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Enabling pinniped conservation by means of non-invasive genetic population analysis

Conservation Genetics Resources volume 13, pages 131–142 (2021)Cite this article

Abstract

Conservation and management of protected species, particularly of elusive species such as pinnipeds, is hampered by knowledge gaps. In the case of studies using genetic data these are often attributed to a lack of representative samples. Therefore, there is a pressing need for the development of minimally invasive sampling protocols suitable for genetic analyses of pinnipeds. The present study evaluated the applicability of various protocols for the collection and processing of samples from harbour seals (Phoca vitulina) and grey seals (Halichoerus grypus), encompassing seven source sample types (blood, skin, hair (plucked/moulted), urine, buccal swabs, scat) and three different extraction methods. Protocols were designed for minimally invasive sampling, but also to evaluate differences in their performance based on cost and time of execution in comparison to traditional sampling approaches. The performance of each protocol was measured following successful DNA isolation, molecular sex determination and sequencing of a mitochondrial DNA fragment (control region). Protocols using plucked hair, urine and buccal swab samples proved effective for collection from individuals in captivity, whereas scat was most applicable for non-invasive sampling in the wild. Furthermore, following a pilot study on scat samples, DNA was found to be viable for genetic analysis after exposure to ambient conditions for up to four weeks. This study provides a useful assessment of the suitability of various minimal and non-invasively collected samples for DNA isolation, amplification and mitochondrial sequencing, enabling the effective design of future sampling strategies and a significant increase of samples available for genetic analysis of pinnipeds.

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Data availability

Data are available via the Electronic Supplementary Material.

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All R code can be provided upon request by contacting the corresponding author.

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Acknowledgements

The authors wish to thank Seal Rescue Ireland, DAERA, Seehundstation Norddeich and Seehundstation Friedrichskoog e.V. for providing samples, Proinsias Hernon for assistance during fieldwork and Javier Burgoa Cardas for assistance with DNA extractions. Prototypes for PB-200 were made available by DNA Genotek (Ottawa, Canada). Our thanks also go to the MFRC/GMIT staff and NPWS staff/rangers for their support.

Funding

Financial support was received from Galway-Mayo Institute of Technology (Research & Innovation Strategic Endowment (RISE) scholarship), the Irish National Parks and Wildlife Service (Grant REF SPU G07-2017) and the Irish Department of Housing, Local Government and Heritage.

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Authors and Affiliations

  1. Marine and Freshwater Research Centre, Department of Natural Science, School of Science & Computing, Galway-Mayo Institute of Technology, Dublin Road, Galway, H91 T8NW, Ireland

    Kristina Steinmetz, Sinéad Murphy & Luca Mirimin

  2. Marine Environment, Water Division, Department of Housing, Local Government and Heritage, 1A, South Mall, Cork, Ireland

    Oliver Ó Cadhla

  3. University of Exeter, Penryn, Cornwall, TR10 9FE, United Kingdom

    James Barnett

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  1. Kristina Steinmetz
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  2. Sinéad Murphy
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  3. Oliver Ó Cadhla
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  5. Luca Mirimin
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Correspondence to Kristina Steinmetz.

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Licences for sampling in the wild were obtained from the Irish National Parks and Wildlife Service (C151/16, C32/17, C33/17, C83/17, C121/17, C59/18, C86/18, C179/18).

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Steinmetz, K., Murphy, S., Ó Cadhla, O. et al. Enabling pinniped conservation by means of non-invasive genetic population analysis. Conservation Genet Resour 13, 131–142 (2021). https://doi.org/10.1007/s12686-020-01182-4

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  • DOI: https://doi.org/10.1007/s12686-020-01182-4

Keywords

  • Non-invasive
  • Population genetics
  • Grey seal
  • Harbour seal