A fine-scale chimpanzee genetic map from population sequencing

Adam Auton, Adi Fledel-Alon, Susanne Pfeifer, Oliver Venn, Laure Ségurel, Teresa Street, Ellen M. Leffler, Rory Bowden, Ivy Aneas, John Broxholme, Peter Humburg, Zamin Iqbal, Gerton Lunter, Julian Maller, Ryan D. Hernandez, Cord Melton, Aarti Venkat, Marcelo A. Nobrega, Ronald Bontrop, Simon MyersPeter Donnelly, Molly Przeworski, Gil McVean

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Abstract

To study the evolution of recombination rates in apes, we developed methodology to construct a fine-scale genetic map from high-throughput sequence data from 10 Western chimpanzees, Pan troglodytes verus. Compared to the human genetic map, broad-scale recombination rates tend to be conserved, but with exceptions, particularly in regions of chromosomal rearrangements and around the site of ancestral fusion in human chromosome 2. At fine scales, chimpanzee recombination is dominated by hotspots, which show no overlap with those of humans even though rates are similarly elevated around CpG islands and decreased within genes. The hotspot-specifying protein PRDM9 shows extensive variation among Western chimpanzees, and there is little evidence that any sequence motifs are enriched in hotspots. The contrasting locations of hotspots provide a natural experiment, which demonstrates the impact of recombination on base composition.

Original languageEnglish (US)
Pages (from-to)193-198
Number of pages6
JournalScience
Volume336
Issue number6078
DOIs
StatePublished - Apr 13 2012

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Auton, A., Fledel-Alon, A., Pfeifer, S., Venn, O., Ségurel, L., Street, T., Leffler, E. M., Bowden, R., Aneas, I., Broxholme, J., Humburg, P., Iqbal, Z., Lunter, G., Maller, J., Hernandez, R. D., Melton, C., Venkat, A., Nobrega, M. A., Bontrop, R., ... McVean, G. (2012). A fine-scale chimpanzee genetic map from population sequencing. Science, 336(6078), 193-198. https://doi.org/10.1126/science.1216872