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Evaluation of novel genomic markers for pedigree construction in an isolated population of Weddell Seals (Leptonychotes weddellii) at White Island, Antarctica

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Abstract

Pedigrees have a long history in classical genetics, agronomics, evolutionary ecology, and ex situ captive breeding. Use of molecular techniques has expanded the variety of species for which pedigrees can be constructed. However, molecular pedigrees almost exclusively consider microsatellite loci, despite advances in high-throughput sequencing allowing development of genomic marker sets in nearly any organism. Here we generate a novel set of genomic SNPs derived from ddRAD sequencing in two populations of Weddell seals (Leptonychotes weddellii) and describe the diversity and differentiation between them. We then compare and contrast parentage assignment rates and accuracy in one population that has been the subject of long-term monitoring. Specifically, we consider pedigrees constructed using two sets of markers (microsatellites and SNPs), two pedigree construction software (CERVUS than Sequoia), as well as varying the groupings of candidate parents (either all individuals simultaneously, only individuals born before a focal year, or only individuals known to have survived to a focal year). ddRAD sequencing returned between 1568 and 3240 loci depending on whether both populations were considered simultaneously or individually. Parentage assignment rates were always higher using CERVUS than Sequoia, with the latter at times either not assigning parentage or creating “inferred parents”. In all cases, “polarizing” the datasets (e.g., including year of birth) significantly improved assignments. This represents one of the first direct comparisons of pedigree construction using different markers in the same set of individuals, and the SNPs described here will be a resource for continued pedigree construction, and future research in Weddell seals.

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Fig. 1

adapted from: Polar Geospatial Center, 2018, “PGC Map Catalog”, https://doi.org/10.7910/DVN/6R8F7U, Harvard Dataverse, V1, Map 16: Victoria Land, August 16, 2021. The inset Antarctic map was obtained from: NOAA National Centers for Environmental Information (NCEI); International Bathymetric Chart of the Southern Ocean (IBCSO); General Bathymetric Chart of the Oceans (GEBCO)

Fig. 2

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Data Availability

Sequencing reads are archived on NCBI (Accessions: SAMN19069034-SAMN19069205). VCF files for whole dataset as well as each of the 10 random subsets are included as supplementary materials.

Code availability

Not applicable.

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Acknowledgements

Field work to collect tissue samples was supported by the National Science Foundation, Division of Polar Programs under grant numbers ANT‐1141326 and ANT‐1640481 to J. J. Rotella, R. A. Garrott and Donald B. Siniff and prior NSF Grants to R. A. Garrott, J. J. Rotella, D. B. Siniff and J. Ward Testa. We would like to thank students in Biol392/592 at the University of Alberta for assistance with preparing samples for sequencing, as well as the staff of the Molecular Biology Services Unit (MBSU) at the University of Alberta for conducting the sequencing.

Funding

Field work to collect tissue samples was supported by the National Science Foundation, Division of Polar Programs under grant numbers ANT‐1141326 and ANT‐1640481 to J. J. Rotella, R. A. Garrott and Donald B. Siniff and prior NSF Grants to R. A. Garrott, J. J. Rotella, D. B. Siniff and J. Ward Testa.

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Authors and Affiliations

  1. Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada

    Joshua M. Miller, Erin O. Campbell & Corey S. Davis

  2. Ecology Department, Montana State University, Bozeman, MT, USA

    Jay J. Rotella & Kaitlin R. Macdonald

  3. NOAA Fisheries, Alaska Fisheries Science Center, Seattle, WA, USA

    Thomas S. Gelatt

Authors
  1. Joshua M. Miller
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  2. Erin O. Campbell
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  3. Jay J. Rotella
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  4. Kaitlin R. Macdonald
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  5. Thomas S. Gelatt
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  6. Corey S. Davis
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Contributions

Conceptualization: JMM, CSD, Data curation: JMM, EOC, CSD, Formal analysis and investigation: JMM, EOC, CSD, Writing—original draft preparation: JMM, Writing—review and editing: EOC, TG, KRM, JJR CSD, Funding acquisition: JR, CSD, Resources: JR, KRM, CSD.

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Correspondence to Joshua M. Miller.

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All authors declare that they have no conflict of interest.

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All tissue samples were collected under Marine Mammal Protection Act Permits and Antarctic Conservation Act Permits and with methods approved by Montana State University’s Institutional Animal Care and Use Committee.

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Miller, J.M., Campbell, E.O., Rotella, J.J. et al. Evaluation of novel genomic markers for pedigree construction in an isolated population of Weddell Seals (Leptonychotes weddellii) at White Island, Antarctica. Conservation Genet Resour 14, 69–80 (2022). https://doi.org/10.1007/s12686-021-01237-0

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