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.
%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
}