Genome-Wide Architecture of Adaptation in Experimentally EvolvedDrosophila

Abstract

The molecular basis of adaptation remains elusive even with the current ease of sequencing the genome and transcriptome. We used experimentally evolved populations of Drosophila in conjunction with statistical learning tools to explore interactions between the genome, the transcriptome, and phenotypes. Our results indicate that transcriptomic measures from adult samples can predict phenotypic characters at many adult ages. Importantly, when comparing the genome and transcriptome in predicting phenotypic characters, we find that the two types of data are comparably useful. When using genome sites as predictors for the expression of the transcriptome, we find that gene expression is influenced by genomic regions across all large chromosome arms. Conversely, we found many genomic regions influencing the expression of numerous genes, which is consistent with widespread pleiotropy. Our results also highlight the power of the combination of experimental evolution, next-generation sequencing, and statistical learning tools in exploring the molecular basis of adaptation.

The Darwinian Core of Evolutionary Theory and the Extended Evolutionary Synthesis: Similarities and Differences

“…Our understanding of the origin of novel trait-variants ("micro-origins") has progressed quite a bit since Darwin's unsuccessful attempts to grapple with this vexed issue through his theory of pangenesis (Geison, 1969;McComas 2012). A large proportion of the explanations for "microorigins" phenomena derives from genetics, involving both mutations in the broadest sense, including chromosomal changes and changes in gene expression (e.g., Dobzhansky, 1937;Graves et al, 2017;Seabra et al, 2018;Fitzgerald & Rosenberg, 2019;Barter et al, 2020;Dowle et al, 2020), as well as the recombinational shuffling of standing genetic variation, especially for quantitative traits (Teotónio et al, 2009;Mueller et al, 2013;Matuszewski et al, 2015;Philips et al, 2018;Hickey & Golding, 2021;Kawecki et al, 2021). The now fairly well accepted role of phenotypic plasticity in preceding and facilitating adaptive evolutionary change (discussed in detail in Pfennig, 2021) also has a bearing on issues in the category "micro-origins".…”