Patterns of genomic variation in three species of Alpine grouse: conservation and management using SNPs

In light of rapidly decreasing levels of biodiversity, conservation efforts towards the sustainable management of species and their ecosystems is becoming increasingly relevant. The black grouse (Lyrurus tetrix), rock ptarmigan (Lagopus muta) and western capercaillie (Tetrao urogallus) are listed as ‘Least Concern’ by the International Union for Conservation of Nature. However, at the southern edges of their ranges, these species are often more fragmented and some populations are classified as threatened. Importantly for conservation actions, the genetic ‘health’ of these elusive species in these regions is poorly understood. Here we use a multispecies, multi-marker approach to identify common factors affecting genetic patterns. Samples were collected predominantly from the Italian Alps over a 20 year period. Data from traditional markers (mitochondrial DNA and microsatellites) as well as genome-wide Single Nucleotide Polymorphisms (SNPs) were generated and compared. SNPs were typed using the Genotyping-by-Sequencing technique to investigate their suitability for this type of conservation application, and applied for the first time for these tetraonids. The black grouse was characterized by a strong pattern of isolation by distance across the Italian Alps, and the results also suggest that there may a barrier to their movement in a heavily urbanized Lombardy Region. The ptarmigan results suggest that this species forms a continuous panmictic population across the study area, confirming that dispersal distances for this species have been underestimated in the Alps. Unexpectedly given its low density and previously estimated range of movement, gene flow is high among capercaillie populations in Trentino-Alto Adige. No genetically isolated populations were identified for any of the species in the Italian Alps; in addition, genetic variability of the black grouse did not decrease over the study period, suggesting that current management practices (including the hunting of both sexes of ptarmigan and male black grouse) are suitable for maintaining current levels of genetic diversity. In general, the SNP results produced more detailed geographical patterns for the data (although they did not contrast with STR results). Therefore, given that the technique was fairly successful even for non-invasive samples, the periodic use of these genomic markers is recommended for the study of populations across all three species ranges, to aid future conservation efforts.