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The Time Scale of Recombination Rate Evolution in Great Apes.

Publication ,  Journal Article
Stevison, LS; Woerner, AE; Kidd, JM; Kelley, JL; Veeramah, KR; McManus, KF; Great Ape Genome Project, ; Bustamante, CD; Hammer, MF; Wall, JD
Published in: Molecular biology and evolution
April 2016

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.

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Published In

Molecular biology and evolution

DOI

EISSN

1537-1719

ISSN

0737-4038

Publication Date

April 2016

Volume

33

Issue

4

Start / End Page

928 / 945

Related Subject Headings

  • Species Specificity
  • Recombination, Genetic
  • Papio
  • Pan troglodytes
  • Linkage Disequilibrium
  • Humans
  • Hominidae
  • Gorilla gorilla
  • Genetic Variation
  • Evolutionary Biology
 

Citation

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Stevison, L. S., Woerner, A. E., Kidd, J. M., Kelley, J. L., Veeramah, K. R., McManus, K. F., … Wall, J. D. (2016). The Time Scale of Recombination Rate Evolution in Great Apes. Molecular Biology and Evolution, 33(4), 928–945. https://doi.org/10.1093/molbev/msv331
Stevison, Laurie S., August E. Woerner, Jeffrey M. Kidd, Joanna L. Kelley, Krishna R. Veeramah, Kimberly F. McManus, Kimberly F. Great Ape Genome Project, Carlos D. Bustamante, Michael F. Hammer, and Jeffrey D. Wall. “The Time Scale of Recombination Rate Evolution in Great Apes.Molecular Biology and Evolution 33, no. 4 (April 2016): 928–45. https://doi.org/10.1093/molbev/msv331.
Stevison LS, Woerner AE, Kidd JM, Kelley JL, Veeramah KR, McManus KF, et al. The Time Scale of Recombination Rate Evolution in Great Apes. Molecular biology and evolution. 2016 Apr;33(4):928–45.
Stevison, Laurie S., et al. “The Time Scale of Recombination Rate Evolution in Great Apes.Molecular Biology and Evolution, vol. 33, no. 4, Apr. 2016, pp. 928–45. Epmc, doi:10.1093/molbev/msv331.
Stevison LS, Woerner AE, Kidd JM, Kelley JL, Veeramah KR, McManus KF, Great Ape Genome Project, Bustamante CD, Hammer MF, Wall JD. The Time Scale of Recombination Rate Evolution in Great Apes. Molecular biology and evolution. 2016 Apr;33(4):928–945.
Journal cover image

Published In

Molecular biology and evolution

DOI

EISSN

1537-1719

ISSN

0737-4038

Publication Date

April 2016

Volume

33

Issue

4

Start / End Page

928 / 945

Related Subject Headings

  • Species Specificity
  • Recombination, Genetic
  • Papio
  • Pan troglodytes
  • Linkage Disequilibrium
  • Humans
  • Hominidae
  • Gorilla gorilla
  • Genetic Variation
  • Evolutionary Biology