Selection on the fly: short term adaptation to an altered sexual selection regime inDrosophila pseudoobscura

Abstract

Experimental evolution studies are powerful approaches to unveil the evolutionary history of lab populations. Such studies have shed light on how selection changes phenotypes and genotypes. Most of these studies have not examined the time course of adaptation under sexual selection manipulation, by resequencing the populations' genomes at multiple time points. Here, we analyse allele frequency trajectories in Drosophila pseudoobscura where we altered their sexual selection regime for 200 generations and sequenced pooled populations at 5 time points. The intensity of sexual selection was either relaxed in monogamous populations (M) or elevated in polyandrous lines (E). We present a comprehensive study of how selection alters population genetics parameters at the chromosome and gene level. We investigate differences in the effective population size - Ne - between the treatments, and perform a genome-wide scan to identify signatures of selection from the time-series data. We found genomic signatures of adaptation to both regimes in D. pseudoobscura. There are more significant variants on E lines as expected from stronger sexual selection. However, we found that the response on the X chromosome was substantial in both treatments, only more marked in E and restricted to chromosome arm XR in M. Ne is lower on the X at the start of the experiment, which might indicate a swift adaptive response at the onset of selection. Additionally, we show that the third chromosome was also affected by elevated polyandry. Its distal end harbours a region showing a strong signal of adaptive divergence in E lines.

PhyloAln: a convenient reference-based tool to align sequences and high-throughput reads for phylogeny and evolution in the omic era

“…To assess PhyloAln’s capability in mapping sequences/reads into reference alignments across diverse species spanning the tree of life and its performance on contaminated data, we constructed a simulated dataset. This dataset comprises genomes from one bacterium ( Escherichia coli (Hayashi, et al 2001)), one plant ( Arabidopsis thaliana (Cheng, et al 2017)), one fungus ( Saccharomyces cerevisiae (Engel, et al 2022)), two vertebrates ( Danio rerio (Howe, et al 2013) and Homo sapiens (Collins, et al 2004)), eight fruit flies ( Scaptodrosophila lebanonensis (Flynn, et al 2020), Drosophila melanogaster (Hoskins, et al 2015), D. simulans (Wang, et al 2023), D. willistoni (Ranz, et al 2023), D. mojavensis (Kim, et al 2021), D. yakuba (Huang, et al 2022), D. busckii (Renschler, et al 2019), D. pseudoobscura (Barata, et al 2023)) and two other insects ( Tribolium castaneum (Herndon, et al 2020) and Aedes aegypti (Matthews, et al 2018)), sourced from the NCBI RefSeq database (Haft, et al 2023) (Table S1). The phylogeny of these species was obtained from the TimeTree database (Kumar, et al 2022).…”