Detecting Natural Selection at the Molecular Level: A Reexamination of Some “Classic” Examples of Adaptive Evolution

摘要

An important criterion used to detect adaptive evolution in DNA sequence data is ω i > 1, where ω i is the ratio of nonsynonymous to synonymous substitution rates in lineage i. However, the evaluation of multiple ω i within a phylogenetic tree can easily inflate the statistical type I error rate. We developed two rigorous methods of analysis that avoid this and other potential pitfalls. We applied these methods to four published examples of adaptive evolution. One case was strongly supported by our reanalysis (abalone sperm lysin), and one was weakly supported (baboon α-globin), but two examples (primate lysozyme and Antarctic fish β-globin) did not show significant evidence of adaptive evolution. Our first method is a “bottom-up” hierarchical maximum likelihood approach, which (1) tests for significant heterogeneity in ω across the phylogeny, (2) locates its source using a sequence of planned comparisons, and (3) tests homogeneous groups of ω for ω > 1, using a modified level of significance that incorporates the pretesting. The second method is a “top-down” log-linear analysis based on estimates of nonsynonymous and synonymous substitutions in pairs of lineages. The log-linear test is applied to pairs of lineages joined at progressively deeper nodes. For each pair, the analysis simultaneously tests for adaptive evolution (ω > 1), a shift in natural selection (ω1 ≠ω2), and unequal evolution rate (the relative rate test). In both tests, we emphasized that the criterion ω1 ≠ ω2 is an important additional indicator of a phylogenetic shift in the balance between natural selection and genetic drift between two related lineages.