Increased genetic marker density reveals high levels of admixture between red deer and introduced Japanese sika in Kintyre, Scotland

Abstract

Hybridization is a natural process at species range boundaries, but increasing numbers of species are hybridizing due to direct or indirect human activities. In such cases of anthropogenic hybridization, subsequent introgression can threaten the survival of native species. To date many such systems have been studied with too few genetic markers to assess the level of threat resulting from advanced backcrossing. Here we use 44,999 single nucleotide polymorphisms and the ADMIXTURE program to study two areas of Scotland where a panel of 22 diagnostic microsatellites previously identified introgression between native red deer (Cervus elaphus) and introduced Japanese sika (Cervus nippon). In Kintyre we reclassify 26% of deer from the pure species categories to the hybrid category whereas in the NW Highlands we only reclassify 2%. As expected, the reclassified individuals are mostly advanced backcrosses. We also investigate the ability of marker panels selected on different posterior allele frequency criteria to find hybrids assigned by the full marker set, and show that in our data, ancestry informative markers (i.e. those that are highly differentiated between the species, but not fixed) are better than diagnostic markers (those markers that are fixed between the species) because they are more evenly distributed in the genome. Diagnostic loci are concentrated on the X chromosome to the detriment of autosomal coverage.

Locus-specific introgression in young hybrid swarms: drift dominates selection

“…We scored genotypes using GenomeStudio using the clusters from Huisman et al (2016), and clustered SNPs manually if they could not be resolved in these clusters (McFarlane et al 2020). All quality control was done in PLINK (Purcell et al 2007).…”

“…Of these 629 SNPs are diagnostic and an additional 3205 SNPs are ancestry informative markers (hereafter together as AIMs) in Kintyre. These AIMs were determined based on having extreme allele frequency differences where the differences in frequency between the two populations was more than 0.95 (McFarlane et al 2020). While one pool of 12 sika from Kintyre were whole genome sequenced for the development of this SNP chip, the focus was on polymorphic SNPs in red deer on Rum (Brauning et al 2015).…”

“…We used the program bgc (Gompert We assigned individuals to three different populations based on their ADMIXTURE estimates and whether the credible intervals from ADMIXTURE overlapped 0 (sika) or (red deer). If an individual's credible intervals overlapped neither 0 or 1 it was considered a hybrid (McFarlane et al 2020). Red deer and sika were each assigned to parental populations, and all admixed individuals were put into a 'hybrid population'.…”

“…Before genomic regions can be considered candidates to be responding to selection, careful consideration of expections due to non-selective forces must be undertaken (Gompert and were introduced to Scotland in the late 19 th century, and have since hybridized with the red deer (Ratcliffe 1987). On the Kintyre peninsula, Argyll, more than 40% of sampled phenotypic red deer and sika individuals are hybrids according to 50 000 SNP markers, with the majority being the result of multiple generations of backcrossing (McFarlane et al 2020).…”

Genetic tools in the management of invasive mammals: recent trends and future perspectives

“…A later study used 61000 SNPs to infer that 62% of Eurasian wolves Canis lupus had some level of admixture with domestic dogs Canis familiaris (Pilot et al ). In a well‐studied hybrid zone between sika deer and red deer in Kintyre, Scotland, an increased panel of 45000 SNPs reclassified 26% of individuals as hybrids that had originally been assigned to one of the parental species from a previous study based on 22 microsatellites (McFarlane et al ). In attempting to preserve Scottish wildcats from extensive introgression with domestic/feral cats, only wildcat individuals with both high genetic scores (using a SNP panel) and high phenotype scores of wildcat ‘purity’ are selected for the captive breeding and reintroduction programmes (Senn et al ).…”