Genome‐wide patterns of latitudinal differentiation among populations of D rosophila melanogaster from N orth A merica

Abstract

Understanding the genetic underpinnings of adaptive change is a fundamental but largely unresolved problem in evolutionary biology. D rosophila melanogaster , an ancestrally tropical insect that has spread to temperate regions and become cosmopolitan, offers a powerful opportunity for identifying the molecular polymorphisms underlying clinal adaptation. Here, we use genome‐wide next‐generation sequencing of DNA pools (‘pool‐seq’) from three populations collected along the N orth A merican east coast to examine patterns of latitudinal differentiation. Comparing the genomes of these populations is particularly interesting since they exhibit clinal variation in a number of important life history traits. We find extensive latitudinal differentiation, with many of the most strongly differentiated genes involved in major functional pathways such as the insulin/ TOR , ecdysone, torso, EGFR , TGF β/ BMP , JAK / STAT , immunity and circadian rhythm pathways. We observe particularly strong differentiation on chromosome 3R , especially within the cosmopolitan inversion In(3R)Payne , which contains a large number of clinally varying genes. While much of the differentiation might be driven by clinal differences in the frequency of In(3R)P , we also identify genes that are likely independent of this inversion. Our results provide genome‐wide evidence consistent with pervasive spatially variable selection acting on numerous loci and pathways along the well‐known North American cline, with many candidates implicated in life history regulation and exhibiting parallel differentiation along the previously investigated Australian cline.

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     Shields DC, Sharp PM, Higgins DG, Wright F. "Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Molecular Biology and Evolution. 1988;5:704-716.

     Not in our library10.1093/oxfordjournals.molbev.a040525

115. 115.

     Sinervo B, Svensson E. Correlational selection and the evolution of genetic architecture. Heredity. 2002;89:329-338.

     Not in our library10.1038/sj.hdy.6800148

116. 116.

     Singh RS, Rhomberg LR. A comprehensive study of genic variation in natural populations of Drosophila melanogaster. II. Estimates of heterozygosity and patterns of geographic differentiation. Genetics. 1987;117:255-271.

     Not in our library10.1093/genetics/117.2.255

117. 117.

     Slatkin M. Spatial patterns in the distributions of polygenic characters. Journal of Theoretical Biology. 1978;70:213-228.

     Not in our library10.1016/0022-5193(78)90348-x

118. 118.

     Stapley J, Reger J, Feulner PGD, et al. Adaptation genomics: the next generation. Trends in Ecology and Evolution. 2010;25:705-712.

     Not in our library10.1016/j.tree.2010.09.002

119. 119.

     Stinchcombe JR, Hoekstra HE. Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity. 2007;100:158-170.

     Not in our library10.1038/sj.hdy.6800937

120. 120.

     Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proceedings of the National Academy of Sciences USA. 2003;100:9440-9445.

     Not in our library10.1073/pnas.1530509100

121. 121.

     Tatar M, Bartke A, Antebi A. The endocrine regulation of aging by insulin-like signals. Science. 2003;299:1346-1351.

     Not in our library10.1126/science.1081447

122. 122.

     Tauber E, Zordan M, Sandrelli F, et al. Natural selection favors a newly derived timeless allele in Drosophila melanogaster. Science. 2007;316:1895-1898.

     Not in our library10.1126/science.1138412

123. 123.

     Teshima KM, Coop G, Przeworski M. How reliable are empirical genomic scans for selective sweeps? Genome Research. 2006;16:702-712.

     Not in our library10.1101/gr.5105206

124. 124.

     Turner TL, Levine MT, Eckert ML, Begun DJ. Genomic analysis of adaptive differentiation in Drosophila melanogaster. Genetics. 2008;179:455-473.

     Not in our library10.1534/genetics.107.083659

125. 125.
     Population-Based Resequencing of Experimentally Evolved Populations Reveals the Genetic Basis of Body Size Variation in Drosophila melanogaster · 2011

     No notice
126. 126.

     Weeks AR, McKechnie SW, Hoffmann AA. Dissecting adaptive clinal variation: markers, inversion and stress/size associations in Drosophila melanogaster from a central field population. Ecology Letters. 2002;5:756-763.

     Not in our library

127. 127.

     Whitlock MC. Evolutionary inference from QST. Molecular Ecology. 2008;17:1885-1896.

     Not in our library10.1111/j.1365-294x.2008.03712.x

128. 128.

     Williams K, Busto M, Suster M, et al. Natural variation in Drosophila melanogaster diapause due to the insulin-regulated PI3-kinase. Proceedings of the National Academy of Sciences USA. 2006;103:15911-15915.

     Not in our library10.1073/pnas.0604592103

129. 129.

     Yagi Y, Ip YT. Helicase89B is a Mot1p/BTAF1 homologue that mediates an antimicrobial response in Drosophila. EMBO Reports. 2005;6:1088-1094.

     Not in our library10.1038/sj.embor.7400542

130. 130.

     Yukilevich R, Turner TL, Aoki F, Nuzhdin SV, True JR. Patterns and processes of genome-wide divergence between North American and African Drosophila melanogaster. Genetics. 2010;186:219-239.

     Not in our library10.1534/genetics.110.117366

Cited by papers we hold 11

• Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila · 2021
  No notice
• Fitness effects for Ace insecticide resistance mutations are determined by ambient temperature · 2020
  Not checked
• Evolutionary genomics can improve prediction of species’ responses to climate change · 2020
  No notice
• Horizons in the evolution of aging · 2018
  No notice
• A Hidden Markov Model Approach for Simultaneously Estimating Local Ancestry and Admixture Time Using Next Generation Sequence Data in Samples of Arbitrary Ploidy · 2017
  No notice
• Using neutral, selected, and hitchhiker loci to assess connectivity of marine populations in the genomic era · 2015
  No notice
• Genetic architecture of natural variation in cuticular hydrocarbon composition in Drosophila melanogaster · 2015
  No notice
• The sleeping beauty: how reproductive diapause affects hormone signaling, metabolism, immune response and somatic maintenance in Drosophila melanogaster. · 2014
  Not checked
• Drosophila Embryogenesis Scales Uniformly across Temperature in Developmentally Diverse Species · 2014
  No notice
• Background Selection as Baseline for Nucleotide Variation across the Drosophila Genome · 2014
  No notice
• Factors that regulate insulin producing cells and their output in Drosophila · 2013
  No notice

Reads

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.