title: Parallel Evolution of Copy-Number Variation across Continents in Drosophila melanogaster.
abstract: Genetic differentiation across populations that is maintained in the presence of gene flow is a hallmark of spatially varying selection. In Drosophila melanogaster, the latitudinal clines across the eastern coasts of Australia and North America appear to be examples of this type of selection, with recent studies showing that a substantial portion of the D. melanogaster genome exhibits allele frequency differentiation with respect to latitude on both continents. As of yet there has been no genome-wide examination of differentiated copy-number variants (CNVs) in these geographic regions, despite their potential importance for phenotypic variation in Drosophila and other taxa. Here, we present an analysis of geographic variation in CNVs in D. melanogaster. We also present the first genomic analysis of geographic variation for copy-number variation in the sister species, D. simulans, in order to investigate patterns of parallel evolution in these close relatives. In D. melanogaster we find hundreds of CNVs, many of which show parallel patterns of geographic variation on both continents, lending support to the idea that they are influenced by spatially varying selection. These findings support the idea that polymorphic CNVs contribute to local adaptation in D. melanogaster In contrast, we find very few CNVs in D. simulans that are geographically differentiated in parallel on both continents, consistent with earlier work suggesting that clinal patterns are weaker in this species.
authors.affiliation: Department of Genetics, Rutgers, The State University of New Jersey dan.schrider@rutgers.edu.
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Schrider
authors.affiliation: Department of Biology and School of Informatics and Computing, Indiana University, Bloomington.
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Hahn
authors.affiliation: Department of Evolution and Ecology, University of California, Davis.
authors.forename: David J
authors.initials: DJ
authors.lastname: Begun
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000818:Animals; D005075:Biological Evolution; D056915:DNA Copy Number Variations; D004331:Drosophila melanogaster / Q000235:genetics*; D019143:Evolution, Molecular; D005260:Female; D005787:Gene Frequency; D014644:Genetic Variation; D005828:Genetics, Population / Q000379:methods; D010802:Phylogeny; D058974:Phylogeography / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic
keywords: copy-number variation; natural selection.; population genetics
references.citation: Trends Genet. 2015 Aug;31(8):434-44
references.pmid: 26072452
references.citation: Genetics. 2003 Oct;165(2):667-73
references.pmid: 14573478
references.citation: PLoS Genet. 2015 May 07;11(5):e1005184
references.pmid: 25950438
references.citation: Mol Ecol. 2012 Oct;21(19):4748-69
references.pmid: 22913798
references.citation: Mol Biol Evol. 2012 Oct;29(10):3237-48
references.pmid: 22617950
references.citation: Mol Biol Evol. 2014 Jul;31(7):1750-66
references.pmid: 24710518
references.citation: Genetics. 2012 Sep;192(1):131-7
references.pmid: 22673805
references.citation: PLoS One. 2012;7(7):e41901
references.pmid: 22848651
references.citation: J Evol Biol. 2008 Nov;21(6):1470-9
references.pmid: 18811666
references.citation: J Hered. 2009 Sep-Oct;100(5):605-17
references.pmid: 19596713
references.citation: Science. 2002 Sep 27;297(5590):2253-6
references.pmid: 12351787
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D555-9
references.pmid: 18948289
references.citation: Mol Biol Evol. 2003 May;20(5):792-9
references.pmid: 12679536
references.citation: Proc Biol Sci. 2010 Nov 7;277(1698):3213-21
references.pmid: 20591863
references.citation: Trends Ecol Evol. 1992 Oct;7(10):340-5
references.pmid: 21236059
references.citation: Annu Rev Med. 2010;61:437-55
references.pmid: 20059347
references.citation: Mol Ecol. 2001 May;10(5):1197-205
references.pmid: 11380877
references.citation: Science. 2010 Jan 15;327(5963):302-5
references.pmid: 20007865
references.citation: Science. 2007 Feb 9;315(5813):848-53
references.pmid: 17289997
references.citation: Evolution. 2010 Nov;64(11):3254-72
references.pmid: 20550573
references.citation: Evolution. 2012 Oct;66(10):3209-23
references.pmid: 23025610
references.citation: PLoS One. 2011;6(12):e29800
references.pmid: 22216356
references.citation: Genome Biol Evol. 2011;3:1014-24
references.pmid: 21979154
references.citation: Genetics. 2013 Jan;193(1):291-301
references.pmid: 23150605
references.citation: Genetics. 2008 May;179(1):455-73
references.pmid: 18493064
references.citation: Mol Biol Evol. 2007 Apr;24(4):1056-67
references.pmid: 17283366
references.citation: PLoS Genet. 2011 Nov;7(11):e1002340
references.pmid: 22072977
references.citation: Nature. 2012 Apr 04;484(7392):55-61
references.pmid: 22481358
references.citation: Genetica. 2004 Mar;120(1-3):5-16
references.pmid: 15088643
references.citation: Nat Genet. 2007 Jul;39(7 Suppl):S37-42
references.pmid: 17597780
references.citation: Genetics. 2004 Oct;168(2):923-31
references.pmid: 15514064
references.citation: PLoS Genet. 2012;8(10):e1002905
references.pmid: 23071443
references.citation: Mol Ecol. 2016 Feb;25(3):723-40
references.pmid: 26523848
references.citation: Genetics. 2011 Jan;187(1):245-60
references.pmid: 21059887
references.citation: J Genet. 2003 Dec;82(3):207-23
references.pmid: 15133196
references.citation: Trends Genet. 2006 Dec;22(12):642-4
references.pmid: 17045359
references.citation: Nat Genet. 2008 Oct;40(10):1199-203
references.pmid: 18776910
references.citation: Genome Biol Evol. 2010 Jan 13;2:83-101
references.pmid: 20333226
references.citation: Annu Rev Genet. 2011;45:203-26
references.pmid: 21854229
references.citation: Science. 2005 Jul 29;309(5735):764-7
references.pmid: 16051794
references.citation: BMC Evol Biol. 2004 Feb 05;4:4
references.pmid: 15018651
references.citation: Mol Ecol. 2015 Apr;24(7):1499-509
references.pmid: 25735402
references.citation: Genetica. 2004 Mar;120(1-3):165-79
references.pmid: 15088656
references.citation: Genetics. 2013 Aug;194(4):937-54
references.pmid: 23733788
references.citation: PLoS Genet. 2013;9(1):e1003242
references.pmid: 23359205
references.citation: PLoS Genet. 2010 Jun 24;6(6):e1000998
references.pmid: 20585622
references.citation: Mol Ecol. 2016 Mar;25(5):1157-74
references.pmid: 26547394
references.citation: Evolution. 2005 Aug;59(8):1721-32
references.pmid: 16331839
references.citation: Trends Genet. 1988 Apr;4(4):106-11
references.pmid: 3149056
references.citation: Bioinformatics. 2009 Jul 15;25(14):1754-60
references.pmid: 19451168
references.citation: Insect Biochem Mol Biol. 2007 May;37(5):512-9
references.pmid: 17456446
references.citation: Genetics. 2012 Oct;192(2):533-98
references.pmid: 22673804
references.citation: Genome Res. 2013 Jan;23(1):89-98
references.pmid: 22936249
references.citation: Genetics. 2014 May;197(1):361-73
references.pmid: 24610860
references.citation: Genetica. 2007 Feb;129(2):133-47
references.pmid: 16955331
references.citation: Genome Res. 2014 Jul;24(7):1193-208
references.pmid: 24714809
references.citation: PLoS Genet. 2010 Jun 17;6(6):e1000924
references.pmid: 20585551
references.citation: Pac Symp Biocomput. 2013;:344-55
references.pmid: 23424139
references.citation: Science. 2008 Jun 20;320(5883):1629-31
references.pmid: 18535209