Selection Signatures from Recent Single

  • Published 2013

Abstract

While the ubiquity of purifying (or negative) selection (the removal of deleterious alleles) at the molecular level is well established, the frequency of positive (or adaptive or Darwinian) selection remains unclear. Because of this, the development of methods to detect the latter is a major growth industry in evolutionary genetics. There is a massive population-genetics literature on this subject, and a partial (but not exhaustive) list of recent reviews includes Kreitman (2000), Nielsen (2001), Ford (2002), Bamshad and Wooding (2003), Schlötterer (2003), Guinand et al. (2004), Storz (2005), Wright and Gaut (2005), Nielsen (2005), Sabeti et al. (2006), Biswas and Akey (2006), Thornton et al. (2007), Pavlidis et al. (2008), Akey (2009), and Stephan (2010a). As detailed in Chapter 8, a single recent event of positive selection can leave a transient signal in the pattern of linked neutral variation, and the detection of such events is the subject of this chapter. Since most approaches for detecting recent/ongoing selection use the segregating variation in a sample from a contemporaneous population, we loosely refer to these as polymorphism-based tests. Because such signals are transient, these methods can only detect an ongoing, or very recent, single event over a very short time window. Hence, they work only over ecological time scales, detecting single events which occured over less thanNe generations ago. In contrast, a history of positive selection on a gene over evolutionary time can leave a cumulative signal in the pattern of substitutions. Divergence-based tests to detect these patterns, which require data on substitutions between species (or very distantlyrelated populations), are developed in Chapter 10 (which also covers tests that jointly use polymorphism and divergence data). These different approaches are complementary, as an adaptive substitution could leave a strong (but fleeting) signature over an ecological time scale, but essentially no signal in that gene over an evolutionary time scale. Likewise, the vast majority of adaptive events that have shaped a gene occurred in its distant past and hence leave no currently-detectable polymorphism pattern. Since the search for sites under selection can be seductive, it is important to stress that the most important point about the methods developed in this chapter are their limitations. They potentially can be useful in detecting some events that involve the signatures from a single selective event at a single site. In principle this allows for a crude localization of the site, and allows the prospect of studying individual (as opposed to cumulative) selective events. As discussed in Chapter 8, one source of these limitations is the nature of the signal left by the sweep itself. First it is very fleeting, typically persisting for between 0.1Ne to Ne generations, depending on the features being examined. Second, only a fraction of such events, even if ongoing or very recent, can be detected. The effect of a weak selection event may be too small to leave a meaningful signal against a noisy molecular background. Finally, even

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@inproceedings{2013SelectionSF, title={Selection Signatures from Recent Single}, author={}, year={2013} }