Allele frequency shift in experimental evolution lines under sex-specific selection

NAISS 2023/5-472


NAISS Medium Compute

Principal Investigator:

David Berger


Uppsala universitet

Start Date:


End Date:


Primary Classification:

10615: Evolutionary Biology



We want to analyze pooled DNA samples from replicated (8) experimental evolution lines of the beetle, Callosobruchus maculatus. The lines have been evolving under three alternative mating regimes for 50 generations. These lines offer a prime opportunity to investigate genome wide consequences of sexually antagonistic (SA) selection (selection acting in opposing directions in males and females). #### DNA pool-seq data By examining shifts in allele frequencies in these lines, we will identify candidate loci under sexually antagonistic selection. This will also allow us to test whether sexually antagonistic selection can maintain genetic variation and potentially also the genomic locations of such loci. We obtained DNA sequences from two separate sequencing efforts of the 8 experimental evolution lines and 2 samples of the ancestral population from which the lines were derived. We re-sequenced one library after quality control, resulting in a total of 21 libraries. DNA came from 80 and 60 pooled individuals for experimental evolution line and ancestral samples, respectively. #Transcriptomic data To refine our analyses and help us identify sex-specific selection and sexual conflict across the genome we will combine the DNA pool-seq data with transcriptome data from the same lines. This effort will allow us to see if sex-bias in gene expression is associated with divergence across the genome between our evolution regimes, and will give insights into how strong genetic constraints are on sex-specific adaptation. We have obtained RNA sequences from mated males and female from the 8 lines (16 libraries). In the end of this year, we will send an additional 32 libraries (16 based on tissue from abdomens and 16 from head tissue) for RNA sequencing, Hence replicating and expanding the first effort. This will offer greater statistical power in our analyses as well as insights on tissue-specific expression. Second, sexual conflict over mating usually occurs when males evolve a trait to enhance their reproductive output at the expense of the reproductive success of their female mating partner. In turn females evolve defense traits that mitigate male harmfulness at the expense of male reproductive success. The level of sexual conflict to differs vastly between the evolution regimes, which offers opportunity to identify loci that underlie this type of male-female coevolution. To search for such loci, we obtained additional RNA sequences from standard females mated to males from one of the 8 experimental evolution lines and an additional 3 samples of unmated standard females (11 libraries). In total there will be 59 RNA libraries that will be analyzed further (27 libraries currently sequenced and on the allocation). All sequencing was done at the SNP&SEQ Technology Platform in Uppsala as 150bp paired-end reads on one NovaSeq S4 lane.