Genomic variation in natural populations of Drosophila melanogaster.
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.
Department of Evolution and Ecology, University of California, Davis, CA 95616, USA. chlangley@ucdavis.edu
Charles H
CH
Langley
Kristian
K
Stevens
Charis
C
Cardeno
Yuh Chwen G
YC
Lee
Daniel R
DR
Schrider
John E
JE
Pool
Sasha A
SA
Langley
Charlyn
C
Suarez
Russell B
RB
Corbett-Detig
Bryan
B
Kolaczkowski
Shu
S
Fang
Phillip M
PM
Nista
Alisha K
AK
Holloway
Andrew D
AD
Kern
Colin N
CN
Dewey
Yun S
YS
Song
Matthew W
MW
Hahn
David J
DJ
Begun
D000349:Africa; D000818:Animals; D002503:Centromere / Q000235:genetics; D002843:Chromatin / Q000235:genetics; D002874:Chromosome Mapping; D004331:Drosophila melanogaster / Q000235:genetics* / Q000502:physiology; D008040:Genetic Linkage; D014644:Genetic Variation; D005828:Genetics, Population; D016678:Genome; D015810:Linkage Disequilibrium; D012641:Selection, Genetic; D013045:Species Specificity; D016615:Telomere / Q000235:genetics; D020506:Untranslated Regions / Q000235:genetics; D014960:X Chromosome / Q000235:genetics
D002843:Chromatin; D020506:Untranslated Regions