Recombination modulates how selection affects linked sites in Drosophila

PLoS Biol. 2012;10(11):e1001422. doi: 10.1371/journal.pbio.1001422. Epub 2012 Nov 13.


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Base Sequence
  • Chromosome Mapping
  • Chromosomes, Insect / genetics
  • Codon / genetics
  • Confidence Intervals
  • Conserved Sequence
  • Drosophila / genetics*
  • Evolution, Molecular
  • Genetic Linkage*
  • Genetic Variation
  • Genetics, Population / methods
  • Genome, Insect*
  • Linear Models
  • Recombination, Genetic*
  • Selection, Genetic*
  • Species Specificity
  • Telomere / genetics


  • Codon