb.2012.0507",
    doi = "10.1098/rstb.2012.0507",
    openalex = "W2144605452",
    references = "doi101146annurevgenet110711155522"
}

Species enter and persist in local communities because of their ecological fit to local conditions, and recently, ecologists have moved from measuring diversity as species richness and evenness, to using measures that reflect species ecological differences. There are two principal approaches for quantifying species ecological differences: functional (trait-based) and phylogenetic pairwise distances between species. Both approaches have produced new ecological insights, yet at the same time methodological issues and assumptions limit them. Traits and phylogeny may provide different, and perhaps complementary, information about species' differences. To adequately test assembly hypotheses, a framework integrating the information provided by traits and phylogenies is required. We propose an intuitive measure for combining functional and phylogenetic pairwise distances, which provides a useful way to assess how functional and phylogenetic distances contribute to understanding patterns of community assembly. Here, we show that both traits and phylogeny inform community assembly patterns in alpine plant communities across an elevation gradient, because they represent complementary information. Differences in historical selection pressures have produced variation in the strength of the trait-phylogeny correlation, and as such, integrating traits and phylogeny can enhance the ability to detect assembly patterns across habitats or environmental gradients.

@article{doi101111ele12161,
    author = "Cadotte, Marc W. and Albert, Cécile H. and Walker, Steve C.",
    title = "The ecology of differences: assessing community assembly with trait and evolutionary distances",
    year = "2013",
    journal = "Ecology Letters",
    abstract = "Species enter and persist in local communities because of their ecological fit to local conditions, and recently, ecologists have moved from measuring diversity as species richness and evenness, to using measures that reflect species ecological differences. There are two principal approaches for quantifying species ecological differences: functional (trait-based) and phylogenetic pairwise distances between species. Both approaches have produced new ecological insights, yet at the same time methodological issues and assumptions limit them. Traits and phylogeny may provide different, and perhaps complementary, information about species' differences. To adequately test assembly hypotheses, a framework integrating the information provided by traits and phylogenies is required. We propose an intuitive measure for combining functional and phylogenetic pairwise distances, which provides a useful way to assess how functional and phylogenetic distances contribute to understanding patterns of community assembly. Here, we show that both traits and phylogeny inform community assembly patterns in alpine plant communities across an elevation gradient, because they represent complementary information. Differences in historical selection pressures have produced variation in the strength of the trait-phylogeny correlation, and as such, integrating traits and phylogeny can enhance the ability to detect assembly patterns across habitats or environmental gradients.",
    url = "https://doi.org/10.1111/ele.12161",
    doi = "10.1111/ele.12161",
    openalex = "W2003019046",
    references = "doi101111j15585646201000960x"
}

I summarize marine studies on plastic versus adaptive responses to global change. Due to the lack of time series, this review focuses largely on the potential for adaptive evolution in marine animals and plants. The approaches were mainly synchronic comparisons of phenotypically divergent populations, substituting spatial contrasts in temperature or CO2 environments for temporal changes, or in assessments of adaptive genetic diversity within populations for traits important under global change. The available literature is biased towards gastropods, crustaceans, cnidarians and macroalgae. Focal traits were mostly environmental tolerances, which correspond to phenotypic buffering, a plasticity type that maintains a functional phenotype despite external disturbance. Almost all studies address coastal species that are already today exposed to fluctuations in temperature, pH and oxygen levels. Recommendations for future research include (i) initiation and analyses of observational and experimental temporal studies encompassing diverse phenotypic traits (including diapausing cues, dispersal traits, reproductive timing, morphology) (ii) quantification of nongenetic trans-generational effects along with components of additive genetic variance (iii) adaptive changes in microbe-host associations under the holobiont model in response to global change (iv) evolution of plasticity patterns under increasingly fluctuating environments and extreme conditions and (v) joint consideration of demography and evolutionary adaptation in evolutionary rescue approaches.

@article{doi101111eva12109,
    author = "Reusch, Thorsten B. H.",
    title = "Climate change in the oceans: evolutionary versus phenotypically plastic responses of marine animals and plants",
    year = "2013",
    journal = "Evolutionary Applications",
    abstract = "I summarize marine studies on plastic versus adaptive responses to global change. Due to the lack of time series, this review focuses largely on the potential for adaptive evolution in marine animals and plants. The approaches were mainly synchronic comparisons of phenotypically divergent populations, substituting spatial contrasts in temperature or CO2 environments for temporal changes, or in assessments of adaptive genetic diversity within populations for traits important under global change. The available literature is biased towards gastropods, crustaceans, cnidarians and macroalgae. Focal traits were mostly environmental tolerances, which correspond to phenotypic buffering, a plasticity type that maintains a functional phenotype despite external disturbance. Almost all studies address coastal species that are already today exposed to fluctuations in temperature, pH and oxygen levels. Recommendations for future research include (i) initiation and analyses of observational and experimental temporal studies encompassing diverse phenotypic traits (including diapausing cues, dispersal traits, reproductive timing, morphology) (ii) quantification of nongenetic trans-generational effects along with components of additive genetic variance (iii) adaptive changes in microbe-host associations under the holobiont model in response to global change (iv) evolution of plasticity patterns under increasingly fluctuating environments and extreme conditions and (v) joint consideration of demography and evolutionary adaptation in evolutionary rescue approaches.",
    url = "https://doi.org/10.1111/eva.12109",
    doi = "10.1111/eva.12109",
    openalex = "W2071187584",
    references = "doi107551mitpress97802625136780010001"
}

@article{doi101007s0043801408892,
    author = "Glasauer, Stella M.K. and Neuhauss, Stephan C. F.",
    title = "Whole-genome duplication in teleost fishes and its evolutionary consequences",
    year = "2014",
    journal = "Molecular Genetics and Genomics",
    url = "https://doi.org/10.1007/s00438-014-0889-2",
    doi = "10.1007/s00438-014-0889-2",
    openalex = "W2065636600",
    references = "doi101038nature06967, doi101038nrg2600, doi101073pnas0900906106, doi101073pnas1011803107, doi101073pnas1206625109, doi101093molbevmsn222, doi101111j15585646200700105x"
}

@article{doi101038514161a,
    author = "Laland, Kevin N. and Uller, Tobias and Feldman, Marc and Sterelny, Kim and Müller, Gerd B. and Moczek, Armin P. and Jablonka, Eva and Odling‐Smee, John and Wray, Gregory A. and Hoekstra, Hopi E. and Futuyma, Douglas J. and Lenski, Richard E. and Mackay, Trudy F. C. and Schluter, Dolph and Strassmann, Joan E.",
    title = "Does evolutionary theory need a rethink?",
    year = "2014",
    journal = "Nature",
    url = "https://doi.org/10.1038/514161a",
    doi = "10.1038/514161a",
    openalex = "W1991285543",
    references = "doi107551mitpress97802625136780010001, openalexw135071171"
}

Phylogenetic niche conservatism (PNC) typically refers to the tendency of closely related species to be more similar to each other in terms of niche than they are to more distant relatives. This has been implicated as a potential driving force in speciation and other species-richness patterns, such as latitudinal gradients. However, PNC has not been very well defined in most previous studies. Is it a pattern or a process? What are the underlying endogenous (e.g. genetic) and exogenous (e.g. ecological) factors that cause niches to be conserved? What degree of similarity is necessary to qualify as PNC? Is it possible for the evolutionary processes causing niches to be conserved to also result in niche divergence in different habitats? Here, we revisit these questions, codifying a theoretical and operational definition of PNC as a mechanistic evolutionary process resulting from several factors. We frame this both from a macroevolutionary and population-genetic perspective. We discuss how different axes of physical (e.g. geographic) and environmental (e.g. climatic) heterogeneity interact with the fundamental process of PNC to produce different outcomes of ecological speciation. We also review tests for PNC, and suggest ways that these could be improved or better utilized in future studies. Ultimately, PNC as a process has a well-defined mechanistic basis in organisms, and future studies investigating ecological speciation would be well served to consider this, and frame hypothesis testing in terms of the processes and expected patterns described herein. The process of PNC may lead to patterns where niches are conserved (more similar than expected), constrained (divergent within a limited subset of available niches), or divergent (less similar than expected), based on degree of phylogenetic relatedness between species.

@article{doi101111brv12154,
    author = "Pyron, R. Alexander and Costa, Gabriel C. and Patten, Michael A. and Burbrink, Frank T.",
    title = "Phylogenetic niche conservatism and the evolutionary basis of ecological speciation",
    year = "2014",
    journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society",
    abstract = "Phylogenetic niche conservatism (PNC) typically refers to the tendency of closely related species to be more similar to each other in terms of niche than they are to more distant relatives. This has been implicated as a potential driving force in speciation and other species-richness patterns, such as latitudinal gradients. However, PNC has not been very well defined in most previous studies. Is it a pattern or a process? What are the underlying endogenous (e.g. genetic) and exogenous (e.g. ecological) factors that cause niches to be conserved? What degree of similarity is necessary to qualify as PNC? Is it possible for the evolutionary processes causing niches to be conserved to also result in niche divergence in different habitats? Here, we revisit these questions, codifying a theoretical and operational definition of PNC as a mechanistic evolutionary process resulting from several factors. We frame this both from a macroevolutionary and population-genetic perspective. We discuss how different axes of physical (e.g. geographic) and environmental (e.g. climatic) heterogeneity interact with the fundamental process of PNC to produce different outcomes of ecological speciation. We also review tests for PNC, and suggest ways that these could be improved or better utilized in future studies. Ultimately, PNC as a process has a well-defined mechanistic basis in organisms, and future studies investigating ecological speciation would be well served to consider this, and frame hypothesis testing in terms of the processes and expected patterns described herein. The process of PNC may lead to patterns where niches are conserved (more similar than expected), constrained (divergent within a limited subset of available niches), or divergent (less similar than expected), based on degree of phylogenetic relatedness between species.",
    url = "https://doi.org/10.1111/brv.12154",
    doi = "10.1111/brv.12154",
    openalex = "W1956587275",
    references = "doi101111j15585646201000960x"
}

Gene flow is a key factor in the evolution of species, influencing effective population size, hybridisation and local adaptation. We analysed local gene flow in eight stands of white oak (mostly Quercus petraea and Q. robur, but also Q. pubescens and Q. faginea) distributed across Europe. Adult trees within a given area in each stand were exhaustively sampled (range [239, 754], mean 423), mapped, and acorns were collected ([17,147], 51) from several mother trees ([3], [47], 23). Seedlings ([65,387], 178) were harvested and geo-referenced in six of the eight stands. Genetic information was obtained from screening distinct molecular markers spread across the genome, genotyping each tree, acorn or seedling. All samples were thus genotyped at 5-8 nuclear microsatellite loci. Fathers/parents were assigned to acorns and seedlings using likelihood methods. Mating success of male and female parents, pollen and seed dispersal curves, and also hybridisation rates were estimated in each stand and compared on a continental scale. On average, the percentage of the wind-borne pollen from outside the stand was 60%, with large variation among stands (21-88%). Mean seed immigration into the stand was 40%, a high value for oaks that are generally considered to have limited seed dispersal. However, this estimate varied greatly among stands (20-66%). Gene flow was mostly intraspecific, with large variation, as some trees and stands showed particularly high rates of hybridisation. Our results show that mating success was unevenly distributed among trees. The high levels of gene flow suggest that geographically remote oak stands are unlikely to be genetically isolated, questioning the static definition of gene reserves and seed stands.

@article{doi101371journalpone0085130,
    author = "Gerber, Sophie and Chadœuf, Joël and Gugerli, Félix and Lascoux, Martin and Buiteveld, J. and Cottrell, Joan and Dounavi, Aikaterini and Fineschi, Silvia and Forrest, Laura L. and Fogelqvist, Johan and Goicoechea, P. G. and Jensen, Jan Svejgaard and Salvini, Daniela and Vendramin, Giovanni G. and Kremer, Antoine",
    title = "High Rates of Gene Flow by Pollen and Seed in Oak Populations across Europe",
    year = "2014",
    journal = "PLoS ONE",
    abstract = "Gene flow is a key factor in the evolution of species, influencing effective population size, hybridisation and local adaptation. We analysed local gene flow in eight stands of white oak (mostly Quercus petraea and Q. robur, but also Q. pubescens and Q. faginea) distributed across Europe. Adult trees within a given area in each stand were exhaustively sampled (range [239, 754], mean 423), mapped, and acorns were collected ([17,147], 51) from several mother trees ([3], [47], 23). Seedlings ([65,387], 178) were harvested and geo-referenced in six of the eight stands. Genetic information was obtained from screening distinct molecular markers spread across the genome, genotyping each tree, acorn or seedling. All samples were thus genotyped at 5-8 nuclear microsatellite loci. Fathers/parents were assigned to acorns and seedlings using likelihood methods. Mating success of male and female parents, pollen and seed dispersal curves, and also hybridisation rates were estimated in each stand and compared on a continental scale. On average, the percentage of the wind-borne pollen from outside the stand was 60\%, with large variation among stands (21-88\%). Mean seed immigration into the stand was 40\%, a high value for oaks that are generally considered to have limited seed dispersal. However, this estimate varied greatly among stands (20-66\%). Gene flow was mostly intraspecific, with large variation, as some trees and stands showed particularly high rates of hybridisation. Our results show that mating success was unevenly distributed among trees. The high levels of gene flow suggest that geographically remote oak stands are unlikely to be genetically isolated, questioning the static definition of gene reserves and seed stands.",
    url = "https://doi.org/10.1371/journal.pone.0085130",
    doi = "10.1371/journal.pone.0085130",
    openalex = "W2092712028",
    references = "doi101111j1365294x200904137x"
}

The genetic diversity of our crop plants has been substantially reduced during the process of domestication and breeding. This reduction in diversity necessarily constrains our ability to expand a crop's range of cultivation into environments that are more extreme than those in which it was domesticated, including into "sustainable" agricultural systems with reduced inputs of pesticides, water, and fertilizers. Conversely, the wild progenitors of crop plants typically possess high levels of genetic diversity, which underlie an expanded (relative to domesticates) range of adaptive traits that may be of agricultural relevance, including resistance to pests and pathogens, tolerance to abiotic extremes, and reduced dependence on inputs. Despite their clear potential for crop improvement, wild relatives have rarely been used systematically for crop improvement, and in no cases, have full sets of wild diversity been introgressed into a crop. Instead, most breeding efforts have focused on specific traits and dealt with wild species in a limited and typically ad hoc manner. Although expedient, this approach misses the opportunity to test a large suite of traits and deploy the full potential of crop wild relatives in breeding for the looming challenges of the 21st century. Here we review examples of hybridization in several species, both intentionally produced and naturally occurring, to illustrate the gains that are possible. We start with naturally occurring hybrids, and then examine a range of examples of hybridization in agricultural settings.

@article{doi103732ajb1400116,
    author = "Warschefsky, Emily and Penmetsa, R. Varma and Cook, Douglas R. and von Wettberg, Eric",
    title = "Back to the wilds: Tapping evolutionary adaptations for resilient crops through systematic hybridization with crop wild relatives",
    year = "2014",
    journal = "American Journal of Botany",
    abstract = {The genetic diversity of our crop plants has been substantially reduced during the process of domestication and breeding. This reduction in diversity necessarily constrains our ability to expand a crop's range of cultivation into environments that are more extreme than those in which it was domesticated, including into "sustainable" agricultural systems with reduced inputs of pesticides, water, and fertilizers. Conversely, the wild progenitors of crop plants typically possess high levels of genetic diversity, which underlie an expanded (relative to domesticates) range of adaptive traits that may be of agricultural relevance, including resistance to pests and pathogens, tolerance to abiotic extremes, and reduced dependence on inputs. Despite their clear potential for crop improvement, wild relatives have rarely been used systematically for crop improvement, and in no cases, have full sets of wild diversity been introgressed into a crop. Instead, most breeding efforts have focused on specific traits and dealt with wild species in a limited and typically ad hoc manner. Although expedient, this approach misses the opportunity to test a large suite of traits and deploy the full potential of crop wild relatives in breeding for the looming challenges of the 21st century. Here we review examples of hybridization in several species, both intentionally produced and naturally occurring, to illustrate the gains that are possible. We start with naturally occurring hybrids, and then examine a range of examples of hybridization in agricultural settings.},
    url = "https://doi.org/10.3732/ajb.1400116",
    doi = "10.3732/ajb.1400116",
    openalex = "W2027144299",
    references = "doi101111evo12399"
}

While homoploid hybridization was viewed as maladaptive by zoologists, the possibility that it might play a creative role in evolution was explored and debated by botanists during the evolutionary synthesis. Owing to his synthetic work on the ecological and genetic factors influencing the occurrence and effects of hybridization, G. Ledyard Stebbins' contributions to this debate were particularly influential. We revisit Stebbins' views on the frequency of hybridization, the evolution of hybrid sterility, and the evolutionary importance of transgressive segregation, introgression, and homoploid hybrid speciation in the context of contemporary evidence. Floristic surveys indicate that ∼10% of plant species hybridize, suggesting that natural hybridization is not as ubiquitous as Stebbins argued. There is stronger support for his contention that chromosomal sterility is of greater importance in plants than in animals and that selection drives the evolution of hybrid sterility. Stebbins' assertions concerning the frequent occurrence of transgressive segregation and introgressive hybridization have been confirmed by contemporary work, but few studies directly link these phenomena to adaptive evolution or speciation. Stebbins proposed a mechanism by which chromosomal rearrangements partially isolate hybrid lineages and parental species, which spurred the development of the recombinational model of homoploid speciation. While this model has been confirmed empirically, the establishment of reproductively independent hybrid lineages is typically associated with the development of both intrinsic and extrinsic reproductive barriers. We conclude by reflecting on outcomes of hybridization not considered by Stebbins and on possible future research that may extend our understanding of the evolutionary role of hybridization beyond Stebbins' legacy.

@article{doi103732ajb1400201,
    author = "Yakimowski, Sarah B. and Rieseberg, Loren H.",
    title = "The role of homoploid hybridization in evolution: A century of studies synthesizing genetics and ecology",
    year = "2014",
    journal = "American Journal of Botany",
    abstract = "While homoploid hybridization was viewed as maladaptive by zoologists, the possibility that it might play a creative role in evolution was explored and debated by botanists during the evolutionary synthesis. Owing to his synthetic work on the ecological and genetic factors influencing the occurrence and effects of hybridization, G. Ledyard Stebbins' contributions to this debate were particularly influential. We revisit Stebbins' views on the frequency of hybridization, the evolution of hybrid sterility, and the evolutionary importance of transgressive segregation, introgression, and homoploid hybrid speciation in the context of contemporary evidence. Floristic surveys indicate that ∼10\% of plant species hybridize, suggesting that natural hybridization is not as ubiquitous as Stebbins argued. There is stronger support for his contention that chromosomal sterility is of greater importance in plants than in animals and that selection drives the evolution of hybrid sterility. Stebbins' assertions concerning the frequent occurrence of transgressive segregation and introgressive hybridization have been confirmed by contemporary work, but few studies directly link these phenomena to adaptive evolution or speciation. Stebbins proposed a mechanism by which chromosomal rearrangements partially isolate hybrid lineages and parental species, which spurred the development of the recombinational model of homoploid speciation. While this model has been confirmed empirically, the establishment of reproductively independent hybrid lineages is typically associated with the development of both intrinsic and extrinsic reproductive barriers. We conclude by reflecting on outcomes of hybridization not considered by Stebbins and on possible future research that may extend our understanding of the evolutionary role of hybridization beyond Stebbins' legacy.",
    url = "https://doi.org/10.3732/ajb.1400201",
    doi = "10.3732/ajb.1400201",
    openalex = "W2184942790",
    references = "doi101016jppees201002002, doi101111evo12399"
}

@article{doi101038nrg3905,
    author = "Sironi, Manuela and Cagliani, Rachele and Forni, Diego and Clerici, Mario",
    title = "Evolutionary insights into host–pathogen interactions from mammalian sequence data",
    year = "2015",
    journal = "Nature Reviews Genetics",
    url = "https://doi.org/10.1038/nrg3905",
    doi = "10.1038/nrg3905",
    openalex = "W1983304589",
    references = "doi101146annurevgenet110711155522"
}

@article{doi101038nrg3982,
    author = "Gilbert, Scott F. and Bosch, Thomas C. G. and Ledón‐Rettig, Cristina C.",
    title = "Eco-Evo-Devo: developmental symbiosis and developmental plasticity as evolutionary agents",
    year = "2015",
    journal = "Nature Reviews Genetics",
    url = "https://doi.org/10.1038/nrg3982",
    doi = "10.1038/nrg3982",
    openalex = "W2219314901",
    references = "doi101146annurevmarine120709142753, doi107551mitpress97802625136780010001"
}

The evolution of life on earth has been driven by a small number of major evolutionary transitions. These transitions have been characterized by individuals that could previously replicate independently, cooperating to form a new, more complex life form. For example, archaea and eubacteria formed eukaryotic cells, and cells formed multicellular organisms. However, not all cooperative groups are en route to major transitions. How can we explain why major evolutionary transitions have or haven't taken place on different branches of the tree of life? We break down major transitions into two steps: the formation of a cooperative group and the transformation of that group into an integrated entity. We show how these steps require cooperation, division of labor, communication, mutual dependence, and negligible within-group conflict. We find that certain ecological conditions and the ways in which groups form have played recurrent roles in driving multiple transitions. In contrast, we find that other factors have played relatively minor roles at many key points, such as within-group kin discrimination and mechanisms to actively repress competition. More generally, by identifying the small number of factors that have driven major transitions, we provide a simpler and more unified description of how life on earth has evolved.

@article{doi101073pnas1421402112,
    author = "West, Stuart A. and Fisher, Roberta M. and Gardner, Andy and Kiers, E. Toby",
    title = "Major evolutionary transitions in individuality",
    year = "2015",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "The evolution of life on earth has been driven by a small number of major evolutionary transitions. These transitions have been characterized by individuals that could previously replicate independently, cooperating to form a new, more complex life form. For example, archaea and eubacteria formed eukaryotic cells, and cells formed multicellular organisms. However, not all cooperative groups are en route to major transitions. How can we explain why major evolutionary transitions have or haven't taken place on different branches of the tree of life? We break down major transitions into two steps: the formation of a cooperative group and the transformation of that group into an integrated entity. We show how these steps require cooperation, division of labor, communication, mutual dependence, and negligible within-group conflict. We find that certain ecological conditions and the ways in which groups form have played recurrent roles in driving multiple transitions. In contrast, we find that other factors have played relatively minor roles at many key points, such as within-group kin discrimination and mechanisms to actively repress competition. More generally, by identifying the small number of factors that have driven major transitions, we provide a simpler and more unified description of how life on earth has evolved.",
    url = "https://doi.org/10.1073/pnas.1421402112",
    doi = "10.1073/pnas.1421402112",
    openalex = "W2160332754",
    references = "doi101098rstb20090095, doi101111j14209101200801681x, doi101146annurevecolsys36102403114735"
}

An enduring mystery of evolutionary genomics concerns the mechanisms responsible for lineage-specific expansions of genome size in eukaryotes, especially in multicellular species. One idea is that all excess DNA is mutationally hazardous, but weakly enough so that genome-size expansion passively emerges in species experiencing relatively low efficiency of selection owing to small effective population sizes. Another idea is that substantial gene additions were impossible without the energetic boost provided by the colonizing mitochondrion in the eukaryotic lineage. Contrary to this latter view, analysis of cellular energetics and genomics data from a wide variety of species indicates that, relative to the lifetime ATP requirements of a cell, the costs of a gene at the DNA, RNA, and protein levels decline with cell volume in both bacteria and eukaryotes. Moreover, these costs are usually sufficiently large to be perceived by natural selection in bacterial populations, but not in eukaryotes experiencing high levels of random genetic drift. Thus, for scaling reasons that are not yet understood, by virtue of their large size alone, eukaryotic cells are subject to a broader set of opportunities for the colonization of novel genes manifesting weakly advantageous or even transiently disadvantageous phenotypic effects. These results indicate that the origin of the mitochondrion was not a prerequisite for genome-size expansion.

@article{doi101073pnas1514974112,
    author = "Lynch, Michael and Marinov, Georgi K.",
    title = "The bioenergetic costs of a gene",
    year = "2015",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "An enduring mystery of evolutionary genomics concerns the mechanisms responsible for lineage-specific expansions of genome size in eukaryotes, especially in multicellular species. One idea is that all excess DNA is mutationally hazardous, but weakly enough so that genome-size expansion passively emerges in species experiencing relatively low efficiency of selection owing to small effective population sizes. Another idea is that substantial gene additions were impossible without the energetic boost provided by the colonizing mitochondrion in the eukaryotic lineage. Contrary to this latter view, analysis of cellular energetics and genomics data from a wide variety of species indicates that, relative to the lifetime ATP requirements of a cell, the costs of a gene at the DNA, RNA, and protein levels decline with cell volume in both bacteria and eukaryotes. Moreover, these costs are usually sufficiently large to be perceived by natural selection in bacterial populations, but not in eukaryotes experiencing high levels of random genetic drift. Thus, for scaling reasons that are not yet understood, by virtue of their large size alone, eukaryotic cells are subject to a broader set of opportunities for the colonization of novel genes manifesting weakly advantageous or even transiently disadvantageous phenotypic effects. These results indicate that the origin of the mitochondrion was not a prerequisite for genome-size expansion.",
    url = "https://doi.org/10.1073/pnas.1514974112",
    doi = "10.1073/pnas.1514974112",
    openalex = "W1946157893",
    references = "doi101073pnas0702207104"
}

Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the 'extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism-environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology.

@article{doi101098rspb20151019,
    author = "Laland, Kevin N. and Uller, Tobias and Feldman, Marcus W. and Sterelny, Kim and Müller, Gerd B. and Moczek, Armin P. and Jablonka, Eva and Odling‐Smee, John",
    title = "The extended evolutionary synthesis: its structure, assumptions and predictions",
    year = "2015",
    journal = "Proceedings of the Royal Society B Biological Sciences",
    abstract = "Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the 'extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism-environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology.",
    url = "https://doi.org/10.1098/rspb.2015.1019",
    doi = "10.1098/rspb.2015.1019",
    openalex = "W2103794982",
    references = "doi101001jama195002910300087029, doi101002jezb21081, doi101017cbo9780511621123, doi101038218525a0, doi10106313050879, doi101086346135, doi101093auk1002507, doi101093oso97801951223430010001, doi101111j155856461982tb05068x, doi101126science1113832, doi101146annureves01110170000245, doi1015159780691209418, doi1015159781400847266, doi1023071367778, doi1023072260026, doi102307jctvjsf433, doi102307jctvx5wbbh, doi105860choice364478, doi105860choice396411, doi105962bhltitle27468, doi107208chicago97802263088830010001, doi107551mitpress97802625136780010001, openalexw2080618944, openalexw227636185"
}

Recent studies have generated an explosion of phylogenetic and biogeographic data and have provided new tools to investigate the processes driving large-scale gradients in species diversity. Fossils and phylogenetic studies of plants and animals demonstrate that tropical regions are the source for almost all groups of organisms, and these groups are composed of a mixture of ancient and recently derived lineages. These findings are consistent with the hypothesis that the large extent of tropical environments during the past 10–50 million years, together with greater climatic stability, has promoted speciation and reduced extinction rates. Energy availability appears to only indirectly contribute to global patterns of species diversity, especially considering how some marine diversity gradients can be completely decoupled from temperature and productivity gradients. Instead, climate stability and time–integrated area together determine the baselines of both terrestrial and marine global diversity patterns. Biotic interactions likely augment diversification and coexistence in the tropics.

@article{doi101146annurevecolsys112414054102,
    author = "Fine, Paul V. A.",
    title = "Ecological and Evolutionary Drivers of Geographic Variation in Species Diversity",
    year = "2015",
    journal = "Annual Review of Ecology Evolution and Systematics",
    abstract = "Recent studies have generated an explosion of phylogenetic and biogeographic data and have provided new tools to investigate the processes driving large-scale gradients in species diversity. Fossils and phylogenetic studies of plants and animals demonstrate that tropical regions are the source for almost all groups of organisms, and these groups are composed of a mixture of ancient and recently derived lineages. These findings are consistent with the hypothesis that the large extent of tropical environments during the past 10–50 million years, together with greater climatic stability, has promoted speciation and reduced extinction rates. Energy availability appears to only indirectly contribute to global patterns of species diversity, especially considering how some marine diversity gradients can be completely decoupled from temperature and productivity gradients. Instead, climate stability and time–integrated area together determine the baselines of both terrestrial and marine global diversity patterns. Biotic interactions likely augment diversification and coexistence in the tropics.",
    url = "https://doi.org/10.1146/annurev-ecolsys-112414-054102",
    doi = "10.1146/annurev-ecolsys-112414-054102",
    openalex = "W1908440753",
    references = "doi101007s116920129171x, doi101016jtree201309012, doi101016s003101829600096x, doi101038nature11631, doi101038nature14324, doi101073pnas0709472105, doi101086282687, doi101086680850, doi101093sysbiosyu131, doi101111j13652699201002375x, doi101111j155856461964tb01674x, doi101111j15585646201000960x, doi101126science2304728895, doi101146annurevecolsys110512135800, doi101146annurevecolsys120213091905, doi101146annurevecolsys33010802150448, doi101371journalpbio1001775, doi101641b570707, doi101666090211, doi1023073071998, doi105860choice332720, doi105860choice485062"
}

@article{doi101038nrg201534,
    author = "Champer, Jackson and Buchman, Anna and Akbari, Omar S.",
    title = "Cheating evolution: engineering gene drives to manipulate the fate of wild populations",
    year = "2016",
    journal = "Nature Reviews Genetics",
    url = "https://doi.org/10.1038/nrg.2015.34",
    doi = "10.1038/nrg.2015.34",
    openalex = "W2263233808",
    references = "alpheyNoneinsect, doi101146annurevento011613162002"
}

Hybridization is a potent evolutionary process that can affect the origin, maintenance, and loss of biodiversity. Because of its ecological and evolutionary consequences, an understanding of hybridization is important for basic and applied sciences, including conservation biology and agriculture. Herein, we review and discuss ideas that are relevant to the recognition of hybrids and hybridization. We supplement this discussion with simulations. The ideas we present have a long history, particularly in botany, and clarifying them should have practical consequences for managing hybridization and gene flow in plants. One of our primary goals is to illustrate what we can and cannot infer about hybrids and hybridization from molecular data; in other words, we ask when genetic analyses commonly used to study hybridization might mislead us about the history or nature of gene flow and selection. We focus on patterns of variation when hybridization is recent and populations are polymorphic, which are particularly informative for applied issues, such as contemporary hybridization following recent ecological change. We show that hybridization is not a singular process, but instead a collection of related processes with variable outcomes and consequences. Thus, it will often be inappropriate to generalize about the threats or benefits of hybridization from individual studies, and at minimum, it will be important to avoid categorical thinking about what hybridization and hybrids are. We recommend potential sampling and analytical approaches that should help us confront these complexities of hybridization.

@article{doi101111eva12380,
    author = "Gompert, Zachariah and Buerkle, C. Alex",
    title = "What, if anything, are hybrids: enduring truths and challenges associated with population structure and gene flow",
    year = "2016",
    journal = "Evolutionary Applications",
    abstract = "Hybridization is a potent evolutionary process that can affect the origin, maintenance, and loss of biodiversity. Because of its ecological and evolutionary consequences, an understanding of hybridization is important for basic and applied sciences, including conservation biology and agriculture. Herein, we review and discuss ideas that are relevant to the recognition of hybrids and hybridization. We supplement this discussion with simulations. The ideas we present have a long history, particularly in botany, and clarifying them should have practical consequences for managing hybridization and gene flow in plants. One of our primary goals is to illustrate what we can and cannot infer about hybrids and hybridization from molecular data; in other words, we ask when genetic analyses commonly used to study hybridization might mislead us about the history or nature of gene flow and selection. We focus on patterns of variation when hybridization is recent and populations are polymorphic, which are particularly informative for applied issues, such as contemporary hybridization following recent ecological change. We show that hybridization is not a singular process, but instead a collection of related processes with variable outcomes and consequences. Thus, it will often be inappropriate to generalize about the threats or benefits of hybridization from individual studies, and at minimum, it will be important to avoid categorical thinking about what hybridization and hybrids are. We recommend potential sampling and analytical approaches that should help us confront these complexities of hybridization.",
    url = "https://doi.org/10.1111/eva.12380",
    doi = "10.1111/eva.12380",
    openalex = "W2301071597",
    references = "doi101111j1365294x200904137x"
}

Hybridization and its consequences have been of longstanding interest to evolutionary biologists. Darwin (1859) included a chapter on hybrids and the expression and causes of hybrid sterility in The Origin of Species, while the main proponents of the neo-Darwinian synthesis discussed the topic at varying length in the mid-1900s (

@article{doi101111mec13685,
    author = "Abbott, Richard J. and Barton, Nick and Good, Jeffrey M.",
    title = "Genomics of hybridization and its evolutionary consequences",
    year = "2016",
    journal = "Molecular Ecology",
    abstract = "Hybridization and its consequences have been of longstanding interest to evolutionary biologists. Darwin (1859) included a chapter on hybrids and the expression and causes of hybrid sterility in The Origin of Species, while the main proponents of the neo-Darwinian synthesis discussed the topic at varying length in the mid-1900s (",
    url = "https://doi.org/10.1111/mec.13685",
    doi = "10.1111/mec.13685",
    openalex = "W2345350775",
    references = "doi101016jppees201002002"
}

Adaptive immunity had been long thought of as an exclusive feature of animals. However, the discovery of the CRISPR-Cas defense system, present in almost half of prokaryotic genomes, proves otherwise. Because of the everlasting parasite-host arms race, CRISPR-Cas has rapidly evolved through horizontal transfer of complete loci or individual modules, resulting in extreme structural and functional diversity. CRISPR-Cas systems are divided into two distinct classes that each consist of three types and multiple subtypes. We discuss recent advances in CRISPR-Cas research that reveal elaborate molecular mechanisms and provide for a plausible scenario of CRISPR-Cas evolution. We also briefly describe the latest developments of a wide range of CRISPR-based applications.

@article{doi101126scienceaad5147,
    author = "Mohanraju, Prarthana and Makarova, Kira S. and Zetsche, Bernd and Zhang, Feng and Koonin, Eugene V. and van der Oost, John",
    title = "Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems",
    year = "2016",
    journal = "Science",
    abstract = "Adaptive immunity had been long thought of as an exclusive feature of animals. However, the discovery of the CRISPR-Cas defense system, present in almost half of prokaryotic genomes, proves otherwise. Because of the everlasting parasite-host arms race, CRISPR-Cas has rapidly evolved through horizontal transfer of complete loci or individual modules, resulting in extreme structural and functional diversity. CRISPR-Cas systems are divided into two distinct classes that each consist of three types and multiple subtypes. We discuss recent advances in CRISPR-Cas research that reveal elaborate molecular mechanisms and provide for a plausible scenario of CRISPR-Cas evolution. We also briefly describe the latest developments of a wide range of CRISPR-based applications.",
    url = "https://doi.org/10.1126/science.aad5147",
    doi = "10.1126/science.aad5147",
    openalex = "W2502856725",
    references = "doi101016jmolcel201403011, doi101093nargkt157, doi107554elife03401"
}

@article{doi101016jtree201711007,
    author = "Struck, Torsten H. and Feder, Jeffrey L. and Bendiksby, Mika and Birkeland, Siri and Cerca, José and Gusarov, Vladimir I. and Kistenich, Sonja and Larsson, Karl‐Henrik and Liow, Lee Hsiang and Nowak, Michael and Stedje, Brita and Bachmann, Lutz and Dimitrov, Dimitar",
    title = "Finding Evolutionary Processes Hidden in Cryptic Species",
    year = "2017",
    journal = "Trends in Ecology \& Evolution",
    url = "https://doi.org/10.1016/j.tree.2017.11.007",
    doi = "10.1016/j.tree.2017.11.007",
    openalex = "W2773211227",
    references = "doi101016jtree201109002, doi101073pnas1403662111, doi101073pnas1607921114, doi101111j15585646201000960x"
}

Human cultural traits-behaviors, ideas, and technologies that can be learned from other individuals-can exhibit complex patterns of transmission and evolution, and researchers have developed theoretical models, both verbal and mathematical, to facilitate our understanding of these patterns. Many of the first quantitative models of cultural evolution were modified from existing concepts in theoretical population genetics because cultural evolution has many parallels with, as well as clear differences from, genetic evolution. Furthermore, cultural and genetic evolution can interact with one another and influence both transmission and selection. This interaction requires theoretical treatments of gene-culture coevolution and dual inheritance, in addition to purely cultural evolution. In addition, cultural evolutionary theory is a natural component of studies in demography, human ecology, and many other disciplines. Here, we review the core concepts in cultural evolutionary theory as they pertain to the extension of biology through culture, focusing on cultural evolutionary applications in population genetics, ecology, and demography. For each of these disciplines, we review the theoretical literature and highlight relevant empirical studies. We also discuss the societal implications of the study of cultural evolution and of the interactions of humans with one another and with their environment.

@article{doi101073pnas1620732114,
    author = "Creanza, Nicole and Kolodny, Oren and Feldman, Marcus W.",
    title = "Cultural evolutionary theory: How culture evolves and why it matters",
    year = "2017",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Human cultural traits-behaviors, ideas, and technologies that can be learned from other individuals-can exhibit complex patterns of transmission and evolution, and researchers have developed theoretical models, both verbal and mathematical, to facilitate our understanding of these patterns. Many of the first quantitative models of cultural evolution were modified from existing concepts in theoretical population genetics because cultural evolution has many parallels with, as well as clear differences from, genetic evolution. Furthermore, cultural and genetic evolution can interact with one another and influence both transmission and selection. This interaction requires theoretical treatments of gene-culture coevolution and dual inheritance, in addition to purely cultural evolution. In addition, cultural evolutionary theory is a natural component of studies in demography, human ecology, and many other disciplines. Here, we review the core concepts in cultural evolutionary theory as they pertain to the extension of biology through culture, focusing on cultural evolutionary applications in population genetics, ecology, and demography. For each of these disciplines, we review the theoretical literature and highlight relevant empirical studies. We also discuss the societal implications of the study of cultural evolution and of the interactions of humans with one another and with their environment.",
    url = "https://doi.org/10.1073/pnas.1620732114",
    doi = "10.1073/pnas.1620732114",
    openalex = "W2737859984",
    references = "doi101002evan20181, doi101002sici1520650520009251aidevan130co27, doi1010079781475729177, doi101007bf02207996, doi101017s0140525x0100396x, doi101017s0140525x06009083, doi101086300102, doi101093biomet333183, doi101126science1170165, doi101126science1185231, doi101257aer91273, doi1015159781400847266, doi101537ase188722495, doi1023071367778, doi1023072485224, doi1023072669574, doi104324978020371075335"
}

A functioning gene drive system could fundamentally change our strategies for the control of vector-borne diseases by facilitating rapid dissemination of transgenes that prevent pathogen transmission or reduce vector capacity. CRISPR/Cas9 gene drive promises such a mechanism, which works by converting cells that are heterozygous for the drive construct into homozygotes, thereby enabling super-Mendelian inheritance. Although CRISPR gene drive activity has already been demonstrated, a key obstacle for current systems is their propensity to generate resistance alleles, which cannot be converted to drive alleles. In this study, we developed two CRISPR gene drive constructs based on the nanos and vasa promoters that allowed us to illuminate the different mechanisms by which resistance alleles are formed in the model organism Drosophila melanogaster. We observed resistance allele formation at high rates both prior to fertilization in the germline and post-fertilization in the embryo due to maternally deposited Cas9. Assessment of drive activity in genetically diverse backgrounds further revealed substantial differences in conversion efficiency and resistance rates. Our results demonstrate that the evolution of resistance will likely impose a severe limitation to the effectiveness of current CRISPR gene drive approaches, especially when applied to diverse natural populations.

@article{doi101371journalpgen1006796,
    author = "Champer, Jackson and Reeves, Riona and Oh, Suh Yeon and Liu, Chen and Liu, Jingxian and Clark, Andrew G. and Messer, Philipp W.",
    title = "Novel CRISPR/Cas9 gene drive constructs reveal insights into mechanisms of resistance allele formation and drive efficiency in genetically diverse populations",
    year = "2017",
    journal = "PLoS Genetics",
    abstract = "A functioning gene drive system could fundamentally change our strategies for the control of vector-borne diseases by facilitating rapid dissemination of transgenes that prevent pathogen transmission or reduce vector capacity. CRISPR/Cas9 gene drive promises such a mechanism, which works by converting cells that are heterozygous for the drive construct into homozygotes, thereby enabling super-Mendelian inheritance. Although CRISPR gene drive activity has already been demonstrated, a key obstacle for current systems is their propensity to generate resistance alleles, which cannot be converted to drive alleles. In this study, we developed two CRISPR gene drive constructs based on the nanos and vasa promoters that allowed us to illuminate the different mechanisms by which resistance alleles are formed in the model organism Drosophila melanogaster. We observed resistance allele formation at high rates both prior to fertilization in the germline and post-fertilization in the embryo due to maternally deposited Cas9. Assessment of drive activity in genetically diverse backgrounds further revealed substantial differences in conversion efficiency and resistance rates. Our results demonstrate that the evolution of resistance will likely impose a severe limitation to the effectiveness of current CRISPR gene drive approaches, especially when applied to diverse natural populations.",
    url = "https://doi.org/10.1371/journal.pgen.1006796",
    doi = "10.1371/journal.pgen.1006796",
    openalex = "W2950981781",
    references = "doi101146annurevento011613162002"
}

Durable crop protection is an essential component of current and future food security. However, the effectiveness of pesticides is threatened by the evolution of resistant pathogens, weeds and insect pests. Pesticides are mostly novel synthetic compounds, and yet target species are often able to evolve resistance soon after a new compound is introduced. Therefore, pesticide resistance provides an interesting case of rapid evolution under strong selective pressures, which can be used to address fundamental questions concerning the evolutionary origins of adaptations to novel conditions. We ask: (i) whether this adaptive potential originates mainly from de novo mutations or from standing variation; (ii) which pre-existing traits could form the basis of resistance adaptations; and (iii) whether recurrence of resistance mechanisms among species results from interbreeding and horizontal gene transfer or from independent parallel evolution. We compare and contrast the three major pesticide groups: insecticides, herbicides and fungicides. Whilst resistance to these three agrochemical classes is to some extent united by the common evolutionary forces at play, there are also important differences. Fungicide resistance appears to evolve, in most cases, by de novo point mutations in the target-site encoding genes; herbicide resistance often evolves through selection of polygenic metabolic resistance from standing variation; and insecticide resistance evolves through a combination of standing variation and de novo mutations in the target site or major metabolic resistance genes. This has practical implications for resistance risk assessment and management, and lessons learnt from pesticide resistance should be applied in the deployment of novel, non-chemical pest-control methods.

@article{doi101111brv12440,
    author = "Hawkins, Nichola J. and Bass, Chris and Dixon, A. L. and Neve, Paul",
    title = "The evolutionary origins of pesticide resistance",
    year = "2018",
    journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society",
    abstract = "Durable crop protection is an essential component of current and future food security. However, the effectiveness of pesticides is threatened by the evolution of resistant pathogens, weeds and insect pests. Pesticides are mostly novel synthetic compounds, and yet target species are often able to evolve resistance soon after a new compound is introduced. Therefore, pesticide resistance provides an interesting case of rapid evolution under strong selective pressures, which can be used to address fundamental questions concerning the evolutionary origins of adaptations to novel conditions. We ask: (i) whether this adaptive potential originates mainly from de novo mutations or from standing variation; (ii) which pre-existing traits could form the basis of resistance adaptations; and (iii) whether recurrence of resistance mechanisms among species results from interbreeding and horizontal gene transfer or from independent parallel evolution. We compare and contrast the three major pesticide groups: insecticides, herbicides and fungicides. Whilst resistance to these three agrochemical classes is to some extent united by the common evolutionary forces at play, there are also important differences. Fungicide resistance appears to evolve, in most cases, by de novo point mutations in the target-site encoding genes; herbicide resistance often evolves through selection of polygenic metabolic resistance from standing variation; and insecticide resistance evolves through a combination of standing variation and de novo mutations in the target site or major metabolic resistance genes. This has practical implications for resistance risk assessment and management, and lessons learnt from pesticide resistance should be applied in the deployment of novel, non-chemical pest-control methods.",
    url = "https://doi.org/10.1111/brv.12440",
    doi = "10.1111/brv.12440",
    openalex = "W2810473995",
    references = "doi101038nrg3483, doi101111mec12415, doi101111mec13360"
}

Current approaches to biodiversity conservation are largely based on geographic areas, ecosystems, ecological communities and species, with less attention ongenetic diversity and the evolutionary continuum from populations to species. Conservation management generally rests on discrete categories, such as identified species, and, for threated taxa, intraspecific units. Species, in particular, provide a common measure of biodiversity yet in both theory and nature, speciation is typically a protracted process progressing from connected populations to unambiguous species with variable rates of phenotypic, ecological and genetic divergence. Thus, most recognised species are not genetically uniform and are sometimes highly structured into historically isolated populations worthy of consideration as intraspecific units that represent unique genetic diversity for conservation. Genome screens offer unprecedented resolution of structure across taxonomic boundaries in species complexes, and have the potential to oversplit species if not interpreted conservatively. This highlights the blurred line between populations and species, and can confound simple dichotomies of ‘species’ versus ‘not species’. At the same time, like plants, there is increasing evidence than even distantly related animal species can hybridize and exchange genes. A review of conservation legislation reveals that legal definitions of ‘species’ are quite flexible and can accommodate a range of infra-specific taxa and divergent populations, as well as taxonomically recognised species. For example, the legislative definition of a species around the world can include: species, subspecies, varieties, and geographically and/or genetically distinct populations. In principle, this flexibility allows for protection of genetic diversity and maintenance of evolutionary processes at a broad range of infra-specific levels. However, evolutionary biologists often fail to adequately justify and then translate their evidence for genetically defined units into categories suited to assessment under local legislation. We recommend that (i). genomic data should be interpreted conservatively when formally naming species, (ii). concomitantly, there should be stronger impetus and a more uniform approach to identifying clearly justified intraspecific units, (iii). guidelines be developed for recognising and labelling intraspecific data that align with best scientific practice, and (iv). that the more nuanced view of species and speciation emerging from genomic analyses is communicated more effectively by scientists to decision makers.

@article{doi103389fevo201800165,
    author = "Coates, David and Byrne, Margaret and Moritz, Craig",
    title = "Genetic Diversity and Conservation Units: Dealing With the Species-Population Continuum in the Age of Genomics",
    year = "2018",
    journal = "Frontiers in Ecology and Evolution",
    abstract = "Current approaches to biodiversity conservation are largely based on geographic areas, ecosystems, ecological communities and species, with less attention ongenetic diversity and the evolutionary continuum from populations to species. Conservation management generally rests on discrete categories, such as identified species, and, for threated taxa, intraspecific units. Species, in particular, provide a common measure of biodiversity yet in both theory and nature, speciation is typically a protracted process progressing from connected populations to unambiguous species with variable rates of phenotypic, ecological and genetic divergence. Thus, most recognised species are not genetically uniform and are sometimes highly structured into historically isolated populations worthy of consideration as intraspecific units that represent unique genetic diversity for conservation. Genome screens offer unprecedented resolution of structure across taxonomic boundaries in species complexes, and have the potential to oversplit species if not interpreted conservatively. This highlights the blurred line between populations and species, and can confound simple dichotomies of ‘species’ versus ‘not species’. At the same time, like plants, there is increasing evidence than even distantly related animal species can hybridize and exchange genes. A review of conservation legislation reveals that legal definitions of ‘species’ are quite flexible and can accommodate a range of infra-specific taxa and divergent populations, as well as taxonomically recognised species. For example, the legislative definition of a species around the world can include: species, subspecies, varieties, and geographically and/or genetically distinct populations. In principle, this flexibility allows for protection of genetic diversity and maintenance of evolutionary processes at a broad range of infra-specific levels. However, evolutionary biologists often fail to adequately justify and then translate their evidence for genetically defined units into categories suited to assessment under local legislation. We recommend that (i). genomic data should be interpreted conservatively when formally naming species, (ii). concomitantly, there should be stronger impetus and a more uniform approach to identifying clearly justified intraspecific units, (iii). guidelines be developed for recognising and labelling intraspecific data that align with best scientific practice, and (iv). that the more nuanced view of species and speciation emerging from genomic analyses is communicated more effectively by scientists to decision makers.",
    url = "https://doi.org/10.3389/fevo.2018.00165",
    doi = "10.3389/fevo.2018.00165",
    openalex = "W2897004916",
    references = "doi101007s116920129171x, doi1010160006320792912013, doi1010160169534794900574, doi101016jcub201709047, doi101016jtree200611004, doi101016jtree200901009, doi101016s0169534700018760, doi101073pnas1607921114, doi10108010635150701701083, doi101111j10958312200500503x, doi101111j1365294x200703529x, doi101146annurevento112408085432, doi101146annureves18110187002421, doi10118617429994716"
}

@article{doi101038s415590180777y,
    author = "Taylor, Scott A. and Larson, Erica L.",
    title = "Insights from genomes into the evolutionary importance and prevalence of hybridization in nature",
    year = "2019",
    journal = "Nature Ecology \& Evolution",
    url = "https://doi.org/10.1038/s41559-018-0777-y",
    doi = "10.1038/s41559-018-0777-y",
    openalex = "W2911246394",
    references = "doi101038nature05706, doi101038ncomms14363, doi101111evo12399, doi101111j14209101201202599x, doi101111mec12415"
}

There is growing evidence that anthropogenic landscapes can strongly influence the evolution of dispersal, particularly through fragmentation, and may drive organisms into an evolutionary trap by suppressing dispersal. However, the influence on dispersal evolution of anthropogenic variation in habitat patch turnover has so far been largely overlooked. In this study, we examined how human-driven variation in patch persistence affects dispersal rates and distances, determines dispersal-related phenotypic specialization, and drives neutral genetic structure in spatially structured populations. We addressed this issue in an amphibian, Bombina variegata, using an integrative approach combining capture-recapture modeling, demographic simulation, common garden experiments, and population genetics. B. variegata reproduces in small ponds that occur either in habitat patches that are persistent (i.e. several decades or more), located in riverine environments with negligible human activity, or in patches that are highly temporary (i.e. a few years), created by logging operations in intensively harvested woodland. Our capture-recapture models revealed that natal and breeding dispersal rates and distances were drastically higher in spatially structured populations (SSPs) in logging environments than in riverine SSPs. Population simulations additionally showed that dispersal costs and benefits drive the fate of logging SSPs, which cannot persist without dispersal. The common garden experiments revealed that toadlets reared in laboratory conditions have morphological and behavioral specialization that depends on their habitat of origin. Toadlets from logging SSPs were found to have higher boldness and exploration propensity than those from riverine SSPs, indicating transgenerationally transmitted dispersal syndromes. We also found contrasting patterns of neutral genetic diversity and gene flow in riverine and logging SSPs, with genetic diversity and effective population size considerably higher in logging than in riverine SSPs. In parallel, intra-patch inbreeding and relatedness levels were lower in logging SSPs. Controlling for the effect of genetic drift and landscape connectivity, gene flow was found to be higher in logging than in riverine SSPs. Taken together, these results indicate that anthropogenic variation in habitat patch turnover may have an effect at least as important as landscape fragmentation on dispersal evolution and the long-term viability and genetic structure of wild populations.

@misc{cayuela2020anthropogenic,
    author = "Cayuela, Hugo",
    title = "Anthropogenic disturbance drives dispersal syndromes, demography, and gene flow in amphibian populations",
    year = "2020",
    publisher = "Dryad",
    abstract = "There is growing evidence that anthropogenic landscapes can strongly influence the evolution of dispersal, particularly through fragmentation, and may drive organisms into an evolutionary trap by suppressing dispersal. However, the influence on dispersal evolution of anthropogenic variation in habitat patch turnover has so far been largely overlooked. In this study, we examined how human-driven variation in patch persistence affects dispersal rates and distances, determines dispersal-related phenotypic specialization, and drives neutral genetic structure in spatially structured populations. We addressed this issue in an amphibian, Bombina variegata, using an integrative approach combining capture-recapture modeling, demographic simulation, common garden experiments, and population genetics. B. variegata reproduces in small ponds that occur either in habitat patches that are persistent (i.e. several decades or more), located in riverine environments with negligible human activity, or in patches that are highly temporary (i.e. a few years), created by logging operations in intensively harvested woodland. Our capture-recapture models revealed that natal and breeding dispersal rates and distances were drastically higher in spatially structured populations (SSPs) in logging environments than in riverine SSPs. Population simulations additionally showed that dispersal costs and benefits drive the fate of logging SSPs, which cannot persist without dispersal. The common garden experiments revealed that toadlets reared in laboratory conditions have morphological and behavioral specialization that depends on their habitat of origin. Toadlets from logging SSPs were found to have higher boldness and exploration propensity than those from riverine SSPs, indicating transgenerationally transmitted dispersal syndromes. We also found contrasting patterns of neutral genetic diversity and gene flow in riverine and logging SSPs, with genetic diversity and effective population size considerably higher in logging than in riverine SSPs. In parallel, intra-patch inbreeding and relatedness levels were lower in logging SSPs. Controlling for the effect of genetic drift and landscape connectivity, gene flow was found to be higher in logging than in riverine SSPs. Taken together, these results indicate that anthropogenic variation in habitat patch turnover may have an effect at least as important as landscape fragmentation on dispersal evolution and the long-term viability and genetic structure of wild populations.",
    url = "https://datadryad.org/dataset/doi:10.5061/dryad.q83bk3jdz",
    doi = "10.5061/dryad.q83bk3jdz"
}

Abstract Loss of biodiversity is among the greatest problems facing the world today. Conservation and the Genomics of Populations gives a comprehensive overview of the essential background, concepts, and tools needed to understand how genetic information can be used to conserve species threatened with extinction, and to manage species of ecological or commercial importance. New molecular techniques, statistical methods, and computer programs, genetic principles, and methods are becoming increasingly useful in the conservation of biological diversity. Using a balance of data and theory, coupled with basic and applied research examples, this book examines genetic and phenotypic variation in natural populations, the principles and mechanisms of evolutionary change, the interpretation of genetic data from natural populations, and how these can be applied to conservation. The book includes examples from plants, animals, and microbes in wild and captive populations. This third edition has been thoroughly revised to include advances in genomics and contains new chapters on population genomics, genetic monitoring, and conservation genetics in practice, as well as new sections on climate change, emerging diseases, metagenomics, and more. More than one-third of the references in this edition were published after the previous edition. Each of the 24 chapters and the Appendix end with a Guest Box written by an expert who provides an example of the principles presented in the chapter from their own work. This book is essential for advanced undergraduate and graduate students of conservation genetics, natural resource management, and conservation biology, as well as professional conservation biologists and policy-makers working for wildlife and habitat management agencies. Much of the book will also interest nonprofessionals who are curious about the role of genetics in conservation and management of wild and captive populations.

@book{doi101093oso97801988565660010001,
    author = "Allendorf, Fred W. and Funk, W. Chris and Aitken, Sally N. and Byrne, Margaret and Luikart, Gordon and Antunes, Agostinho",
    title = "Conservation and the Genomics of Populations",
    year = "2022",
    abstract = "Abstract Loss of biodiversity is among the greatest problems facing the world today. Conservation and the Genomics of Populations gives a comprehensive overview of the essential background, concepts, and tools needed to understand how genetic information can be used to conserve species threatened with extinction, and to manage species of ecological or commercial importance. New molecular techniques, statistical methods, and computer programs, genetic principles, and methods are becoming increasingly useful in the conservation of biological diversity. Using a balance of data and theory, coupled with basic and applied research examples, this book examines genetic and phenotypic variation in natural populations, the principles and mechanisms of evolutionary change, the interpretation of genetic data from natural populations, and how these can be applied to conservation. The book includes examples from plants, animals, and microbes in wild and captive populations. This third edition has been thoroughly revised to include advances in genomics and contains new chapters on population genomics, genetic monitoring, and conservation genetics in practice, as well as new sections on climate change, emerging diseases, metagenomics, and more. More than one-third of the references in this edition were published after the previous edition. Each of the 24 chapters and the Appendix end with a Guest Box written by an expert who provides an example of the principles presented in the chapter from their own work. This book is essential for advanced undergraduate and graduate students of conservation genetics, natural resource management, and conservation biology, as well as professional conservation biologists and policy-makers working for wildlife and habitat management agencies. Much of the book will also interest nonprofessionals who are curious about the role of genetics in conservation and management of wild and captive populations.",
    url = "https://doi.org/10.1093/oso/9780198856566.001.0001",
    doi = "10.1093/oso/9780198856566.001.0001",
    openalex = "W4224274233",
    references = "doi101002evl3189, doi101007s10531020019800, doi101016jppees201002002, doi101046j14209101200100339x, doi101093czzow088, doi101093genetics902349, doi101111gcb13976"
}