Genomic analyses of gray wolf (Canis lupus) populations in Eurasia

Abstract

Wide-ranging species such as the gray wolf (Canis lupus) can disperse several hundred kilometers, although recent studies demonstrate that their population structure at times reflect physical, environmental, or ecological boundaries. For certain populations this structuring represents long-standing isolation and genetic drift, whereas for others there does not appear to be obvious barriers to dispersal. In Eurasia, especially in the western part, north-south gene flow may be more limited than that occurring east-west because of physical features including mountain chains and water. We examined gray wolf genomic profiles from across Eurasia to determine broad-scale population genetic structure. We expected to find stronger north-south than east-west structuring, and a higher degree of isolation and genetic drift in peninsular populations. Methods: The analyses included over 700 wolves genotyped on the Illumina CanineHD BeadChip with more than 170,000 single nucleotide polymorphism (SNP) loci, encompassing previous and recently genotyped profiles. These comprise samples from central and eastern Russia and the Caucasus, and in Europe we sampled wolves from the Dinaric-Balkans, Italy, and Iberia in the south to Scandinavia in the north. After merging data sets, we filtered for individual and SNP genotyping quality, minor allele frequency, and loci in Hardy-Weinberg and linkage disequilibrium. We examined population genetic structure by comparing results from principal component analyses and maximum-likelihood methods, assessed population differentiation, and evaluated the relationship among populations with TreeMix. Results: We detected population clusters in central and eastern Russia, Caucasus, Iberia, Italy, the Carpathian Mountains, the Dinaric-Balkan region, northcentral Europe, and Scandinavia. Italy emerged as the most divergent population and, in general, our findings indicate higher east-west than north-south gene flow. Finer-scale genetic structure across relatively short geographic distances was observed in the Carpathian Mountains versus neighbouring regions north and south, between Dinaric and Italian wolves, and between Dinaric and Balkan wolves. Population differentiation results reflected protracted isolation and genetic drift in the Iberian, Italian, and Scandinavian wolves, which contrasted with limited genetic differentiation in other areas, particularly between wolves in central and eastern Russia. The TreeMix results also reflected the isolation and genetic drift observed in peninsular populations, especially for Scandinavia and Italy.