Ancestral population reconstitution from isofemale lines as a tool for experimental evolution.

Pierre Nouhaud,Ray Tobler,Christian Schlötterer,Viola Nolte

doi:10.1002/ece3.2402

Abstract

Experimental evolution is a powerful tool to study adaptation under controlled conditions. Laboratory natural selection experiments mimic adaptation in the wild with better‐adapted genotypes having more offspring. Because the selected traits are frequently not known, adaptation is typically measured as fitness increase by comparing evolved populations against an unselected reference population maintained in a laboratory environment. With adaptation to the laboratory conditions and genetic drift, however, it is not clear to what extent such comparisons provide unbiased estimates of adaptation. Alternatively, ancestral variation could be preserved in isofemale lines that can be combined to reconstitute the ancestral population. Here, we assess the impact of selection on alleles segregating in newly established Drosophila isofemale lines. We reconstituted two populations from isofemale lines and compared them to two original ancestral populations (AP) founded from the same lines shortly after collection. No significant allele frequency changes could be detected between both AP and simulations showed that drift had a low impact compared to Pool‐Seq‐associated sampling effects. We conclude that laboratory selection on segregating variation in isofemale lines is too weak to have detectable effects, which validates ancestral population reconstitution from isofemale lines as an unbiased approach for measuring adaptation in evolved populations.

Highlights

Combining experimental evolution and high-throughput sequencing is a powerful approach to study adaptation (Barrick and Lenski 2013; Achaz et al 2014; Long et al 2015; Schlo€tterer et al 2015)
We used Pool-Seq to compare allele frequency estimates from ancestral populations (AP) established from freshly collected isofemale lines to populations reconstituted from the same isofemale lines after several years of maintenance in the laboratory (RAPs)
We attribute the lower number of SNPs in D. melanogaster to coverage fluctuations, which differ between the libraries of AP and reconstituted ancestral population (RAP) due to the modifications in library preparation protocols for RAPs

Summary

Introduction

Combining experimental evolution and high-throughput sequencing is a powerful approach to study adaptation (Barrick and Lenski 2013; Achaz et al 2014; Long et al 2015; Schlo€tterer et al 2015). By monitoring allele frequency changes (AFCs) in populations exposed to new environments, evolve and resequence approaches (E&R, Turner et al 2011) permit the identification of targets of selection and provide new insights into fundamental evolutionary questions such as the genomic architecture of adaptive traits (Burke et al 2010; Parts et al 2011; Orozco-terWengel et al 2012; Remolina et al 2012), the reproducibility of evolution (Teotonio et al 2009; Chan et al 2012; Tenaillon et al 2012; Burke et al 2014), or the tempo of evolutionary change

Methods

Results

Conclusion