title: Recombination modulates how selection affects linked sites in Drosophila.
abstract: One of the most influential observations in molecular evolution has been a strong association between local recombination rate and nucleotide polymorphisms across the genome. This is interpreted as evidence for ubiquitous natural selection. The alternative explanation, that recombination is mutagenic, has been rejected by the absence of a similar association between local recombination rate and nucleotide divergence between species. However, many recent studies show that recombination rates are often very different even in closely related species, questioning whether an association between recombination rate and divergence between species has been tested satisfactorily. To circumvent this problem, we directly surveyed recombination across approximately 43% of the D. pseudoobscura physical genome in two separate recombination maps and 31% of the D. miranda physical genome, and we identified both global and local differences in recombination rate between these two closely related species. Using only regions with conserved recombination rates between and within species and accounting for multiple covariates, our data support the conclusion that recombination is positively related to diversity because recombination modulates Hill-Robertson effects in the genome and not because recombination is predominately mutagenic. Finally, we find evidence for dips in diversity around nonsynonymous substitutions. We infer that at least some of this reduction in diversity resulted from selective sweeps and examine these dips in the context of recombination rate.
authors.affiliation: Biology Department, Duke University, Durham, North Carolina, United States of America. suzanne.mcgaugh@duke.edu
authors.forename: Suzanne E
authors.initials: SE
authors.lastname: McGaugh
authors.forename: Caiti S S
authors.initials: CS
authors.lastname: Heil
authors.forename: Brenda
authors.initials: B
authors.lastname: Manzano-Winkler
authors.forename: Laurence
authors.initials: L
authors.lastname: Loewe
authors.forename: Steve
authors.initials: S
authors.lastname: Goldstein
authors.forename: Tiffany L
authors.initials: TL
authors.lastname: Himmel
authors.forename: Mohamed A F
authors.initials: MA
authors.lastname: Noor
mesh_terms: D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping; D059006:Chromosomes, Insect / Q000235:genetics; D003062:Codon / Q000235:genetics; D016001:Confidence Intervals; D017124:Conserved Sequence; D004330:Drosophila / Q000235:genetics*; D019143:Evolution, Molecular; D008040:Genetic Linkage; D014644:Genetic Variation; D005828:Genetics, Population / Q000379:methods; D049750:Genome, Insect; D016014:Linear Models; D011995:Recombination, Genetic; D012641:Selection, Genetic; D013045:Species Specificity; D016615:Telomere / Q000235:genetics
chemical_list: D003062:Codon