The determination of independent genome sequences from two natural populations of Drosophila melanogaster (37 from North America and 6 from Africa) provides a unique new opportunity to investigate the forces shaping genomic polymorphism and divergence. Evidence of interactions between natural selection and linkage is abundant not only in the centromere- and telomere-proximal regions, but throughout the euchromatic arms. Linkage disequilibrium which decays within 1 kbp, exhibits a strong bias toward the coupling of the more frequent alleles and supports a high resolution map of the recombination rate. The juxtaposition of population genetics statistics in small windows to gene structures and chromatin states yields a rich, high resolution annotation. 5'and 3' UTRs are enriched for regions of reduced polymorphism relative to lineage specific divergence. Exons overlap with windows of excess relative polymorphism. Epigenetic marks associated with active transcription starts sites overlap with regions of reduced relative polymorphism and relatively reduced estimates of the rate of recombination. The rate of adaptive nonsynonymous fixation increases with the rate of crossing over per bp. Both duplications and deletions are enriched near origins of replication and their density also correlates negatively with the rate of crossing over. Available demographic models of X and autosome descent cannot account for the X's increased divergence and loss of diversity associated with the out-of-africa migration. Comparative analysis of the variation among these genomes to genomes from D. simulana suggests that many targets of directional selection may be shared between these species.
- linkage disequilibrium
- background selection
- geographic differentiation, mutation, recombination, chromatin states and copy number variation
- natural selection, polymorphism, divergence, frequency spectrum
- Received December 22, 2011.
- Accepted May 24, 2012.
- Copyright © 2012, The Genetics Society of America