"What man that sees the ever-whirling wheel
Of Change, the which all mortal things doth sway,
But that therby doth find, and plainly feel,
How Mutability in them doth play"
Folio 41v , c. AD 1200
The Faerie Queene,, bk. VII, ch. VI, 1596
he genetic information specifies everything about an organism and its potential. Genotype specifies possible phenotypes, therefore, phenotypic change follows genetic change. This obviously should be one of the areas where evolutionary change is seen, and genetic change is truly the most important for understanding evolutionary processes.
Extremely extensive genetic change has been observed, both in the lab and in the wild. We have seen genomes irreversibly and heritably altered by numerous phenomena, including gene flow, random genetic drift, natural selection, and mutation. Observed mutations have occurred by mobile introns, gene duplications, recombination, transpositions, retroviral insertions (horizontal gene transfer), base substitutions, base deletions, base insertions, and chromosomal rearrangements. Chromosomal rearrangements include genome duplication (e.g. polyploidy), unequal crossing over, inversions, translocations, fissions, fusions, chromosome duplications and chromosome deletions (Futuyma 1998, pp. 267-271, 283-294).
Once the genetic material was elucidated, it was obvious that for macroevolution to proceed vast amounts of change was necessary in the genetic material. If the general observation of geneticists was that of genomic stasis and recalcitrance to significant genetic change, it would be weighty evidence against the probability of macroevolution. For instance, it is possible that whenever we introduce mutations into an organism's genome, the DNA could back-mutate to its former state. However, the opposite is the case—the genome is incredibly plastic, and genetic change is heritable and essentially irreversible (Lewin 1999).
Cladistic classification, and thus, phylogenetic reconstruction, is largely based on the various distinguishing morphological characteristics of species. Macroevolution requires that organisms' morphologies have changed throughout evolutionary history; thus, we should observe morphological change and variation in modern populations.
There have been numerous observations of morphological change in populations of organisms (Endler 1986). Examples are the change in color of some organ, such as the yellow body or brown eyes of Drosophila, coat color in mice (Barsh 1996), scale color in fish (Houde 1988), and plumage pattern in birds (Morton 1990). Almost every imaginable heritable variation in size, length, width, or number of some physical aspect of animals has been recorded (Johnston and Selander 1973; Futuyma 1998, p. 247-262). This last fact is extremely important for common descent, since the major morphological differences between many species (e.g. species of amphibians, reptiles, mammals, and birds) are simple alterations in size of certain aspects of their respective parahomologous structures.
One of the major differences between organisms is their capacity for various functions. The ability to occupy one niche over another is invariably due to differing functions. Thus, functional change must be extremely important for macroscopic macroevolutionary change.
Many organisms have been observed to acquire various new functions which they did not have previously (Endler 1986). Bacteria have acquired resistance to viruses (Luria and Delbruck 1943) and to antibiotics (Lederberg and Lederberg 1952). Bacteria have also evolved the ability to synthesize new amino acids and DNA bases (Futuyma 1998, p. 274). Unicellular organisms have evolved the ability to use nylon and pentachlorophenol (which are both unnatural manmade chemicals) as their sole carbon sources (Okada et al. 1983; Orser and Lange 1994). The acquisition of this latter ability entailed the evolution of an entirely novel multienzyme metabolic pathway (Lee et al. 1998). Bacteria have evolved to grow at previously unviable temperatures (Bennett et al. 1992). In E. coli, we have seen the evolution (by artificial selection) of an entirely novel metabolic system including the ability to metabolize a new carbon source, the regulation of this ability by new regulatory genes, and the evolution of the ability to transport this new carbon source across the cell membrane (Hall 1982).
Such evolutionary acquisition of new function is also common in metazoans. We have observed insects become resistant to insecticides (Ffrench-Constant et al. 2000), animals and plants acquire disease resistance (Carpenter and O'Brien 1995; Richter and Ronald 2000), crustaceans evolve new defenses to predators (Hairston 1990), amphibians evolve tolerance to habitat acidification (Andren et al. 1989), and mammals acquire immunity to poisons (Bishop 1981). Recent beneficial mutations are also known in humans, such as the famous apolipoprotein AI Milano mutation that confers lowered risk to cardiovascular disease in its carriers.
A very general conclusion made from the theory of common descent is that life, as a whole, was different in the past. The predicted evolutionary pattern is that the farther back we look back in time, the more different life should appear from the modern biosphere. More recent fossils should be more similar to contemporary life forms than older fossils.
This point is related to, yet subtly different from, prediction 1.4 and prediction 1.5 concerning predicted common ancestors. As we have seen, the standard phylogenetic tree predicts many common ancestors and their morphologies. However, given what we know of modern species dynamics and recent extinction rates, we know that the majority of organisms will eventually go extinct (Diamond 1984a; Diamond 1984b; Wilson 1992, ch. 12; Futuyma 1998, pp. 722-723). By extrapolation, the majority of past organisms also have gone extinct. Thus, we should reasonably expect that the predicted common ancestors had many other descendants and relatives that did not leave descendants which survive today. In short, we predict that the majority of fossil species that we find should not be the actual common ancestors of modern species, but rather they should be related organisms that eventually ended in extinction.
The oldest rocks we find on the earth are about 4 Bya (billion years ago), and they are devoid of any life. The oldest potential fossil evidence for life are fossil bacteria from the Apex Chert of Australia (3.46 Bya), though these fossils are currently embroiled controversy and may not represent traces of life. The next oldest fossils are well-accepted fossil bacteria and bacterial mats (stromatolites) from South Africa that date to 3.4 Bya. Thus, the oldest fossil prokaryotes date to 3.4 to 3.5 Byr. For nearly the next billion years, rocks from the Archean have no multicellular life at all, just prokaryotes. The oldest eukaryote fossils are acritarchs dating to about 1.75 Byr. For another 1000 million years, there is still no evidence of multicellular life.
Near the Precambrian/Cambrian transition, only 580 Mya, in the Ediacaran and Burgess shale faunas we finally find the first fossils of multicellular animals. However, they are very unusual, mostly small, soft-bodied metazoans, and most are superficially unlike anything found today. Precisely as we would expect from the standard phylogenetic tree, the earliest fossils of multi-cellular life are very simple sponges and sea anemone-like organisms (sea anemones and jellyfish are both cnidarians). Around 20 million years later, we find the first evidence of simple mollusks, worms, and echinoderms (organisms similar to starfish and sea cucumbers). Another ~15 million years later, the very first vertebrates appear, though most people would strain to recognize them as such. They are small worm-like and primitive fish-like organisms, without bones, jaws, or fins (excepting a single dorsal fin).
As we progress through the Phanerozoic, life gets progressively more similar to modern biota. In the Cambrian (~540 to 500 Mya), we find predominantly invertebrate sea organisms, such as trilobites, sponges, and echinoderms. During the next 100 million years sea life is dominated by invertebrates and strange jawless fish, which besides chordate worms are the only vertebrates around at the time. More familiar jawed fish only appear during the late Silurian, about 410 Mya. Ninety percent of the earth's sediments, up until the Devonian (~400 Mya), are devoid of any land animals.
During the Devonian, we finally find the first evidence of insects. For the next 100 million years, through the Carboniferous up until the Permian (~300 Mya), there are no land reptiles, no birds, nor mammals—only amphibians and insects. The land is covered by ferns—no pine trees or oaks or anything resembling them.
During the Mesozoic (from 250 to 65 Mya) life is dominated by monstrously large reptiles, the dinosaurs. The predominant plants are unusual gymnosperms, like the cycads. Nothing even resembling a modern mammal is found until the Jurassic, about 190 Mya. Even then, these "mammals" are small and appear half-reptile/half-rodent—far removed from the large megafauna yet to come. Ninety percent of the sediments on the earth which contain fossils of living organisms have no evidence of flowers—these appear for the first time just before the Paleocene (~65 Mya). Likewise, the earth's record of life is devoid of any hardwood forests until the beginning of the Cenozoic (~65 Mya to the present).
During the Cenozoic, mammals and birds finally come to prominence on the land, much as we find today. By the Pleistocene (2 Mya), the earth's biota closely, yet imperfectly, resembles what we presently find on the earth. Notable exceptions are the recent megafauna that covered the continents with organisms like mammoths, giant sloths, and saber-toothed tigers (Futuyma 1998, pp. 130, 169-199).
This falsification would be simple and facile—the sediments of the earth could contain a composition of species very similar to modern life as far back as we can see in the sequential layers.
The most useful definition of species (which does not assume evolution) for sexual metazoans is the Biological Species Concept: species are groups of actually or potentially interbreeding natural populations that are reproductively isolated from other such groups (Mayr 1942).
If branching of existing species into new species occurred gradually in the past, we should see all possible degrees of speciation or genetic isolation today, ranging from fully interbreeding populations, to partially interbreeding populations, to populations that interbreed with reduced fertility or with complete infertility, to completely genetically isolated populations.
There are countless cases of distinct species which can, in unusual or limited circumstances, form hybrids. One example is the West European carrion crow (Corvus corone) and the Asian hooded crow (Corvus cornix), which have distinct ranges meeting in a narrow "hybrid zone". Another are the Platte river species of sucker fish of the Catostomus genus which live together and only rarely interbreed (Futuyma 1998, p. 454).
One of the most striking instances of partial or incomplete speciation are the numerous "ring species" (for review see Irwin et al. 2001). Ring species, such as the salamander Ensatina, form a chain of interbreeding populations which loop around some geographical feature; where the populations meet on the other side, they behave as completely different species. In the case of Ensatina, the subspecies form a ring around the Central Valley of California—the subspecies freely interbreed and hybridize on the east, west, and north sides of the valley, but where they coexist on the south side they are incapable of hybridizing and act as separate species (Moritz et al. 1982; Futuyma 1998, pp. 455-456).
Another example of a ring species is the gull genus Larus. L. argentatus and L. fuscus were originally identified as distinct species in England. However, there is a continuous ring of Larus hybrids extending to the east and west all the way round the North Pole. Only in England are they incapable of interbreeding.
The Great Tit, Parus major, similarly forms a ring species around the mountains of Central Asia, freely interbreeding everywhere except in Northern China (Smith 1993, pp. 227-230).
Many species can hybridize, but the resulting offspring have reduced fertility. One example is the English shrew (genus Sorex) whose hybrids are reproductively disadvantaged due to chromosomal differences. This has also been seen in lab experiments mating Utah and California strains of Drosophila pseudoobscura. Another example are the frogs Bombina bombina and Bombina variegata, whose hybrids have low fitness (i.e. they do not reproduce very successfully) (Barton and Gale 1993).
Many other species can mate and produce viable hybrids, but the hybrids are infertile. This has been observed in species of amphibians (like certain frog species of the Rana genus) and mammals like Equus (where matings of horse and ass result in a sterile mule). Another example is the newt Triturus cristatus and T. marmoratus, in which hybrid infertility is due to unpaired chromosomes (Smith 1993, pp. 253, 264).
Other species are able to mate with successful fertilization, but mortality occurs in embryogenesis. Such is the case with the frog species Rana pipiens and R. sylvatica (Futuyma 1998, p. 460). This phenomenon has also been observed in Drosophila. Additional examples are also found in plants such as the cotton species Gossypium hirsutum and G. barbadense (Smith 1993; Futuyma 1998, ch. 15 and 16).
If all known species were completely genetically isolated from one another, and there were no instances of hybrids, it would be very difficult to reasonably justify the postulation of millions upon millions of gradual speciation events in the past.
The standard phylogenetic tree illustrates countless speciation events; each common ancestor also represents at least one speciation event. Thus we should be able to observe actual speciation, if even only very rarely. Current estimates from the fossil record and measured mutational rates place the time required for full reproductive isolation in the wild at ~3 million years on average (Futuyma 1998, p. 510). Consequently, observation of speciation in nature should be a possible but rare phenomenon. However, evolutionary rates in laboratory organisms can be much more rapid than rates inferred from the fossil record, so it is still possible that speciation may be observed in common lab organisms (Gingerich 1983).
Speciation of numerous plants, both angiosperms and ferns (such as hemp nettle, primrose, radish and cabbage, and various fern species) has been seen via hybridization and polyploidization since the early 20th century. Several speciation events in plants have been observed that did not involve hybridization or polyploidization (such as maize and S. malheurensis).
Some of the most studied organisms in all of genetics are the Drosophila species, which are commonly known as fruitflies. Many Drosophila speciation events have been extensively documented since the seventies. Speciation in Drosophila has occurred by spatial separation, by habitat specialization in the same location, by change in courtship behavior, by disruptive natural selection, and by bottlenecking populations (founder-flush experiments), among other mechanisms.
Several speciation events have also been seen in laboratory populations of houseflies, gall former flies, apple maggot flies, flour beetles, Nereis acuminata (a worm), mosquitoes, and various other insects. Green algae and bacteria have been classified as speciated due to change from unicellularity to multicellularity and due to morphological changes from short rods to long rods, all the result of selection pressures.
Speciation has also been observed in mammals. Six instances of speciation in house mice on Madeira within the past 500 years have been the consequence of only geographic isolation, genetic drift, and chromosomal fusions. A single chromosomal fusion is the sole major genomic difference between humans and chimps, and some of these Madeiran mice have survived nine fusions in the past 500 years (Britton-Davidian et al. 2000).
More detail and many references are given in the Observed Instances of Speciation FAQ.
Observed rates of evolutionary change in modern populations must be greater than or equal to rates observed in the fossil record.
Here I can do no better than to quote George C. Williams writing on this very issue:
"The question of evolutionary rate is indeed a serious theoretical challenge, but the reason is exactly opposite of that inspired by most people's intuitions. Organisms in general have not done nearly as much evolving as we should reasonably expect. Long-term rates of change, even in lineages of unusually rapid evolution, are almost always far slower than they theoretically could be." (Williams 1992, p. 128)
In 1983, Phillip Gingerich published a famous study analyzing 512 different observed rates of evolution (Gingerich 1983). The study centered on rates observed from three classes of data: (1) lab experiments, (2) historical colonization events, and (3) the fossil record. A useful measure of evolutionary rate is the darwin, which is defined as a change in an organism's character by a factor of e per million years (where e is the base of natural log). The average rate observed in the fossil record was 0.6 darwins; the fastest rate was 32 darwins. The latter is the most important number for comparison; rates of evolution observed in modern populations should be equal to or greater than this rate.
The average rate of evolution observed in historical colonization events in the wild was 370 darwins—over 10 times the required minimum rate. In fact, the fastest rate found in colonization events was 80,000 darwins, or 2500 times the required rate. Observed rates of evolution in lab experiments are even more impressive, averaging 60,000 darwins and as high as 200,000 darwins (or over 6000 times the required rate).
A more recent paper evaluating the evolutionary rate in guppies in the wild found rates ranging from 4000 to 45,000 darwins (Reznick 1997). Note that a sustained rate of "only" 400 darwins is sufficient to transform a mouse into an elephant in a mere 10,000 years (Gingerich 1983).
One of the most extreme examples of rapid evolution was when the hominid cerebellum doubled in size within ~100,000 years during the Pleistocene (Rightmire 1985). This "unique and staggering" acceleration in evolutionary rate was only 7 darwins (Williams 1992, p. 132). This rate converts to a minuscule 0.02% increase per generation, at most. For comparison, the fastest rate observed in the fossil record in the Gingerich study was 37 darwins over one thousand years, and this corresponds to, at most, a 0.06% change per generation.
If modern observed rates of evolution were unable to account for the rates found in the fossil record, the theory of common descent would be extremely difficult to justify, to put it mildly. For example, Equus evolutionary rates during the late Cenozoic could be consistently found to be greater than 80,000 darwins. Given the observed rates in modern populations, a rate that high would be impossible to explain. Since the average rate of evolution in colonization events is ~400 darwins, even an average rate of 4000 darwins in the fossil record would constitute a robust falsification.
Rates of genetic change, as measured by nucleotide substitutions, must also be consistent with the rate required from the time allowed in the fossil record and the sequence differences observed between species.
What we must compare are the data from three independent sources: (1) fossil record estimates of the time of divergence of species, (2) nucleotide differences between species, and (3) the observed rates of mutation in modern species. The overall conclusion is that these three are entirely consistent with one another.
For example, consider the human/chimp divergence, one of the most well-studied evolutionary relationships. Chimpanzees and humans are thought to have diverged, or shared a common ancestor, about 6 Mya, based on the fossil record (Stewart and Disotell 1998). The genomes of chimpanzees and humans are very similar; their DNA sequences overall are 98% identical (King and Wilson 1975; Sverdlov 2000). The greatest differences between these genomes are found in pseudogenes, non-translated sequences, and fourfold degenerate third-base codon positions. All of these are very free from selection constraints, since changes in them have virtually no functional or phenotypic effect, and thus most mutational changes are incorporated and retained in their sequences. For these reasons, they should represent the background rate of spontaneous mutation in the genome. These regions with the highest sequence dissimilarity are what should be compared between species, since they will provide an upper limit on the rate of evolutionary change.
Given a divergence date of 6 Mya, the maximum inferred rate of nucleotide substitution in the most divergent regions of DNA in humans and chimps is ~1.3 x 10-9 base substitutions per site per year. Given a generation time of 15-20 years, this is equivalent to a substitution rate of ~2 x 10-8 per site per generation (Crowe 1993; Futuyma 1998, p. 273).
Background spontaneous mutation rates are extremely important for cancer research, and they have been studied extensively in humans. A review of the spontaneous mutation rate observed in several genes in humans has found an average background mutation rate of 1-5 x 10-8 base substitutions per site per generation. This rate is a very minimum, because its value does not include insertions, deletions, or other base substitution mutations that can destroy the function of these genes (Giannelli et al. 1999; Mohrenweiser 1994, pp. 128-129). Thus, the fit amongst these three independent sources of data is extremely impressive.
Similar results have been found for many other species (Kumar and Subramanian 2002; Li 1997, pp. 180-181, 191). In short, the observed genetic rates of mutation closely match inferred rates based on paleological divergence times and genetic genomic differences. Therefore, the observed rates of mutation can easily account for the genetic differences observed between species as different as mice, chimpanzees, and humans.
It is entirely plausible that measured genetic mutation rates from observations of modern organisms could be orders of magnitude less than that required by rates inferred from the fossil record and sequence divergence.
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