Abstract
The survival of indigenous European wildcat (Felis silvestris silvestris) populations can be locally threatened by introgressive hybridization with free-ranging domestic cats. Identifying pure wildcats and investigating the ancestry of admixed individuals becomes thus a conservation priority. We analyzed 63k cat Single Nucleotide Polymorphisms (SNPs) with multivariate, Bayesian and gene-search tools to better evaluate admixture levels between domestic and wild cats collected in Europe, timing and ancestry proportions of their hybrids and backcrosses, and track the origin (wild or domestic) of the genomic blocks carried by admixed cats, also looking for possible deviations from neutrality in their inheritance patterns. Small domestic ancestry blocks were detected in the genomes of most admixed cats, which likely originated from hybridization events occurring from 6 to 22 generations in the past. We identified about 1,900 outlier coding genes with excess of wild or domestic ancestry compared to random expectations in the admixed individuals. More than 600 outlier genes were significantly enriched for Gene Ontology (GO) categories mainly related to social behavior, functional and metabolic adaptive processes (wild-like genes), involved in cognition and neural crest development (domestic-like genes), or associated with immune system functions and lipid metabolism (parental-like genes). These kinds of genomic ancestry analyses could be reliably applied to unravel the admixture dynamics in European wildcats, as well as in other hybridizing populations, in order to design more efficient conservation plans.
Highlights
Anthropogenic hybridization, the cross-breeding of genetically differentiated taxa due to human alterations of habitats and populations, is one of the major threats to the conservation of native plants and animals[1,2,3]
Quality-control and filtering procedures yielded a final sample set consisting of 80 presumed European wildcats (WC), 44 domestic cats (DC) and 22 known or presumed WC x DC admixed individuals (Supplementary Fig. S1), previously identified from STR assignment and multivariate analyses[20,21,27,37], successfully typed for 57,302 autosomal Single Nucleotide Polymorphisms (SNPs), hereafter referred to as the 57k SNP panel set (35,228 after linkage disequilibrium pruning, hereafter referred to as the 35k Linkage Disequilibrium (LD)-pruned SNP panel set)
More than 78% of the genetic variability of the sampled cats was explained by the first two components of a preliminary Principal Component Analysis (PCA) performed in SVS using the 57k SNP panel set (Fig. 1), which clearly distinguished domestic from wildcats
Summary
Anthropogenic hybridization, the cross-breeding of genetically differentiated taxa due to human alterations of habitats and populations, is one of the major threats to the conservation of native plants and animals[1,2,3].
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