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Mol Biol Evol. 2016 Apr;33(4):928-45. doi: 10.1093/molbev/msv331. Epub 2015 Dec 15.

The Time Scale of Recombination Rate Evolution in Great Apes.

Author information

1
Institute for Human Genetics, University of California San Francisco Department of Biological Sciences, Auburn University lss0021@auburn.edu wallj@humgen.ucsf.edu.
2
Arizona Research Laboratories, Division of Biotechnology, University of Arizona Department of Genetics, University of Arizona.
3
Department of Human Genetics, University of Michigan Department of Computational Medicine & Bioinformatics, University of Michigan.
4
School of Biological Sciences, Washington State University Department of Genetics, Stanford University.
5
Arizona Research Laboratories, Division of Biotechnology, University of Arizona Department of Ecology and Evolution, Stony Brook University.
6
Department of Biology, Stanford University Department of Biomedical Informatics, Stanford University.
7
Department of Genetics, Stanford University.
8
Arizona Research Laboratories, Division of Biotechnology, University of Arizona Department of Ecology and Evolutionary Biology, University of Arizona Department of Anthropology, University of Arizona.
9
Institute for Human Genetics, University of California San Francisco Department of Epidemiology & Biostatistics, University of California San Francisco lss0021@auburn.edu wallj@humgen.ucsf.edu.

Abstract

We present three linkage-disequilibrium (LD)-based recombination maps generated using whole-genome sequence data from 10 Nigerian chimpanzees, 13 bonobos, and 15 western gorillas, collected as part of the Great Ape Genome Project (Prado-Martinez J, et al. 2013. Great ape genetic diversity and population history. Nature 499:471-475). We also identified species-specific recombination hotspots in each group using a modified LDhot framework, which greatly improves statistical power to detect hotspots at varying strengths. We show that fewer hotspots are shared among chimpanzee subspecies than within human populations, further narrowing the time scale of complete hotspot turnover. Further, using species-specific PRDM9 sequences to predict potential binding sites (PBS), we show higher predicted PRDM9 binding in recombination hotspots as compared to matched cold spot regions in multiple great ape species, including at least one chimpanzee subspecies. We found that correlations between broad-scale recombination rates decline more rapidly than nucleotide divergence between species. We also compared the skew of recombination rates at centromeres and telomeres between species and show a skew from chromosome means extending as far as 10-15 Mb from chromosome ends. Further, we examined broad-scale recombination rate changes near a translocation in gorillas and found minimal differences as compared to other great ape species perhaps because the coordinates relative to the chromosome ends were unaffected. Finally, on the basis of multiple linear regression analysis, we found that various correlates of recombination rate persist throughout the African great apes including repeats, diversity, and divergence. Our study is the first to analyze within- and between-species genome-wide recombination rate variation in several close relatives.

KEYWORDS:

PRDM9; hotspots; primates; recombination

PMID:
26671457
PMCID:
PMC5870646
DOI:
10.1093/molbev/msv331
[Indexed for MEDLINE]
Free PMC Article

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