Despite Darwinian expectations, there is no single, agreed upon Tree of Life. Efforts to derive such a tree, which would coherently describe the descent of all life from a common ancestor, are bedeviled by scientists offering pesky evidence that disturbs the tidy evolutionary story.
A recent paper in the journal Biological Reviews of the Cambridge Philosophical Society offers some striking comments about the prevalence of discordance among phylogenetic trees. It acknowledges that “phylogenetic conflict is common, and frequently the norm rather than the exception.” Many had hoped that collecting more data would resolve some of these problems, but the paper observes that, “Phylogenetic conflict has become a more acute problem with the advent of genomescale data sets.” The paper explains how this problem has gotten worse as time goes on:
Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species.
(Liliana M. Dávalos, Andrea L. Cirranello, Jonathan H. Geisler, and Nancy B. Simmons, “Understanding phylogenetic incongruence: lessons from phyllostomid bats,” Biological Reviews of the Cambridge Philosophical Society, Vol. 87:991-1024 (2012).)
Meanwhile, bats are posing phylogenetic conundrums for evolutionary biologists in an entirely different way — ways that include both morphological and molecular data. As we’ve discussed here before on ENV, it’s long been known that both bats and whales use echolocation, even though their supposed distant common ancestor did not have this trait. Evolutionary biologists long-believed this was a case of convergent morphological evolution. In the past we covered an article in Current Biology explaining the “surprising” finding that echolocation in bats and whales also involves genetic convergence:
Only microbats and toothed whales have acquired sophisticated echolocation, indispensable for their orientation and foraging. Although the bat and whale biosonars originated independently and differ substantially in many aspects, we here report the surprising finding that the bottlenose dolphin, a toothed whale, is clustered with microbats in the gene tree constructed using protein sequences encoded by the hearing gene Prestin.
(Ying Li, Zhen Liu, Peng Shi, and Jianzhi Zhang, “The hearing gene Prestin unites echolocating bats and whales,” Current Biology, 20(2):R55-R56 (January, 2010) (internal citations removed).)
Of course the authors try to massage away this result, which doesn’t fit with the standard mammalian phylogeny. They try to explain it by appealing to convergent evolution — at the genetic level. In fact, another paper called this data, “one of the best examples of convergent molecular evolution discovered to date.” (The first bat study mentioned in this post uses similar appeals to “convergence” to explain away why the bat genetic data won’t fit a tree.) But a recent 2012 study titled “Parallel Evolution of Auditory Genes for Echolocation in Bats and Toothed Whales” has expanded what we know about the extent of unexpected “convergent” similarity among bat and whale genes. According to the paper:
The ability of bats and toothed whales to echolocate is a remarkable case of convergent evolution. Previous genetic studies have documented parallel evolution of nucleotide sequences in Prestin and KCNQ4, both of which are associated with voltage motility during the cochlear amplification of signals. Echolocation involves complex mechanisms. The most important factors include cochlear amplification, nerve transmission, and signal re-coding. Herein, we screen three genes that play different roles in this auditory system. Cadherin 23 (Cdh23) and its ligand, protocadherin 15 (Pcdh15), are essential for bundling motility in the sensory hair. Otoferlin (Otof) responds to nerve signal transmission in the auditory inner hair cell. Signals of parallel evolution occur in all three genes in the three groups of echolocators — two groups of bats (Yangochiroptera and Rhinolophoidea) plus the dolphin.
(Yong-Yi Shen, Lu Liang, Gui-Sheng Li, Robert W. Murphy, Ya-Ping Zhang, “Parallel Evolution of Auditory Genes for Echolocation in Bats and Toothed Whales,” PLoS Genetics, Vol. 8(6): e1002788 (June, 2012).)
The paper concludes, “The independent origins of echolocation involve the same genes that have evolved in precisely identical ways.” But this is hardly the only known example of molecular convergent evolution.
In his book The Cell’s Design, chemist and Darwin-skeptic Fazale Rana reviewed the technical literature and documented over 100 reported cases of convergent genetic evolution. Each case shows an example where biological similarity — even at the genetic level — is not the result of inheritance from a common ancestor. So what does this do to the main assumption of tree-building that biological similarity implies inheritance from a common ancestor? With so many exceptions to the rule, you wonder if the rule itself is valid.