title: Genome-wide analysis of long-term evolutionary domestication in Drosophila melanogaster.
abstract: Experimental evolutionary genomics now allows biologists to test fundamental theories concerning the genetic basis of adaptation. We have conducted one of the longest laboratory evolution experiments with any sexually-reproducing metazoan, Drosophila melanogaster. We used next-generation resequencing data from this experiment to examine genome-wide patterns of genetic variation over an evolutionary time-scale that approaches 1,000 generations. We also compared measures of variation within and differentiation between our populations to simulations based on a variety of evolutionary scenarios. Our analysis yielded no clear evidence of hard selective sweeps, whereby natural selection acts to increase the frequency of a newly-arising mutation in a population until it becomes fixed. We do find evidence for selection acting on standing genetic variation, as independent replicate populations exhibit similar population-genetic dynamics, without obvious fixation of candidate alleles under selection. A hidden-Markov model test for selection also found widespread evidence for selection. We found more genetic variation genome-wide, and less differentiation between replicate populations genome-wide, than arose in any of our simulated evolutionary scenarios.
authors.affiliation: University of California, Irvine, Department of Ecology and Evolutionary Biology, Irvine, CA, 92617, USA.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Phillips
authors.affiliation: University of California, Irvine, Department of Ecology and Evolutionary Biology, Irvine, CA, 92617, USA.|Genescient Inc., Fountain Valley, CA 92708, USA.
authors.forename: Anthony D
authors.initials: AD
authors.lastname: Long
authors.affiliation: University of California, Irvine, Department of Ecology and Evolutionary Biology, Irvine, CA, 92617, USA.
authors.forename: Zachary S
authors.initials: ZS
authors.lastname: Greenspan
authors.affiliation: University of California, Irvine, Department of Ecology and Evolutionary Biology, Irvine, CA, 92617, USA.|Genescient Inc., Fountain Valley, CA 92708, USA.
authors.forename: Lee F
authors.initials: LF
authors.lastname: Greer
authors.affiliation: Oregon State University, Department of Integrative Biology, Corvallis, OR 97331, USA.
authors.forename: Molly K
authors.initials: MK
authors.lastname: Burke
authors.affiliation: Genescient Inc., Fountain Valley, CA 92708, USA.
authors.forename: Bryant
authors.initials: B
authors.lastname: Villeponteau
authors.affiliation: Genescient Inc., Fountain Valley, CA 92708, USA.
authors.forename: Kennedy C
authors.initials: KC
authors.lastname: Matsagas
authors.affiliation: Genescient Inc., Fountain Valley, CA 92708, USA.
authors.forename: Cristina L
authors.initials: CL
authors.lastname: Rizza
authors.affiliation: University of California, Irvine, Department of Ecology and Evolutionary Biology, Irvine, CA, 92617, USA.|Genescient Inc., Fountain Valley, CA 92708, USA.
authors.forename: Laurence D
authors.initials: LD
authors.lastname: Mueller
authors.affiliation: University of California, Irvine, Department of Ecology and Evolutionary Biology, Irvine, CA, 92617, USA.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Rose
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D000483:Alleles; D000818:Animals; D005075:Biological Evolution; D002454:Cell Differentiation; D003198:Computer Simulation; D000071278:Domestication; D004331:Drosophila melanogaster / Q000235:genetics* / Q000502:physiology*; D005260:Female; D005787:Gene Frequency; D014644:Genetic Variation; D005828:Genetics, Population; D049750:Genome, Insect; D023281:Genomics; D006579:Heterozygote; D008390:Markov Chains; D012641:Selection, Genetic