Bayesian analyses of admixture in wild and domestic cats (Felis silvestris) using linked microsatellite loci

Abstract

Methods recently developed to infer population structure and admixture mostly use individual genotypes described by unlinked neutral markers. However, Hardy-Weinberg and linkage disequilibria among independent markers decline rapidly with admixture time, and the admixture signals could be lost in a few generations. In this study, we aimed to describe genetic admixture in 182 European wild and domestic cats (Felis silvestris), which hybridize sporadically in Italy and extensively in Hungary. Cats were genotyped at 27 microsatellites, including 21 linked loci mapping on five distinct feline linkage groups. Genotypes were analysed with structure 2.1, a Bayesian procedure designed to model admixture linkage disequilibrium, which promises to assess efficiently older admixture events using tightly linked markers. Results showed that domestic and wild cats sampled in Italy were split into two distinct clusters with average proportions of membership Q > 0.90, congruent with prior morphological identifications. In contrast, free-living cats sampled in Hungary were assigned partly to the domestic and the wild cat clusters, with Q < 0.50. Admixture analyses of individual genotypes identified, respectively, 5/61 (8%), and 16-20/65 (25-31%) hybrids among the Italian wildcats and Hungarian free-living cats. Similar results were obtained in the past using unlinked loci, although the new linked markers identified additional admixed wildcats in Italy. Linkage analyses confirm that hybridization is limited in Italian, but widespread in Hungarian wildcats, a population that is threatened by cross-breeding with free-ranging domestic cats. The total panel of 27 loci performed better than the linked loci alone in the identification of domestic and known hybrid cats, suggesting that a large number of linked plus unlinked markers can improve the results of admixture analyses. Inferred recombination events led to identify the population of origin of chromosomal segments, suggesting that admixture mapping experiments can be designed also in wild populations.

European wildcat populations are subdivided into five main biogeographic groups: consequences of Pleistocene climate changes or recent anthropogenic fragmentation?

“…2003; Lecis et al. 2006). At K varying from 3 to 5, the European wildcat populations were gradually assigned to distinct clusters (Fig.…”

“…2003; Lecis et al. 2006; Oliveira et al. 2008b), we confirmed the domestic × wildcat admixed composition of wild‐living cats in Scotland and Hungary.…”

Molecular detection of hybridization between sympatric kangaroo species in south-eastern Australia

“…Although the evolutionary consequences of hybridization can be deleterious, causing sterility or reduced fertility of offspring or resulting in a loss of genetic integrity and homogenization of gene pools (Rhymer and Simberloff, 1996), in some circumstances it may be beneficial by allowing the incorporation of novel genetic diversity and promoting adaptation to new environments or even speciation (Dowling and Secor, 1997;Martinsen et al, 2001;Salzburger et al, 2002;Smith et al, 2003). Although initially considered rare and usually deleterious among mammals, hybridization has been identified, to varying degrees, in various wild eutherian mammal taxa including cetaceans (Willis et al, 2004), seals (Lancaster et al, 2006;Kingston and Gwilliam, 2007), canids (Vila et al, 2003;Verardi et al, 2006), felids (Pierpaoli et al, 2003;Lecis et al, 2006), leporids (Thulin et al, 2006;MeloFerreira et al, 2007), martens (Kyle et al, 2003) and squirrels (Ermakov et al, 2006;Spiridonova et al, 2006). However, despite many macropodid marsupial species readily hybridizing in captivity (Close and Lowry, 1990), relatively few instances of natural hybridization have been reported in marsupials, with the exception of several parapatric rock-wallaby species (Briscoe et al, 1982;Eldridge et al, 1991;Eldridge and Close, 1992;Bee and Close, 1993).…”

Toward a genome-wide approach for detecting hybrids: informative SNPs to detect introgression between domestic cats and European wildcats (Felis silvestris)

“…The survival and conservation of indigenous populations of the European wildcat might be locally threatened by introgressive hybridization with feral domestic cats (Felis silvestris catus). Over the last decade, the genotyping of highly polymorphic molecular markers (specifically microsatellites, short tandem repeats) and partial mitochondrial DNA sequences, combined with new Bayesian statistical tools, have radically improved the knowledge on wildcat population genetics and admixture with the domestic cat (for example, Beaumont et al, 2001;Randi et al, 2001;Pierpaoli et al, 2003;Kitchener et al, 2005;Lecis et al, 2006;Oliveira et al, 2008a, b;O'Brien et al, 2009;Hertwig et al, 2009;Eckert et al, 2010;Mattucci et al, 2013). Wildcats have been domesticated from African wildcat (F.s.…”