Identification of Ancestry Informative Marker (AIM) Panels to Assess Hybridisation between Feral and Domestic Sheep

Abstract

Hybridisation of wild populations with their domestic counterparts can lead to the loss of wildtype genetic integrity, outbreeding depression, and loss of adaptive features. The Mediterranean island of Sardinia hosts one of the last extant autochthonous European mouflon (Ovis aries musimon) populations. Although conservation policies, including reintroduction plans, have been enforced to preserve Sardinian mouflon, crossbreeding with domestic sheep has been documented. We identified panels of single nucleotide polymorphisms (SNPs) that could act as ancestry informative markers able to assess admixture in feral x domestic sheep hybrids. The medium-density SNP array genotyping data of Sardinian mouflon and domestic sheep (O. aries aries) showing pure ancestry were used as references. We applied a two-step selection algorithm to this data consisting of preselection via Principal Component Analysis followed by a supervised machine learning classification method based on random forest to develop SNP panels of various sizes. We generated ancestry informative marker (AIM) panels and tested their ability to assess admixture in mouflon x domestic sheep hybrids both in simulated and real populations of known ancestry proportions. All the AIM panels recorded high correlations with the ancestry proportion computed using the full medium-density SNP array. The AIM panels proposed here may be used by conservation practitioners as diagnostic tools to exclude hybrids from reintroduction plans and improve conservation strategies for mouflon populations.

Genetic characterization and implications for conservation of the last autochthonous Mouflon population in Europe

“…We argue that these sub-populations should be considered as separate management units and preserved from contacts with genetically uncharacterized and known mouflon x sheep hybrid populations, such as the Mount Lerno population. Hybridization of wild populations with their domestic counterparts can lead to the loss of wildtype genetic integrity, outbreeding depression, and loss of adaptive features 53 – 55 . Morphological features are rarely informative to discriminate hybrids from pure mouflons especially when several events of backcrosses occurred 55 .…”

“…Hybridization of wild populations with their domestic counterparts can lead to the loss of wildtype genetic integrity, outbreeding depression, and loss of adaptive features 53 – 55 . Morphological features are rarely informative to discriminate hybrids from pure mouflons especially when several events of backcrosses occurred 55 . Conversely, molecular investigations have the power to identify mixed ancestry components even with reduced panels of selected ancestry informative markers and are the only diagnostic tools able to effectively identify hybrids before carrying out restocking actions 26 , 55 .…”

“…Morphological features are rarely informative to discriminate hybrids from pure mouflons especially when several events of backcrosses occurred 55 . Conversely, molecular investigations have the power to identify mixed ancestry components even with reduced panels of selected ancestry informative markers and are the only diagnostic tools able to effectively identify hybrids before carrying out restocking actions 26 , 55 . Our study prompts for initiatives to restore the habitat connectivity between Montes Forest and Mount Tonneri and promotes controlled inter-population exchange in order to improve the overall genetic diversity and counteract the effects of population fragmentation 56 , 57 .…”

Current and Forthcoming Approaches for Benchmarking Genetic and Genomic Diversity

“…The European mouflon (Ovis aries musimon), the wild relative of the domestic sheep, became extinct from mainland Europe by the Neolithic, but remnants from the first wave of sheep domestication that brought them to the Mediterranean isles of Corsica and Sardinia established feral populations (Chessa et al, 2009). Now considered "historically autochthonous, " the species is protected by regional laws after almost becoming extinct due to intense hunting and erosion of its habitat (Somenzi et al, 2020). There has also been evidence of extensive hybridization with domestic sheep since Roman times, with confirmed adaptive introgression of loci related to immunity mechanisms from mouflon to sheep, but not the other way round (Barbato et al, 2017).…”

“…Yet, as individuals are being relocated within the islands and to mainland Europe, it would be important for future management to know the ancestry of individuals. Somenzi et al (2020) used a machine learning procedure to screen more than 50,000 SNPs from non-admixed mouflons and sheep form Sardinia, and from confirmed admixed individuals, generating panels of reduced numbers of SNPs which could be used as Ancestry Informative Markers (AIMs). These AIMs represented fast, low-cost tools to identify the ancestry of a given individual, therefore the study provided both a tool to contribute to the conservation of this species, and also a new methodology that can be applied to the conservation of other wildlife in risk of hybridization with domestic species.…”