DOI: 10.5061/dryad.fxpnvx0nd
title: Genomic processes underlying rapid adaptation of a natural Chironomus riparius population to unintendedly applied experimental selection pressures

description: Evolve and Resquence (E&R) studies are a useful tool to study
 genomic processes during rapid adaptation, e.g. in the framework of
 adaptive responses to global climate change. We applied different thermal
 regimes to a natural Chironomus riparius (Diptera) population in an
 E&R framework to infer its evolutionary potential for rapid
 thermal adaptation. We exposed two replicates to three temperatures each
 (14°C, 20°C and 26°C) for more than two years, the experiment thus lasting
 22, 44 or 65 generations, respectively. The two higher temperatures
 presented a priori moderate, respectively strong selection pressures.
 Life-cycle fitness tests revealed no appreciable adaptation to thermal
 regimes but a common adaptation of all six replicates likely to the
 rearing conditions, presumably increased larval density and water quality.
 Genomic analyses showed a strong, genome-wide selective response in all
 replicates (mean s of selected SNPs = 0.305). This genomic response was
 significantly similar at all genomic levels among all replicates (SNPs, 10
 kb windows, genes, exons, regions of elevated allele frequency change
 (REA)). The intersections among the replicates exposed to the same
 temperature were either insignificant or underrepresented. This confirmed
 a selective response to identical selection pressure(s), however, not to
 thermal regime. Genes closest to the SNP with the highest selection
 coefficient per REA were enriched for GO terms related to ion transport,
 regulation of transcription and signal transduction, which supported the
 presumed acting selection pressures. Our study showed the evolutionary
 potential for rapid adaptation by genome-wide and probably polygenic
 selection on standing genetic variation in C. riparius. However,
 because of the impossibility to accurately predict the acting selective
 regime in evolutionary experiments, we discuss the sobering perspectives
 for inferring the evolutionary potential of natural populations with this
 approach.
description: DNA was extracted from the ancestral population and each replicate using the Quiagen blood and tissue extraction kit on pooled samples of 80 larval head capsules, respectively. Integrity and quality of extracted DNA was controlled using electrophoresis, and the DNA concentration for each samples measured with a Qubit fluorimeter (Invitrogen). Whole genome pool-sequencing was carried out on an Illumina MySeq with 250bp paired end reads. Reads were trimmed using the wrapper tool autotrim (Waldvogel <i>et al.</i> 2018) that integrates trimmomatic (Bolger<i> et al.</i> 2014) for trimming and fastQC (Andrews 2010) for quality control. The trimmed reads were then mapped on the latest <i>C. riparius</i> reference genome (Schmidt<i> et al.</i> 2019) using the BWA mem algorithm (Li & Durbin 2009). Low quality reads were subsequently filtered and SNPs were initially called using samtools (Li <i>et al.</i> 2011). The pipelines Popoolation and Popoolation2 (Robert Kofler <i>et al.</i> 2011; R. Kofler <i>et al.</i> 2011) were used to call SNPs, remove indels, and to estimate genetic diversity as Watterson’s theta in the ancestral population and each evolved replicate.