RT Journal Article
SR Electronic
T1 The Time-Scale of Recombination Rate Evolution in Great Apes
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 013755
DO 10.1101/013755
A1 Laurie S Stevison
A1 August E Woerner
A1 Jeffrey M Kidd
A1 Joanna L Kelley
A1 Krishna R Veeramah
A1 Kimberly F. McManus
A1 Great Ape Genome Project
A1 Carlos D Bustamante
A1 Michael F Hammer
A1 Jeffrey D Wall
YR 2015
UL http://biorxiv.org/content/early/2015/01/13/013755.abstract
AB We present three linkage-disequilibrium (LD)-based recombination maps generated using whole-genome sequencing data of 10 Nigerian chimpanzees, 13 bonobos, and 15 western gorillas, collected as part of the Great Ape Genome Project (Prado-Martinez et al. 2013). Using species-specific PRDM9 sequences to predict potential binding sites, we identified an important role for PRDM9 in predicting recombination rate variation broadly across great apes. Our results are contrary to previous research that PRDM9 is not associated with recombination in western chimpanzees (Auton et al. 2012). Additionally, we show that fewer hotspots are shared among chimpanzee subspecies than within human populations, further narrowing the time-scale of complete hotspot turnover. We quantified the variation in the biased distribution of recombination rates towards recombination hotspots across great apes. 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, based on multiple linear regression analysis, we found that various correlates of recombination rate persist throughout primates including repeats, diversity, divergence and local effective population size (Ne). Our study is the first to analyze within-and between-species genome-wide recombination rate variation in several close relatives.