Academic journal article Genetics

Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism across the Genomes of Three Related Populus Species

Academic journal article Genetics

Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism across the Genomes of Three Related Populus Species

Article excerpt

Amajor goal in evolutionary genetics is to understandhow genomic variation is established and maintained within and between species (Nordborg et al. 2005; Begun et al. 2007) and how different evolutionary forces have substantial impacts in shaping genetic variation throughout the genome (Hellmann et al. 2005). Under the neutral theory, genetic variation is the manifestation of the balance between mutation and genetic drift(Kimura 1983). Demographic fluctuations, such as population expansion and/or bottlenecks, can cause patterns of genome-wide variation deviating from the standard neutral model in various ways (Li and Durbin 2011). It is now clear, however, that natural selection-via positive selection favoring beneficial mutations (genetic hitchhiking) and/or purifying selection against deleterious mutations (background selection)-plays an important role in molding the landscape of nucleotide polymorphism in many species (Begun and Aquadro 1992; Begun et al. 2007; Cutter and Choi 2010; Mackay et al. 2012).

If natural selection is pervasive across the genome, patterns of genetic variation at linked neutral sites can be influenced by selection in a number of ways. First, positive correlations between levels of neutral polymorphism and recombination rates are expected since linked selection is expected to remove more neutral polymorphism in low-recombination regions compared to high-recombination regions and such a pattern is unlikely to be generated by demographic processes alone (Begun and Aquadro 1992; Kulathinal et al. 2008; McGaugh et al. 2012; Campos et al. 2014; Charlesworth and Campos 2014). Second, in addition to influencing the level of neutral variability, recombination rate can affect the efficacy of selection through the process known as Hill-Robertson interference (HBI) (Hill and Robertson 1966). If HRI is operating, genetic linkage effects in regions of low recombination will reduce the local effective population size (Ne) and accordingly reduce the efficacy of selection (Nes), since the effects of selection are determined by the product of Ne and the selection coefficient on a mutation (s) (Kimura 1983). We would therefore expect both a reduced fixation of favorable mutations and an increased frequency of deleterious mutations in these regions (Hill and Robertson 1966; Haddrill et al. 2007; Campos et al. 2014). Third, signatures and magnitudes of linked selection are sensitive to the density of important functional sites (e.g., gene density) within specific genomic regions (Flowers et al. 2012). In accordance with the view that genes represent the most likely targets of natural selection, regions with a high density of genes are expected to have undergone stronger effects of linked selection and exhibit lower levels of neutral polymorphism (Nordborg et al. 2005; Flowers et al. 2012). Therefore, a positive or negative covariation of recombination rate and gene density would act to either obscure or strengthen the signatures of linked selection across the genome (Cutter and Payseur 2003; Cutter and Choi 2010; Flowers et al. 2012). Finally, a distinctive signature of recurrent selective sweeps is the local reduction of linked neutral polymorphism in regions experiencing frequent adaptive substitutions (Andolfatto 2007). A substantial number of adaptive substitutions are likely composed of amino acid substitutions, and a negative correlation between neutral polymorphism and nonsynonymous divergence can thus be particularly informative of the prevalence of selective sweeps (Macpherson et al. 2007). With the advance of nextgeneration sequencing technology, sufficient genome-wide data among multiple related species are becoming available (Luikart et al. 2003; Ellegren 2014). Phylogenetic comparative approaches will thus place us in a stronger position to understand how various evolutionary forces have interacted to shape the heterogeneous patterns of nucleotide polymorphism across the genome (Hufford et al. 2012; Cutter and Payseur 2013; Lawrie and Petrov 2014). …

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