Genomic variation in natural populations of Drosophila melanogaster

Genetics. 2012 Oct;192(2):533-98. doi: 10.1534/genetics.112.142018. Epub 2012 Jun 5.


This report of independent genome sequences of two natural populations of Drosophila melanogaster (37 from North America and 6 from Africa) provides unique insight into forces shaping genomic polymorphism and divergence. Evidence of interactions between natural selection and genetic linkage is abundant not only in centromere- and telomere-proximal regions, but also throughout the euchromatic arms. Linkage disequilibrium, which decays within 1 kbp, exhibits a strong bias toward coupling of the more frequent alleles and provides a high-resolution map of recombination rate. The juxtaposition of population genetics statistics in small genomic windows with gene structures and chromatin states yields a rich, high-resolution annotation, including the following: (1) 5'- and 3'-UTRs are enriched for regions of reduced polymorphism relative to lineage-specific divergence; (2) exons overlap with windows of excess relative polymorphism; (3) epigenetic marks associated with active transcription initiation sites overlap with regions of reduced relative polymorphism and relatively reduced estimates of the rate of recombination; (4) the rate of adaptive nonsynonymous fixation increases with the rate of crossing over per base pair; and (5) both duplications and deletions are enriched near origins of replication and their density correlates negatively with the rate of crossing over. Available demographic models of X and autosome descent cannot account for the increased divergence on the X and loss of diversity associated with the out-of-Africa migration. Comparison of the variation among these genomes to variation among genomes from D. simulans suggests that many targets of directional selection are shared between these species.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Africa
  • Animals
  • Centromere / genetics
  • Chromatin / genetics
  • Chromosome Mapping
  • Drosophila melanogaster / genetics*
  • Drosophila melanogaster / physiology
  • Genetic Linkage*
  • Genetic Variation*
  • Genetics, Population
  • Genome*
  • Linkage Disequilibrium
  • Selection, Genetic
  • Species Specificity
  • Telomere / genetics
  • Untranslated Regions / genetics
  • X Chromosome / genetics


  • Chromatin
  • Untranslated Regions