Comparison of Fine-Scale Recombination Rates in Humans and Chimpanzees

Winckler, Wendy; Myers, Simon; Richter, Daniel J.; Onofrio, Robert C.; McDonald, Gavin J.; Bontrop, Ronald E.; McVean, Gil; Gabriel, Stacey; Reich, David; Donnelly, Peter; Altshuler, David

doi:10.1126/science.1105322

Cited by 339 publications

(351 citation statements)

References 22 publications

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“…But the assumption may not be as applicable to the fine scale. Indeed, analyses of LD data in humans and chimpanzees indicate that although rates >50 kb are weakly correlated , hotspot locations differ markedly between the two species (Wall et al 2003;Ptak et al 2004Ptak et al , 2005Winckler et al 2005). If HRI exerts its effects over very short distances, and fine-scale rates have changed markedly between species, some of the signal could be masked as a result.…”

Section: Discussionmentioning

confidence: 99%

“…At a finer scale, recombination rates may have changed substantially: Although fine-scale rates may be partially conserved Ptak et al 2005), hotspot locations seem to differ markedly between human and chimpanzee (Wall et al 2003;Ptak et al 2004Ptak et al , 2005Winckler et al 2005). Rapid turnover of hotspots could lead human fine-scale rates to be poor proxies for the fine-scale recombination environment for much of the phylogeny.…”

Section: Relevance Of Human Recombination Ratesmentioning

confidence: 99%

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No effect of recombination on the efficacy of natural selection in primates

Bullaughey¹,

Przeworski²,

Coop³

2008

Genome Res.

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Population genetic theory suggests that natural selection should be less effective in regions of low recombination, potentially leading to differences in rates of adaptation among recombination environments. To date, this prediction has mainly been tested in Drosophila, with somewhat conflicting results. We investigated the association between human recombination rates and adaptation in primates, by considering rates of protein evolution (measured by d N /d S ) between human, chimpanzee, and rhesus macaque. We found no correlation between either broad-or fine-scale rates of recombination and rates of protein evolution, once GC content is taken into account. Moreover, genes in regions of very low recombination, which are expected to show the most pronounced reduction in the efficacy of selection, do not evolve at a different rate than other genes. Thus, there is no evidence for differences in the efficacy of selection across recombinational environments. An interesting implication is that indirect selection for recombination modifiers has probably been a weak force in primate evolution.

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Section: Discussionmentioning

confidence: 99%

Section: Relevance Of Human Recombination Ratesmentioning

confidence: 99%

No effect of recombination on the efficacy of natural selection in primates

Bullaughey¹,

Przeworski²,

Coop³

2008

Genome Res.

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show abstract

“…A persistently puzzling feature of real SNP clusters is their evolutionary transience Winckler et al 2005). If a region of DNA has a structure such that it attracts a higher mutation rate, why should this change over relatively short tracts of time?…”

Section: Discussionmentioning

confidence: 99%

“…This clustering is widely interpreted as reflecting mutation hotspots (Rogozin & Pavlov 2003), though the forces responsible remain poorly understood. Particularly puzzling is the observation that clusters appear to be short-lived, with many or most of those present in humans not being present in chimpanzees Winckler et al 2005;Jeffreys & Neumann 2009). Nonetheless, the distribution of SNPs along a chromosome is often used to infer the action of natural selection (Voight et al 2006;Wang et al 2006;Oleksyk et al 2008).…”

Section: Introductionmentioning

confidence: 99%

Even small SNP clusters are non-randomly distributed: is this evidence of mutational non-independence?

Amos

2010

Proc. R. Soc. B.

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Single nucleotide polymorphisms (SNPs) are distributed highly non-randomly in the human genome through a variety of processes from ascertainment biases (i.e. the preferential development of SNPs around interesting genes) to the action of mutation hotspots and natural selection. However, with more systematic SNP development, one might expect an increasing proportion of SNPs to be distributed more or less randomly. Here, I test this null hypothesis using stochastic simulations and compare this output with that of an alternative hypothesis that mutations are more likely to occur near existing SNPs, a possibility suggested both by molecular studies of meiotic mismatch repair in yeast and by data showing that SNPs cluster around heterozygous deletions. A purely Poisson process generates SNP clusters that differ from equivalent data from human chromosome 1 in both the frequency of different-sized clusters and the SNP density within each cluster, even for small clusters of just four or five SNPs, while clusters on the X chromosome differ from those on the autosomes. In contrast, modest levels of mutational non-independence generate a reasonable fit to the real data for both cluster frequency and density, and also exhibit the evolutionary transience noted for 'mutation hotspots'. Mutational nonindependence therefore provides an interesting new hypothesis that appears capable of explaining the distribution of SNPs in the human genome.

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“…Attempts to elucidate the determinants of recombination have identified numerous factors of influence, many of which appear to be conserved across eukaryotes (Lichten and Goldman, 1995;Roeder, 1997;Hassold et al, 2000;Keeney, 2001;Petes, 2001;Page and Hawley, 2003). New hypotheses have emerged, for example, that variation in epigenetic features could explain the variation in the rates of recombination between closely related species (Myers et al, , 2008Ptak et al, 2005;Winckler et al, 2005). The continued study of recombination between closely related species has the potential to illuminate more decisive determinants and how they change over time.…”

Section: Determinants and Correlatesmentioning

confidence: 99%

Recombination rate variation in closely related species

2011

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Despite their importance to successful meiosis and various evolutionary processes, meiotic recombination rates sometimes vary within species or between closely related species. For example, humans and chimpanzees share virtually no recombination hotspot locations in the surveyed portion of the genomes. However, conservation of recombination rates between closely related species has also been documented, raising an apparent contradiction. Here, we evaluate how and why conflicting patterns of recombination rate conservation and divergence may be observed, with particular emphasis on features that affect recombination, and the scale and method with which recombination is surveyed. Additionally, we review recent studies identifying features influencing fine-scale and broad-scale recombination patterns and informing how quickly recombination rates evolve, how changes in recombination impact selection and evolution in natural populations, and more broadly, which forces influence genome evolution.

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Comparison of Fine-Scale Recombination Rates in Humans and Chimpanzees

Cited by 339 publications

References 22 publications

No effect of recombination on the efficacy of natural selection in primates

No effect of recombination on the efficacy of natural selection in primates

Even small SNP clusters are non-randomly distributed: is this evidence of mutational non-independence?

Recombination rate variation in closely related species

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