Academic journal article Genetics

Soft Selective Sweeps in Complex Demographic Scenarios

Academic journal article Genetics

Soft Selective Sweeps in Complex Demographic Scenarios

Article excerpt

(ProQuest: ... denotes formulae omitted.)

ADAPTATION can proceed from standing genetic varia- tion or mutations that are not initially present in the population. When adaptation requires de novo mutations, the waiting time until adaptation occurs depends on the product of the mutation rate toward adaptive alleles and the population size. In large populations, or when the muta- tion rate toward adaptive alleles is high, adaptation can be fast, whereas in small populations the speed of adaptation will often be limited by the availability of adaptive mutations.

Whether adaption is mutation limited or not has impor- tant implications for the dynamics of adaptive alleles. In a mutation-limited scenario, only a single adaptive mutation typically sweeps through the population and all individuals in a population sample that carry the adaptive allele coalesce into a single ancestor with the adaptive mutation (Figure 1A). This process is referred to as a " hard" selective sweep (Hermisson and Pennings 2005). Hard selective sweeps leave characteristic signatures in population genomic data, such as a reduction in genetic diversity around the adaptive site (Maynard Smith and Haigh 1974; Kaplan et al. 1989; Kim and Stephan 2002) and the presence of a single, long haplo- type (Hudson et al. 1994; Sabeti et al. 2002; Voight et al. 2006). In non-mutation-limited scenarios, by contrast, several adaptive mutations of independent origin can sweep through the population at the same time, producing so-called "soft" selective sweeps (Pennings and Hermisson 2006a). In a soft sweep, individuals that carry the adaptive allele collapse into distinct clusters in the genealogy and several haplotypes can be frequent in the population (Figure 1A). As a result, soft sweeps leave more subtle signatures in population genomic data than hard sweeps and are thus more difficult to detect. For example, diversity is not necessarily reduced in the vicinity of the adaptive locus in a soft sweep because a larger proportion of the ancestral variation present prior to the onset of selection is preserved (Innan and Kim 2004; Przeworski et al. 2005; Pennings and Hermisson 2006b; Burke 2012; Peter et al. 2012).

There is mounting evidence that adaptation is not mutation limited in many species, even when it requires a specific nucleotide mutation in the genome (Messer and Petrov 2013). Recent case studies have revealed many examples where, at the same locus, several adaptive mutations of independent mutational origin swept through the population at the same time, producing soft selective sweeps. For instance, soft sweeps have been observed during the evolution of drug resistance in HIV (Fischer et al. 2010; Messer and Neher 2012; Pennings et al. 2014) and malaria (Nair et al. 2007), pesticide and viral resistance in fruit flies (Catania et al. 2004; Aminetzach et al. 2005; Chung et al. 2007; Karasov et al. 2010; Schmidt et al. 2010), warfarin resistance in rats (Pelz et al. 2005), and color patterns in beach mice (Hoekstra et al. 2006; Domingues et al. 2012). Even in the global human population, adaptation has produced soft selective sweeps, as evidenced by the parallel evolution of lactase persistence in Eurasia and Africa through recurrent mutations in the lac- tase enhancer (Bersaglieri et al. 2004; Tishkoff et al. 2007; Enattah et al. 2008; Jones et al. 2013) and the mutations in the gene G6PD that evolved independently in response to malaria (Louicharoen et al. 2009). Some of these sweeps arose from standing genetic variation while others involved recur- rent de novo mutation. For the remainder of our study, we focus on the latter scenario of adaptation arising from de novo mutation.

The population genetics of adaptation by soft selective sweeps was first investigated in a series of articles by Hermisson and Pennings (Hermisson and Pennings 2005; Pennings and Hermisson 2006a,b). They found that in a hap- loid population of constant size the key evolutionary parameter that determines whether adaptation from de novo mutations is more likely to produce hard or soft sweeps is the population- scale mutation rate Q =2NeUA,whereNe isthevarianceef- fective population size in a Wright-Fisher model and UA is the rate at which the adaptive allele arises per individual per gen- eration. …

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