Abstract
We deployed admixture mapping on a sample of 386 deer from a hybrid swarm between native red deer (Cervus elaphus) and introduced Japanese sika (Cervus nippon) sampled in Kintyre, Scotland to search for quantitative trait loci (QTLs) underpinning phenotypic differences between the species. These two species are highly diverged genetically [Fst between pure species, based on 50K single nucleotide polymorphism (SNPs) = 0.532] and phenotypically: pure red have on average twice the carcass mass of pure sika in our sample (38.7 kg vs 19.1 kg). After controlling for sex, age, and population genetic structure, we found 10 autosomal genomic locations with QTL for carcass mass. Effect sizes ranged from 0.191 to 1.839 kg and as expected, in all cases the allele derived from sika conferred lower carcass mass. The sika population was fixed for all small carcass mass alleles, whereas the red deer population was typically polymorphic. GO term analysis of genes lying in the QTL regions are associated with oxygen transport. Although body mass is a likely target of selection, none of the SNPs marking QTL are introgressing faster or slower than expected in either direction.
Highlights
A major goal of evolutionary genetics is to understand the relationship between phenotypic and genetic variation
The mean number of single nucleotide polymorphism (SNPs) included in the sparse effects was 58.1 (6–179), but only 9 (10 in run C, Supplementary Table S1) SNPs had a posterior inclusion probability (PIP) above the threshold of 0.1
We have identified 10 autosomal SNPs that are related to carcass mass, which are associated with 7 chromosomes, 45 genes, and 297 GO: Molecular Function (GO) terms
Summary
A major goal of evolutionary genetics is to understand the relationship between phenotypic and genetic variation. In the context of hybridization, it is informative to understand the genetic architecture of the phenotypic traits that differ between hybridizing species. This is relevant when human influences lead to increased hybridization (Grabenstein and Taylor 2018) and there is the potential for extinction via hybridization to decrease biodiversity (Rhymer and Simberloff 1996; Brennan et al 2015; Todesco et al 2016). Genetic mapping in hybrid zones is powerful because of the opportunity to use admixture mapping on recombinant individuals (Rieseberg and Buerkle 2002). Natural hybrid zones can be extremely powerful for detecting QTLs when both the phenotype and genotypes are divergent between the two parental populations and when there are individuals sampled across the ancestry and phenotype spectrum (Buerkle and Lexer 2008)
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