title: Rapid genomic changes in Drosophila melanogaster adapting to desiccation stress in an experimental evolution system.
abstract: BACKGROUND
  Experimental evolution studies, coupled with whole genome resequencing and advances in bioinformatics, have become a powerful tool for exploring how populations respond to selection at the genome-wide level, complementary to genome-wide association studies (GWASs) and linkage mapping experiments as strategies to connect genotype and phenotype. In this experiment, we analyzed genomes of Drosophila melanogaster from lines evolving under long-term directional selection for increased desiccation resistance in comparison with control (no-selection) lines.
  
  
  RESULTS
  We demonstrate that adaptive responses to desiccation stress have exerted extensive footprints on the genomes, manifested through a high degree of fixation of alleles in surrounding neighborhoods of eroded heterozygosity. These patterns were highly convergent across replicates, consistent with signatures of 'soft' selective sweeps, where multiple alleles present as standing genetic variation become beneficial and sweep through the replicate populations at the same time. Albeit much less frequent, we also observed line-unique sweep regions with zero or near-zero heterozygosity, consistent with classic, or 'hard', sweeps, where novel rather than pre-existing adaptive mutations may have been driven to fixation. Genes responsible for cuticle and protein deubiquitination seemed to be central to these selective sweeps. High divergence within coding sequences between selected and control lines was also reflected by significant results of the McDonald-Kreitman and Ka/Ks tests, showing that as many as 347 genes may have been under positive selection.
  
  
  CONCLUSIONS
  Desiccation stress, a common challenge to many organisms inhabiting dry environments, proves to be a very potent selecting factor having a big impact on genome diversity.
authors.affiliation: Biocomplexity Institute, Virginia Tech, Blacksburg, VA, 24061, USA.
authors.forename: Lin
authors.initials: L
authors.lastname: Kang
authors.affiliation: Institute of Evolution, University of Haifa, Abba Khoushy Ave 199, Haifa, Israel.
authors.forename: Dau Dayal
authors.initials: DD
authors.lastname: Aggarwal
authors.affiliation: Institute of Evolution, University of Haifa, Abba Khoushy Ave 199, Haifa, Israel.
authors.forename: Eugenia
authors.initials: E
authors.lastname: Rashkovetsky
authors.affiliation: Institute of Evolution, University of Haifa, Abba Khoushy Ave 199, Haifa, Israel.
authors.forename: Abraham B
authors.initials: AB
authors.lastname: Korol
authors.affiliation: Biocomplexity Institute, Virginia Tech, Blacksburg, VA, 24061, USA. pawel@vbi.vt.edu.
authors.forename: Pawel
authors.initials: P
authors.lastname: Michalak
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000483:Alleles; D000818:Animals; D003681:Dehydration / Q000235:genetics*; D004331:Drosophila melanogaster / Q000235:genetics* / Q000502:physiology; D019143:Evolution, Molecular; D005260:Female; D014644:Genetic Variation; D049750:Genome, Insect; D005838:Genotype; D008297:Male; D009154:Mutation; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D013312:Stress, Physiological
keywords: Desiccation stress; Drosophila; Evolutionary genomics; Experimental evolution; Rapid adaptation; Selective sweep