Detecting selection from microbial sequence data.

<p>The phylogeny shows the evolutionary history of 20 sequences sampled evenly from four divergent populations. d_N/d_S methods test for selection by comparing the rates of non-synonymous and synonymous substitution occurring between divergent lineages (i.e., only substitutions that have occurred on the black branches) with those expected under neutrality. In contrast, the McDonald-Kreitman test for selection compares the ratio of non-synonymous and synonymous polymorphisms that are present within populations (due to substitutions occurring on red branches) with the ratio of non-synonymous and synonymous fixed differences that are present between populations (due to substitutions occurring on black branches). The phylogeny can also be used to detect selection by identifying parallel evolution, whereby recurrent mutations occur at a site or across a gene during the evolutionary history of a sample (for example, substitution X on the phylogeny).