title: A fine-scale chimpanzee genetic map from population sequencing.
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.
authors.affiliation: Wellcome Trust Centre for Human Genetics, Oxford , UK.
authors.forename: Adam
authors.initials: A
authors.lastname: Auton
authors.forename: Adi
authors.initials: A
authors.lastname: Fledel-Alon
authors.forename: Susanne
authors.initials: S
authors.lastname: Pfeifer
authors.forename: Oliver
authors.initials: O
authors.lastname: Venn
authors.forename: Laure
authors.initials: L
authors.lastname: Ségurel
authors.forename: Teresa
authors.initials: T
authors.lastname: Street
authors.forename: Ellen M
authors.initials: EM
authors.lastname: Leffler
authors.forename: Rory
authors.initials: R
authors.lastname: Bowden
authors.forename: Ivy
authors.initials: I
authors.lastname: Aneas
authors.forename: John
authors.initials: J
authors.lastname: Broxholme
authors.forename: Peter
authors.initials: P
authors.lastname: Humburg
authors.forename: Zamin
authors.initials: Z
authors.lastname: Iqbal
authors.forename: Gerton
authors.initials: G
authors.lastname: Lunter
authors.forename: Julian
authors.initials: J
authors.lastname: Maller
authors.forename: Ryan D
authors.initials: RD
authors.lastname: Hernandez
authors.forename: Cord
authors.initials: C
authors.lastname: Melton
authors.forename: Aarti
authors.initials: A
authors.lastname: Venkat
authors.forename: Marcelo A
authors.initials: MA
authors.lastname: Nobrega
authors.forename: Ronald
authors.initials: R
authors.lastname: Bontrop
authors.forename: Simon
authors.initials: S
authors.lastname: Myers
authors.forename: Peter
authors.initials: P
authors.lastname: Donnelly
authors.forename: Molly
authors.initials: M
authors.lastname: Przeworski
authors.forename: Gil
authors.initials: G
authors.lastname: McVean
mesh_terms: D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping; D002889:Chromosomes, Human, Pair 2 / Q000235:genetics; D033481:Chromosomes, Mammalian / Q000235:genetics*; D018899:CpG Islands; D019143:Evolution, Molecular; D005260:Female; D014644:Genetic Variation; D006239:Haplotypes; D059014:High-Throughput Nucleotide Sequencing; D011495:Histone-Lysine N-Methyltransferase / Q000235:genetics; D006801:Humans; D008297:Male; D002679:Pan troglodytes / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D011495:Histone-Lysine N-Methyltransferase; C544431:PRDM9 protein, human