Development of SNP markers identifying European wildcats, domestic cats, and their admixed progeny

Abstract

Introgression can be an important evolutionary force but it can also lead to species extinction and as such is a crucial issue for species conservation. However, introgression is difficult to detect, morphologically as well as genetically. Hybridization with domestic cats (Felis silvestris catus) is a major concern for the conservation of European wildcats (Felis s. silvestris). The available morphologic and genetic markers for the two Felis subspecies are not sufficient to reliably detect hybrids beyond first generation. Here we present a single nucleotide polymorphism (SNP) based approach that allows the identification of introgressed individuals. Using high-throughput sequencing of reduced representation libraries we developed a diagnostic marker set containing 48 SNPs (Fst > 0.8) which allows the identification of wildcats, domestic cats, their hybrids and backcrosses. This allows assessing introgression rate in natural wildcat populations and is key for a better understanding of hybridization processes.

Assessing patterns of hybridization between North Atlantic eels using diagnostic single-nucleotide polymorphisms

“…Simulations showed a high discriminatory power of the markers, as we were able to correctly identify 100% of F1 hybrids and 99% of backcrosses with pure parental species. Our results confirm that SNPs are effective markers to study hybridization and detect introgression (Hohenlohe et al, , 2013Amish et al, 2012;Nussberger et al, 2013). Because of their relatively low mutation rate and consequently low number of alleles, SNPs are more likely to be diagnostic loci than highly polymorphic markers such as microsatellites that present a higher probability of allele sharing between related species due to homoplasy (Balloux and Goudet, 2002).…”

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

“…Similar studies in other species have also been conducted, such as for European bison (Bison bonasus; Tokarska et al, 2009), Atlantic salmon (Salmo salar; Glover et al, 2010), red fox (Vulpes vulpes; Sacks and Louie, 2008) and chicken breeds (Gärke et al, 2012). Recently, Nussberger et al (2013) developed a diagnostic marker set containing 48 SNPs that allows the identification of wildcats, domestic cats, their hybrids and backcrosses, and have demonstrated their accurate genotyping in single hairs (Nussberger et al, 2014). However, these authors used a restricted set of reference Toward a genome-wide approach for detecting hybrids R Oliveira et al samples, and the choice of highly differentiated traits/loci from a small panel of parental individuals has been considered to possibly overlook population differentiation (Brumfield et al, 2003;Schlötterer, 2004;Morin et al, 2009).…”

“…Further genotyping of additional populations should help to validate the selected SNPs. In addition, the possible combination of the SNPs described in our study with the ones developed by Nussberger et al (2013) can eventually maximize the hybrid detection. Nevertheless, the new throughput technologies under development for domestic cats will soon allow the evaluation of the entire genome of F. silvestris species, supporting the identification of more diagnostic loci and potentially indicating areas of the genome involved with domestication (Montague et al, 2014;Tamazian et al, 2014).…”

“…Specifically, the recent sequencing of the domestic cat genome (Pontius et al, 2007;Mullikin et al, 2010;Montague et al, 2014;Tamazian et al, 2014), which has included SNP discovery in the African wildcat subspecies (Felis silvestris cafra), provides useful reference data for the discovery of new nuclear markers for assessing the introgression of domestic cat genes in the wild counterparts. Nussberger et al (2013) recently described a set of 48 nuclear SNPs for identifying European wildcats, domestic cats and their admixed progeny. However, this work used a limited number of SNPs and reference samples solely from Switzerland.…”

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

“…The use of more informative DNA markers (e.g., ancestral informative SNPs; Nussberger et al. 2013; Oliveira et al. 2015) or variation at domestication genes identified through entire genome analyses (Montague et al.…”