Castoe et al., “Evidence for an ancient adaptive episode of convergent molecular evolution” PNAS, April 29, 2009, published on line, doi: 10.1073/pnas.0900233106
Abstract: …..These results indicate that nonneutral convergent molecular evolution in mitochondria can occur at a scale and intensity far beyond what has been documented previously, and they highlight the vulnerability of standard phylogenetic methods to the presence of nonneutral convergent sequence evolution.
I left a comment on the preprint version of this paper at Nature precedings. http://precedings.nature.com/documents/2123/version/1#comments
Indeed, convergent evolution is extremely common. The best illustration of this is a phenomenon I termed ‘genetic nonequidistance to a more complex outgroup’. Thus, relative to a complex outgroup such as human, some sister species from a simple clade are not equidistant to human. The more complex sister species is always closer to human than the simpler sister species. In all five cases (except plants) examined where difference in complexity of the sister species can be inferred (octopus vs. cockle, Terebratulina vs. Lingula, bird vs. snake, dragonfly vs. louse, and smut vs. yeast), the more complex species always show greater sequence similarity to humans.
Because these sister species are separated from humans for the same amount of time, their different sequence similarity to humans must be due to convergent evolution. Thus, sequence similarity to complex species or humans cannot be used to infer closer genealogy with humans.
The sister grouping of chimpanzees and humans really has no other non-ambiguous support other than sequence similarity as measured by percent identity. The premise for this approach has now been nullified by the phenomenon of genetic non-equidistance to a more complex outgroup despite equidistance in time or genealogy. The same premise for grouping an ape (chimpanzee) with human to the exclusion of another ape (orangutan) would equally justify the obviously absurd grouping of human with a mollusk (octopus) to the exclusion of another mollusk (cockle), or with a brachiopod (Terebratulina) to the exclusion of another brachiopod (Lingula), or with a reptile (bird) to the exclusion of another reptile (snake).
The molecular clock hypothesis, i.e., vastly different species have very similar mutation rates, is a tautological interpretation of the ‘genetic equidistance’ result. It is falsified by the ‘genetic nonequidistance’ phenomenon as discussed above. I have recently come up with the ‘maximum genetic diversity’ (MGD) hypothesis to explain equally well both the equidistance and the nonequidistance phenomenon. See my paper posted here, “Inverse relationship between genetic diversity and epigenetic complexity”.
Below is a paragraph from one of my recent manuscripts discussing one of the best facts (newly reported in Nature this year) that simply cannot be reconciled in any way with the sister grouping of humans and chimpanzees but fully supports the MGD hypothesis and the sister grouping of humans and pongids.
Consistent with low genetic diversity in humans, human specific segmented duplications show lower copy number polymorphisms in humans than chimpanzee specific segmented duplications do in chimpanzees . Similarly, those duplications shared among human, chimpanzees, and orangutans, or those shared among human, chimpanzees, orangutans, and monkeys are also less polymorphic in humans than in chimpanzees, indicating clearly that duplications that are shared because of common ancestry are less polymorphic in humans than in chimpanzees. In contrast, the duplications shared between human and chimpanzees are equally polymorphic in humans and chimpanzees. This unusual result contradicts the sister grouping of humans and chimpanzees, because both the MGD and the bottleneck hypothesis would predict lower polymorphism in humans if these duplications are shared because of common ancestry. However, it is fully consistent with the interpretation that the shared duplications between humans and chimpanzees are not due to common ancestry but are due to common selection of independent duplications. Common selection leading to shared sequences is well established . The MGD hypothesis interprets many of the shared sequences between human and chimpanzees as a result of common selection rather than common ancestry. The similar selection pressure leads to similar levels of polymorphism. This result is thus one of the best that simply cannot be reconciled in any way with the sister grouping of humans and chimpanzees but fully supports the MGD hypothesis and the sister grouping of humans and pongids.
Ref: 54. Marques-Bonet T, Kidd JM, Ventura M, Graves TA, Cheng Z, et al. (2009) A burst of segmental duplications in the genome of the African great ape ancestor. Nature 457: 877-881. http://www.publicacions.ub.es/refs/micoshumans.pdf
55. Bull JJ, Badgett MR, Wichman HA, Huelsenbeck JP, Hillis DM, et al. (1997) Exceptional convergent evolution in a virus. Genetics 147: 1497-1507.