Low concordance of short‐term and long‐term selection responses in experimental Drosophila populations

Abstract

Experimental evolution is becoming a popular approach to study the genomic selection response of evolving populations. Computer simulation studies suggest that the accuracy of the signature increases with the duration of the experiment. Since some assumptions of the computer simulations may be violated, it is important to scrutinize the influence of the experimental duration with real data. Here, we use a highly replicated Evolve and Resequence study in Drosophila simulans to compare the selection targets inferred at different time points. At each time point, approximately the same number of SNPs deviates from neutral expectations, but only 10% of the selected haplotype blocks identified from the full data set can be detected after 20 generations. Those haplotype blocks that emerge already after 20 generations differ from the others by being strongly selected at the beginning of the experiment and display a more parallel selection response. Consistent with previous computer simulations, our results demonstrate that only Evolve and Resequence experiments with a sufficient number of generations can characterize complex adaptive architectures.

Fine Mapping without Phenotyping: Identification of Selection Targets in Secondary Evolve and Resequence Experiments

“…Consistent with previous computer simulation studies ( Baldwin-Brown et al 2014 ; Kofler and Schlötterer 2014 ; Kessner and Novembre 2015 ) and empirical results ( Langmüller and Schlötterer 2020 ), we observe reduced power for experimental designs with shorter experimental duration (supplementary fig. S3, Supplementary Material online).…”

Increased time sampling in an evolve‐and‐resequence experiment with outcrossing Saccharomyces cerevisiae reveals multiple paths of adaptive change

“…Pie charts above the five most significant peaks show the proportion of significant sites in each region exhibiting each pattern time point sampling-provided that the experiment is highly replicated. This conclusion is consistent with recent work in Drosophila that empirically demonstrates the importance of experimental length in accurately identifying targets of selection (Langmüller and Schlötterer, 2020). In general, we expect these recommendations should also apply to E&R work in which the goal is to identify haplotype blocks underlying selection, rather than candidate SNPs Michalak et al, 2018).…”

A morphological trait involved in reproductive isolation between Drosophila sister species is sensitive to temperature

“…This suggests that as flies adapt to the laboratory environment, the plasticity of ventral branches form toward temperature tends to be lost and ventral branches tend to be more rounded. Recent studies show that Drosophila flies can adapt to a laboratory environment in 20 generations only, which corresponds to about 8 months (Langmüller & Schlötterer, 2020).…”

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Phenotypic plasticity, the capacity for one genotype to generate multiple phenotypes in response to environmental variation, is a pervasive feature of biological systems (Debat & David, 2001;Klingenberg, 2019). The connection between plasticity and speciation is multifaceted (Lafuente & Beldade, 2019). On the one hand, plasticity can be heritable and modified by selection.

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“…and the "plasticity-first" model (Levis & Pfennig, 2016). A key feature of all these views is that the phenotypic change triggered by the plastic response, which allows the colonization of the new niches, is a phenocopy, that is, that the phenotypic change can be developmentally triggered by environmental variation or genetic variation interchangeably (Lafuente & Beldade, 2019). As we learn more about the genes mediating phenotypic plasticity (Gibert, 2017), it appears that similar phenotypic changes, either environmentally or genetically induced, can sometimes involve the same genetic loci.…”