Locus‐specific introgression in young hybrid swarms: Drift may dominate selection

Abstract

The rate of hybridization between closely related species that have recently come into secondary contact is increasing, due to human-assisted migration and environmental change (Grabenstein & Taylor, 2018;Parmesan & Yohe, 2003). While such hybridization is not necessarily negative (Hamilton & Miller, 2016), in many cases hybridization can cause problems for native species. If F1s are

Admixture mapping reveals loci for carcass mass in red deer x sika hybrids in Kintyre, Scotland

“…Additionally, Bayesian genomic clines, which can be used to compare the rate and extent of introgression in hybrid populations ( Gompert and Buerkle 2011 ; Gompert and Buerkle 2012 ), were used to quantify locus-specific introgression. We found that red deer and sika in Scotland are quite genetically diverged, with a genome-wide F st of 0.532 (95% confidence interval: 0.529–0.534; McFarlane et al 2020 ), although it should be noted that there is substantial variation in divergence across the genome ( McFarlane et al 2021 ). We also found substantial variation in the rate of introgression, indicating the potential for some SNPs to be under selection ( McFarlane et al 2021 ).…”

“…We found that red deer and sika in Scotland are quite genetically diverged, with a genome-wide F st of 0.532 (95% confidence interval: 0.529–0.534; McFarlane et al 2020 ), although it should be noted that there is substantial variation in divergence across the genome ( McFarlane et al 2021 ). We also found substantial variation in the rate of introgression, indicating the potential for some SNPs to be under selection ( McFarlane et al 2021 ). If there is an SNP for carcass mass that is in a causal region, or in linkage disequilibrium (LD) with a causal region, we should have high power to detect it, based on the F st between red deer and sika, the large phenotypic divergence and the estimated number of generations since admixture began (approximately 6–7; Crawford and Nielsen 2013 ; McFarlane et al 2020 ).…”

“…In a previous study, we used genomic clines in the program bgc to look for SNPs that could be associated with either reproductive isolation or adaptive introgression ( i.e. , those SNPs are introgressing either slower or faster than the genome average; Gompert and Buerkle 2011 ; Gompert and Buerkle 2012 ; McFarlane et al 2021 ). We have previously reported that 11.4% of SNPs have cline centers more extreme than the genome average and 17.6% of SNPs have introgressed at rates more extreme than the genome average ( McFarlane et al 2021 ).…”

“…, those SNPs are introgressing either slower or faster than the genome average; Gompert and Buerkle 2011 ; Gompert and Buerkle 2012 ; McFarlane et al 2021 ). We have previously reported that 11.4% of SNPs have cline centers more extreme than the genome average and 17.6% of SNPs have introgressed at rates more extreme than the genome average ( McFarlane et al 2021 ). However, we found that these patterns could be driven by either genetic drift or selection ( McFarlane et al 2021 ).…”

“…We have previously reported that 11.4% of SNPs have cline centers more extreme than the genome average and 17.6% of SNPs have introgressed at rates more extreme than the genome average ( McFarlane et al 2021 ). However, we found that these patterns could be driven by either genetic drift or selection ( McFarlane et al 2021 ). For this reason, we wanted to determine if any QTLs associated with carcass mass had significant genomic cline parameters, as these would be independent analyses suggesting selection on specific SNPs.…”