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The use of museum skins for genomic analyses of temporal genetic diversity in wild species

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Abstract

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.

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Acknowledgements

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.

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Author notes

  1. Astrid Vik Stronen and Laura Iacolina contributed equally.

Authors and Affiliations

  1. Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark

    Astrid Vik Stronen, Laura Iacolina & Cino Pertoldi

  2. Biology Department, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000, Ljubljana, Slovenia

    Astrid Vik Stronen

  3. Aalborg Zoo, Mølleparkvej 63, 9000, Aalborg, Denmark

    Laura Iacolina & Cino Pertoldi

  4. Animal Genetics Laboratory, Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen, Böszörményi street 138, Debrecen, 4032, Hungary

    Szilvia Kusza

  5. Department of Zoology, Charles University, Viničná 7, 128 44, Prague, Czech Republic

    Pavel Hulva

  6. Department of Biology and Ecology, Charles University of Ostrava, Chittussiho 10, 710 00, Ostrava, Czech Republic

    Pavel Hulva

  7. Department of Zoology, Faculty of Biology, Ivan Franko National University of Lviv, Hrushevskyi Street, 4, Lviv, 79005, Ukraine

    Ihor Dykyy

  8. Natural Resources Institute Finland, Box 16, 96500, Rovaniemi, Finland

    Ilpo Kojola

  9. Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30, Gothenburg, Sweden

    Søren Faurby

  10. Gothenburg Global Biodiversity Centre, Box 461, 405 30, Gothenburg, Sweden

    Søren Faurby

Authors
  1. Astrid Vik Stronen
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  2. Laura Iacolina
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  3. Cino Pertoldi
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  4. Szilvia Kusza
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  5. Pavel Hulva
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  6. Ihor Dykyy
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  7. Ilpo Kojola
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  8. Søren Faurby
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Correspondence to Astrid Vik Stronen.

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Stronen, A.V., Iacolina, L., Pertoldi, C. et al. The use of museum skins for genomic analyses of temporal genetic diversity in wild species. Conservation Genet Resour 11, 499–503 (2019). https://doi.org/10.1007/s12686-018-1036-x

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