Convergent evolution and discordant phylogenetic signals are subjects that have been much discussed here at ENV (for example, here). The fact that there is so much phylogenetic conflict at every level of the tree of life undermines one of the arguments for common descent (that the nested hierarchical distribution of similarities and differences reveals a family-tree like pattern).
One particularly striking case of parallel evolution was presented in a paper in Biology Direct last year. The authors reported on a phylogenetic analysis of genes that facilitate the production of tetrahymanol, a compound that can be synthesized without molecular oxygen (Takishita et al., 2012).
When a phylogeny was constructed for genes encoding the enzyme responsible for synthesis of tetrahymanol (squalene-tetrahymanol cyclase, or STC), it was found that the “sequences from phylogenetically diverged eukaryotes (ciliates, excavates, a fungus, and an animal) formed a monophyletic group within the SHC radiation with 100% ML bootstrap support and a posterior probability of 1.00 in Bayesian analysis.” This renders vertical inheritance of STC implausible since that would require “dozens of parallel losses of the STC genes in many eukaryotic lineages that currently lack this gene.”
The authors attempt to account for the incongruity by positing that “the STC gene has been laterally transferred among phylogenetically diverged eukaryotes through an unknown mechanism.” They thus attribute the shared genes to horizontal gene transfer (with no offered mechanism), a proposition that has become a catch-all to explain away severe conflicts between evolutionary phylogenies.
Indeed, the authors were unable to “find any traces of putative LGT vectors such as transposable elements in the flanking regions of the STC genes in the genomes from the ciliates Tetrahymena and Paramecium,” and they admittedly know of “no distantly-related STC homologue encoded in any mitochondrial genome characterized to date,” meaning that “there is no evidence linking [the] findings to endosymbiotic gene transfer from the mitochondrial (or plastid) ancestor and no other reason to think these organelles are relevant to this case of gene transfer.”
This example is just a particularly striking representation of a much larger problem. As has been noted, “phylogenetic conflict is common, and frequently the norm rather than the exception” (D�valos et al., 2012).
Is it possible that the real reason for such striking and widespread phylogenetic discordance is that evolutionary biologists are looking at biology through the wrong lens? Could the reason that there is so much difficulty in correlating organisms to a tree be that no such tree exists?