Demographic Histories and Patterns of Linkage Disequilibrium in Chinese and Indian Rhesus Macaques

Hernández, Ryan D.; Hubisz, Melissa J.; Wheeler, David A.; Smith, David Glenn; Ferguson, Betsy; Rogers, Jeffrey; Nazareth, Lynne V.; Indap, Amit; Bourquin, Traci; Mcpherson, John Douglas; Muzny, Donna M.; Gibbs, Richard A.; Nielsen, Rasmus; Bustamante, Carlos D.

doi:10.1126/science.1140462

Cited by 159 publications

(209 citation statements)

References 15 publications

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“…Therefore, unsorted ancestral polymorphisms could not entirely explain the high proportion of inconsistent regions observed between the CE macaque and CR macaque. Furthermore, by combining previous single nucleotide polymorphism (SNP) data from IR and CR macaque populations with data from our own sequenced CR and CE macaque individuals 8 , we noted that our CE macaque individual clustered within the CR macaque population (Supplementary Section 4). This supports the occurrence of strong gene flow from the CR to the CE macaque genome.…”

Section: E T T E R Smentioning

confidence: 75%

Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques

et al. 2011

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Section: E T T E R Smentioning

confidence: 75%

Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques

et al. 2011

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“…Indeed, HRI is thought to play a fundamental role in shaping the evolution of recombination rates in small effective populations, such as those found in these three primate species (Stone and Verrelli 2006;Hernandez et al 2007), as modifier alleles that increase recombination locally can be selected if they reduce HRI (Felsenstein 1974;Felsenstein and Yokoyama 1976;Otto and Lenormand 2002;Barton and Otto 2005). Intuitively, this phenomenon occurs because a modifier allele produces, and so resides on, haplotypes with greater fitness (e.g., with fewer deleterious or more advantageous mutations) and as a result tends to hitchhike to fixation.…”

Section: Discussionmentioning

confidence: 99%

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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“…Investigations by Andrade et al (2004), Doxiadis et al (2003Doxiadis et al ( , 2006, Ferguson et al (2007), Hernandez et al (2007), Smith (1998, 2004), Kanthaswamy et al (2006), Malhi et al (2007), Morin et al (1997), Penedo et al (2005), Satkoski et al (2007), and Viray et al (2001) have all characterized the genetic composition of rhesus macaque populations in the wild and in captivity. Most of these studies have reported discrete genetic differences between Indian and Chinese rhesus macaques and much greater genetic heterogeneity and substructuring in the latter than in the former.…”

Section: Introductionmentioning

confidence: 99%

Hybridization and Stratification of Nuclear Genetic Variation in Macaca mulatta and M. fascicularis

et al. 2008

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Genotypes for 13 short tandem repeats (STRs) were used to assess the genetic diversity within and differentiation among populations of rhesus macaques (Macaca mulatta) from mainland Asia and long-tailed macaques (M. fascicularis) from mainland and insular Southeast Asia. These animals were either recently captured in the wild or derived from wild-caught founders maintained in captivity for biomedical research.A large number of alleles is shared between the two macaque species but a significant genetic division between them persists. This distinction is more clear-cut among populations that are not, or are unlikely to have recently been, geographically contiguous. Our results suggest there has been significant interspecies nuclear gene flow between rhesus macaques and long-tailed macaques on the mainland. Comparisons of mainland and island populations of long-tailed macaques reflect marked genetic subdivisions due to barriers to migration. Geographic isolation has restricted gene flow, allowing island populations to become subdivided and genetically differentiated. Indonesian long-tailed macaques show evidence of long-term separation and genetic isolation from the mainland populations, while long-tailed macaques from the Philippines and Mauritius both display evidence of founder effects and subsequent isolation, with the impact from genetic drift being more profound in the latter.

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Demographic Histories and Patterns of Linkage Disequilibrium in Chinese and Indian Rhesus Macaques

Cited by 159 publications

References 15 publications

Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques

Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques

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

Hybridization and Stratification of Nuclear Genetic Variation in Macaca mulatta and M. fascicularis

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