title: Genomics of Parallel Experimental Evolution in Drosophila.
abstract: What are the genomic foundations of adaptation in sexual populations? We address this question using fitness-character and whole-genome sequence data from 30 Drosophila laboratory populations. These 30 populations are part of a nearly 40-year laboratory radiation featuring 3 selection regimes, each shared by 10 populations for up to 837 generations, with moderately large effective population sizes. Each of 3 sets of the 10 populations that shared a selection regime consists of 5 populations that have long been maintained under that selection regime, paired with 5 populations that had only recently been subjected to that selection regime. We find a high degree of evolutionary parallelism in fitness phenotypes when most-recent selection regimes are shared, as in previous studies from our laboratory. We also find genomic parallelism with respect to the frequencies of single-nucleotide polymorphisms, transposable elements, insertions, and structural variants, which was expected. Entirely unexpected was a high degree of parallelism for linkage disequilibrium. The evolutionary genetic changes among these sexual populations are rapid and genomically extensive. This pattern may be due to segregating functional genetic variation that is abundantly maintained genome-wide by selection, variation that responds immediately to changes of selection regime.
authors.affiliation: Joint School of Nanoscience and Nanoengineering, North Carolina A&T State University and UNC Greensboro, Greensboro, NC.
authors.forename: J L
authors.initials: JL
authors.lastname: Graves
authors.affiliation: Department of Biology, The University of Texas at Tyler, Tyler, TX.
authors.forename: K L
authors.initials: KL
authors.lastname: Hertweck
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, Irvine, CA.
authors.forename: M A
authors.initials: MA
authors.lastname: Phillips
authors.affiliation: School of Life Sciences, University of Nevada, Las Vegas, NV.
authors.forename: M V
authors.initials: MV
authors.lastname: Han
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, Irvine, CA.
authors.forename: L G
authors.initials: LG
authors.lastname: Cabral
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, Irvine, CA.
authors.forename: T T
authors.initials: TT
authors.lastname: Barter
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, Irvine, CA.
authors.forename: L F
authors.initials: LF
authors.lastname: Greer
authors.affiliation: Department of Integrative Biology, Oregon State University, Corvallis, OR.
authors.forename: M K
authors.initials: MK
authors.lastname: Burke
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, Irvine, CA.
authors.forename: L D
authors.initials: LD
authors.lastname: Mueller
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, Irvine, CA.
authors.forename: M R
authors.initials: MR
authors.lastname: Rose
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000483:Alleles; D000818:Animals; D005075:Biological Evolution; D030561:Databases, Nucleic Acid; D004330:Drosophila / Q000235:genetics; D004331:Drosophila melanogaster / Q000235:genetics; D019143:Evolution, Molecular; D005787:Gene Frequency / Q000235:genetics; D056084:Genetic Fitness / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics; D023281:Genomics / Q000379:methods*; D015810:Linkage Disequilibrium / Q000235:genetics; D023421:Models, Animal; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012641:Selection, Genetic / Q000235:genetics*
keywords: adaptation; experimental evolution; population genomics