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

McFarlane, S. Eryn LU ; Hunter, Darren C. ; Senn, Helen V. ; Smith, Stephanie L. ; Holland, Rebecca ; Huisman, Jisca and Pemberton, Josephine M. (2019) In Evolutionary Applications
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... (More)

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.

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author
organization
publishing date
type
Contribution to journal
publication status
epub
subject
keywords
admixture, ancestry informative markers, anthropogenic hybridization, C. nippon, Cervus elaphus, diagnostic markers, genomics, introgression
in
Evolutionary Applications
publisher
Wiley-Blackwell
external identifiers
  • scopus:85074752494
ISSN
1752-4563
DOI
10.1111/eva.12880
language
English
LU publication?
yes
id
a0603fca-7bb1-4b43-93f9-8486f471beea
date added to LUP
2019-12-06 11:05:50
date last changed
2020-01-13 02:34:46
@article{a0603fca-7bb1-4b43-93f9-8486f471beea,
  abstract     = {<p>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.</p>},
  author       = {McFarlane, S. Eryn and Hunter, Darren C. and Senn, Helen V. and Smith, Stephanie L. and Holland, Rebecca and Huisman, Jisca and Pemberton, Josephine M.},
  issn         = {1752-4563},
  language     = {eng},
  publisher    = {Wiley-Blackwell},
  series       = {Evolutionary Applications},
  title        = {Increased genetic marker density reveals high levels of admixture between red deer and introduced Japanese sika in Kintyre, Scotland},
  url          = {http://dx.doi.org/10.1111/eva.12880},
  doi          = {10.1111/eva.12880},
  year         = {2019},
}