Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster

Begun, David J.; Aquadro, Charles F.

doi:10.1038/356519a0

Cited by 928 publications

(792 citation statements)

References 22 publications

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“…While this is so, it may not be possible to move far enough away from potential targets of selection to completely eliminate any bias (as discussed above). Moreover, it is essential to omit regions with lowered recombination rates, where the impact of linked selection will be strongest (Begun and Aquadro 1992). As a corollary to this, demographic estimation performed from regions of the genome at differing genetic distances from regions experiencing selection should recover different parameter estimates (Gazave et al 2014).…”

Section: Discussionmentioning

confidence: 99%

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

2016

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The availability of large-scale population genomic sequence data has resulted in an explosion in efforts to infer the demographic histories of natural populations across a broad range of organisms. As demographic events alter coalescent genealogies, they leave detectable signatures in patterns of genetic variation within and between populations. Accordingly, a variety of approaches have been designed to leverage population genetic data to uncover the footprints of demographic change in the genome. The vast majority of these methods make the simplifying assumption that the measures of genetic variation used as their input are unaffected by natural selection. However, natural selection can dramatically skew patterns of variation not only at selected sites, but at linked, neutral loci as well. Here we assess the impact of recent positive selection on demographic inference by characterizing the performance of three popular methods through extensive simulation of data sets with varying numbers of linked selective sweeps. In particular, we examined three different demographic models relevant to a number of species, finding that positive selection can bias parameter estimates of each of these models-often severely. We find that selection can lead to incorrect inferences of population size changes when none have occurred. Moreover, we show that linked selection can lead to incorrect demographic model selection, when multiple demographic scenarios are compared. We argue that natural populations may experience the amount of recent positive selection required to skew inferences. These results suggest that demographic studies conducted in many species to date may have exaggerated the extent and frequency of population size changes.KEYWORDS population genetics; positive selection; demographic inference T HE widespread availability of population genomic data has spurred a new generation of studies aimed at understanding the histories of natural populations from a host of model and nonmodel organisms alike. In particular, genomescale variation data allows for inference of demographic factors such as population size changes, the timing and ordering of population splits, migration rates between populations, and the founding of admixed populations (Pool et al. 2010;Pickrell and Pritchard 2012;Sousa and Hey 2013). Such efforts can refine our picture of demographic events inferred from the archaeological record (e.g., Fagundes et al. 2007;Goebel et al. 2008), or reveal such events in species where no archaeological data are available, and can aid conservation efforts by complementing census data (e.g., Hájková et al. 2007;Garrick et al. 2015).Population genomic data sets are well suited for this task simply because demographic changes leave their mark on patterns of genetic variation. Recent population growth, for example, will result in an excess of rare variation compared to equilibrium expectations (Fu 1997), while population contraction will result in an excess of intermediate frequency alleles (Maruyama and Fuerst 198...

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Section: Discussionmentioning

confidence: 99%

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

2016

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“…This relationship was initially attributed to Hill-Robertson effects of increased efficacy of selection in areas of increased recombination (Comeron et al 1999;Hey and Kliman 2002;Kliman and Hey 1993). Because in areas of reduced recombination, fixation probabilities of novel mutations will be affected by the fixation probabilities of mutations at linked sites, the ability of natural selection to discriminate among variants will be compromised with increased linkage among sites (Aquadro 1997;Begun and Aquadro 1992;Hill and Robertson 1966).…”

Section: Codon Usage and Recombination Ratementioning

confidence: 99%

“…This relationship was initially attributed to Hill-Robertson effects; if codon bias in Drosophila were under selection for translational efficiency, then the efficacy of this selection should increase with increased recombination, leading to increased codon bias in regions of high recombination. This is because regions of reduced recombination are generally subject to weaker purifying selection and less effective positive selection due to linkage among sites (Aquadro 1997;Begun and Aquadro 1992;Hill and Robertson 1966). However, given that 21 of 22 optimal codons in Drosophila end in G or C, the positive correlation between codon bias and recombination rate in Drosophila can also be attributed to a recombination-associated bias in patterns of neutral point substitution towards increased GC (Marais et al , 2003Singh et al 2004).…”

Section: Introductionmentioning

confidence: 99%

Codon Bias and Noncoding GC Content Correlate Negatively with Recombination Rate on the Drosophila X Chromosome

2005

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Abstract. The patterns and processes of molecular evolution may differ between the X chromosome and the autosomes in Drosophila melanogaster. This may in part be due to differences in the effective population size between the two chromosome sets and in part to the hemizygosity of the X chromosome in Drosophila males. These and other factors may lead to differences both in the gene complements of the X and the autosomes and in the properties of the genes residing on those chromosomes. Here we show that codon bias and recombination rate are correlated strongly and negatively on the X chromosome, and that this correlation cannot be explained by indirect relationships with other known determinants of codon bias. This is in dramatic contrast to the weak positive correlation found on the autosomes. We explored possible explanations for these patterns, which required a comprehensive analysis of the relationships among multiple genetic properties such as protein length and expression level. This analysis highlights conserved features of coding sequence evolution on the X and the autosomes and illuminates interesting differences between these two chromosome sets.

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“…These results have been confirmed and extended by Kaplan et al (1988), and Wiehe & Stephan (1993). Reduced heterozygosity in regions of low recombination in Drosophila, found by Begun & Aquadro (1991) and others, has been attributed to the effects of hitch-hiking, although Charlesworth et al (1993) have proposed an alternative explanation.…”

Section: Introductionmentioning

confidence: 99%

Genetic hitch-hiking in a subdivided population

1998

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SummaryThe problem of genetic hitch-hiking in a geographically subdivided population is analysed under the assumption that migration rates among populations are relatively small compared with the selection coefficient for a newly arising advantageous allele. The approximate method used in the paper is valid when the number of emigrants per generation (Nm) is less than one. The approximate analysis shows that hitch-hiking can result in substantial differences among populations in the frequencies of neutral alleles closely linked to the advantageous allele. Thus, in cases for which genetic hitch-hiking is thought to be responsible for low levels of genetic variability in regions of the genome with restricted crossing over, it might be possible to find confirmatory evidence for that hypothesis by finding unusual patterns of geographic differentiation in the same regions of the genome.

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Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster

Cited by 928 publications

References 22 publications

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

Codon Bias and Noncoding GC Content Correlate Negatively with Recombination Rate on the Drosophila X Chromosome

Genetic hitch-hiking in a subdivided population

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