D N / d S does not show positive selection drives separation of polar‐tropical SAR11 populations

Abstract

Mol Syst Biol. 8: 625 Large‐scale sequencing of environmental microorganisms (including genomes, metagenomes, and metatranscriptomes) now allows researchers to apply sequence‐based evolutionary genetics approaches to microbial ecology questions, including studying how microbes adapt to a diversity of natural environments. There is, however, a danger for misapplication and misinterpretation if the caveats and limitations of these evolutionary methods are not fully appreciated. Here, we highlight an example of such problems in an evolutionary analysis of potential positive selection within strains of SAR11 marine bacteria (Brown et al , 2012). We feel that these issues deserve wider recognition, particularly as evolutionary approaches become more widespread among environmental microbiologists. In the vast majority of genes, the ratio (ω) of non‐synonymous substitutions per non‐synonymous site ( d N ) to synonymous substitutions per synonymous site ( d S ) is 1, then this may be indicative of positive selection favoring amino‐acid replacements (Hughes and Nei, 1988, Hughes, 1999). If ω is not statistically different from 1, then there is evidence for neither purifying nor positive selection. Positive selection is not the only factor that can cause ω to be >1; since ω is a ratio, an unusually high ω value may indicate either an unusually high d N or an unusually low d S . For example, purifying selection on synonymous mutations can lead to a low d S and thus high ω (Parmley and Hurst, 2007). Approaches for calculating d S and d N can be classified into two categories, based on whether the underlying nucleotide evolutionary model takes into account the base/codon frequency bias (Supplementary Table S1; Zhang et al , 2006). For instance, the Yang and Nielsen method (YN00) considers the base/codon …