The use of museum skins for genomic analyses of temporal genetic diversity in wild species
Analyses of museum specimens can help illuminate temporal changes in wildlife genetics and distributions, and the objective of our study was to evaluate the suitability of skin samples from the past century for genomic analyses. We examined two European species with extensive genomic resources and existing data: the wild boar (Sus scrofa) and the wolf (Canis lupus). Populations of both species declined during the twentieth century, followed by a strong recovery. Moreover, Carpathian Mountain wolves are genetically divergent from Northern European lowland wolves, and their evolutionary history is incompletely understood. We analysed genetic variation from skins of 14 European and Near Eastern wild boars (1903–1948) and 18 Carpathian and Northern wolves (1938–1998). Samples were genotyped in duplicates with standard Illumina single nucleotide polymorphism (SNP) arrays (wild boar 60 K and wolves 170 K), and we retained SNPs with a genotyping rate of > 90%. We obtained a final set of 1595 SNPs for six wild boars (genotyping rate 0.99) and 1806 SNPs for 18 wolves (genotyping rate 0.96). We merged the best performing duplicate with modern data and calculated polymorphism (P), observed (HO) and expected (HE) heterozygosity per population. Our findings underline the difficulties in obtaining quality genomic profiles from museum skins, though a limited number of SNPs provided insights for future research. Wild boars exhibited lower polymorphism in historical than modern samples. In contrast, patterns in wolves appeared spatial rather than temporal, with higher P, HO and HE observed in Carpathian than Northern wolves across historical and modern samples.
KeywordsCanis lupus Historic samples Museum collections Single nucleotide polymorphism Sus scrofa
We thank Marcel Eras, Bendegúz Mihalik, Massimo Scandura, Frank Zachos, and staff from the Mammal Research Institute Polish Academy of Sciences. We gratefully acknowledge the assistance of the National History Museums in Vienna and Hungary, the University of Sassari, the Finnish Museum of Natural History, the National Museum Prague and Silesian Museum Opava of the Czech Republic, and the Slovak National Museum in obtaining skin samples and information. AVS and SF were supported by the Danish Natural Science Research Council (AVS #1337-00007, SF #4090-00227), LI by the European Union’s Horizon 2020 (MCSA-IF #656697). The work was supported by the Aalborg Zoo Conservation Foundation.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
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