Genomic Trajectories to Desiccation Resistance: Convergence and Divergence Among Replicate Selected Drosophila Lines

Philippa C Griffin, Sandra Hangartner, Alexandre Fournier-Level, Ary Anthony Hoffmann

Research output: Contribution to journalArticleResearchpeer-review

20 Citations (Scopus)

Abstract

Adaptation to environmental stress is critical for long-term species persistence.With climate change and other anthropogenic stressors compounding natural selective pressures, understanding the nature of adaptation is as important as ever in evolutionary biology. In particular, the number of alternative molecular trajectories available for an organism to reach the same adaptive phenotype remains poorly understood. Here we investigate this issue in a set of replicated Drosophila melanogaster lines selected for increased desiccation resistance, a classical physiological trait that has been closely linked to Drosophila species distributions. We used pooled whole-genome sequencing (Pool-Seq) to compare the genetic basis of their selection responses using a matching set of replicated control lines for characterising laboratory adaptation, as well as the original base population. The ratio of effective population size to census size was high over the generations of the experiment at 0.52—0.88 for all selected and control lines. While selected SNPs in replicates of the same treatment (desiccation-selection or lab adaptation) tended to change frequency in the same direction, suggesting some commonality in the selection response, candidate SNP and gene lists often differed among replicates. Three of the five desiccation-selection replicates showed significant overlap at the gene and network level. All five replicates showed enrichment for ovary-expressed genes, suggesting maternal effects on the selected trait. Divergence between pairs of replicate lines for desiccation candidate SNPs was greater than between pairs of control lines. This difference also far exceeded the divergence between pairs of replicate lines for neutral SNPs. Overall, while there was overlap in the direction of allele frequency changes and the network and functional categories affected by desiccation selection, replicates showed unique responses at all levels likely reflecting hitchhiking effects, and highlighting the challenges in identifying candidate genes from these types of experiments when traits are likely to be polygenic.
Original languageEnglish
Pages (from-to)871-890
Number of pages20
JournalGenetics
Volume205
Issue number2
DOIs
Publication statusPublished - 1 Feb 2017

Keywords

  • pool-seq
  • climate adaptation
  • experimental evolution
  • natural variation
  • population genomics

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