%0 Journal Article %1 langley2012genomic %A Langley, C H %A Stevens, K %A Cardeno, C %A Lee, Y C %A Schrider, D R %A Pool, J E %A Langley, S A %A Suarez, C %A Corbett-Detig, R B %A Kolaczkowski, B %A Fang, S %A Nista, P M %A Holloway, A K %A Kern, A D %A Dewey, C N %A Song, Y S %A Hahn, M W %A Begun, D J %D 2012 %J Genetics %K Drosophila hitchhiking population_genomics recombination selection %N 2 %P 533-598 %R 10.1534/genetics.112.142018 %T Genomic variation in natural populations of Drosophila melanogaster %U http://www.ncbi.nlm.nih.gov/pubmed/22673804 %V 192 %X 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.

@article{langley2012genomic, abstract = {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.}, added-at = {2015-04-01T17:40:53.000+0200}, author = {Langley, C H and Stevens, K and Cardeno, C and Lee, Y C and Schrider, D R and Pool, J E and Langley, S A and Suarez, C and Corbett-Detig, R B and Kolaczkowski, B and Fang, S and Nista, P M and Holloway, A K and Kern, A D and Dewey, C N and Song, Y S and Hahn, M W and Begun, D J}, biburl = {https://www.bibsonomy.org/bibtex/2a6f05afb18970aa6e438b9aa73c066a9/peter.ralph}, doi = {10.1534/genetics.112.142018}, interhash = {07bdab3d788c9139dbd99624135d9db5}, intrahash = {a6f05afb18970aa6e438b9aa73c066a9}, journal = {Genetics}, keywords = {Drosophila hitchhiking population_genomics recombination selection}, month = oct, number = 2, pages = {533-598}, pmid = {22673804}, timestamp = {2015-04-01T17:40:53.000+0200}, title = {Genomic variation in natural populations of \textit{{Drosophila} melanogaster}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22673804}, volume = 192, year = 2012 }