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 (SNPs) 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 may dominate selection

“…in line with the gene-based theory of conservation (Petit, 2004). In our study area, we found approximately 43% of individuals are hybrids (McFarlane, Hunter, et al, 2020; and in the present study, we have identified 60 SNPs with both an excessive negative α and excessive negative β estimate, indicative of introgressive alleles moving from the introduced sika into the native red deer faster than expected.…”

“…Hybrid deer tend towards an intermediate phenotype and thus are smaller, have smaller antlers, and are more likely to have the spots typical of sika than parental species red deer (Bartos et al, 1981). Initial hybridization may be constrained by the substantial size difference between species, but it is clear that at least some F1s and many backcrosses are fertile (Harrington, 1979;McFarlane, Hunter, et al, 2020;. While there is a trend from red deer in the north to sika in the south of Kintyre, the distribution of hybrids does not follow a cline, being instead concentrated in specific areas (Senn et al, 2010), and we have thus recently redefined this system as a "bivariate hybrid zone" (McFarlane, Hunter, et al, 2020;McFarlane & Pemberton, 2019;.…”

Genome-Scale Phylogenetic and Population Genetic Studies Provide Insight Into Introgression and Adaptive Evolution of Takifugu Species in East Asia

“…Conversely, hybridization is also considered as “genetic pollution,” which will accelerate the extinction of native species ( Simon et al, 2020 ). Moreover, human activities are impacting the genetic makeup of an increasing number of native species ( McFarlane et al, 2020 ). On the other hand, frequent gene exchange makes elucidating the lineage relationships between species complicated, and thus, it is difficult to identify their lineages and evolutionary history accurately through a few genes or the mitochondrial genome.…”

How long‐term studies reveal otherwise hidden phenomena: The Long‐Term Animal Research Seminar Series

“…Finally, Eryn McFarlane highlighted her work on anthropogenic hybridization between red deer ( Cervus elaphus ) and introduced sika deer ( Cervus nippon ). She found that a large proportion of the population were hybrid individuals and that locus‐specific introgression of alleles from sika into red deer could lead to the loss of endemic genetic variation 21 …”