Rapid genomic changes in Drosophila melanogaster adapting to desiccation stress in an experimental evolution system

Lin Kang, Dau Dayal Aggarwal, Eugenia Rashkovetsky, Abraham B. Korol, Pawel Michalak

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Article number233
JournalBMC Genomics
Volume17
Issue number1
DOIs
StatePublished - 15 Mar 2016

Bibliographical note

Funding Information:
The authors would like to thank two anonymous reviewers for their constructive criticism. The study was supported by Binational USA-Israel Science Foundation (grant BSF # 2011438).

Publisher Copyright:
© 2016 Kang et al.

Keywords

  • Desiccation stress
  • Drosophila
  • Evolutionary genomics
  • Experimental evolution
  • Rapid adaptation
  • Selective sweep

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

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