Natural selection and phylogenetic analysis

If Darwin were to survey the entirety of the biological sciences today, he would be pleased to observe how central phylogenies and “tree thinking” are to integrative research (1). Biologists of all stripes now realize that phylogenies are not exotic, but fundamental and routine tools for understanding not only history but mechanism, organization, and function of biological networks at all levels, from molecular and cellular to ecological. The last two decades have seen an explosion of sophisticated statistical methods for inferring phylogenetic trees (2), and these methods are remarkably robust to a variety of forces that can conceivably derail phylogenetic analysis and lead researchers to incorrect conclusions about phylogenetic relationships—forces such as vagaries of the molecular clock, changing base compositions of DNA sequences, even evolutionary convergence, whether driven by natural selection or simple biases of mutation. Yet some genes in some groups of species exhibit evolutionary convergence on such a vast scale that even the best phylogenetic methods fail and erroneous relationships result. The report by Castoe et al. in this issue of PNAS (3) documents an example of rampant convergence in the mitochondrial DNA of snakes, and it raises intriguing questions as to how widespread such convergence is in molecular data. Ways in which natural selection can influence phylogenetic reconstruction. Colors of branches correspond to different species from which sequences are sampled, except in E, wherein colors indicate different rates of evolution at a site. (A) A gene tree of five species whose evolution is largely neutral or dominated by stabilizing selection. (B) Violations of the molecular clock caused by directional selection along lineages. (C and D) Contrast between shared polymorphisms commonly observed between closely related species at neutral loci (C) versus reciprocal monophyly of alleles between closely related species driven by selective sweeps (D). (E) Heterotachy, the …