Department of Biology

Aarhus University Seal

Eva Egelyng Sigsgaard

Individual haplotyping of whale sharks from seawater environmental DNA

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

  • Laurence Dugal, Australian Institute of Marine Science, University of Western Australia, Australia
  • Luke Thomas, Australian Institute of Marine Science, University of Western Australia, Australia
  • Mads Reinholdt Jensen
  • Eva Egelyng Sigsgaard
  • Tiffany Simpson, Curtin University of Technology, Australia
  • Simon Jarman, University of Western Australia, Australia
  • Philip Francis Thomsen
  • Mark Meekan, Australian Institute of Marine Science, University of Western Australia, Australia

Population genetic data can provide valuable information on the demography of a species. For rare and elusive marine megafauna, samples for generating the data are traditionally obtained from tissue biopsies, which can be logistically difficult and expensive to collect and require invasive sampling techniques. Analysis of environmental DNA (eDNA) offers an alternative, minimally invasive approach to provide important genetic information. Although eDNA approaches have been studied extensively for species detection and biodiversity monitoring in metabarcoding studies, the potential for the technique to address population-level questions remains largely unexplored. Here, we applied “eDNA haplotyping” to obtain estimates of the intraspecific genetic diversity of a whale shark (Rhincodon typus) aggregation at Ningaloo reef, Australia. Over 2 weeks, we collected seawater samples directly behind individual sharks prior to taking a tissue biopsy sample from the same animal. Our data showed a 100% match between mtDNA sequences recovered in the eDNA and tissue sample for all 28 individuals sampled. In the seawater samples, >97% of all reads were assigned to six dominant haplotypes, and a clear dominant signal (~99% of sample reads) was recovered in each sample. Our study demonstrates accurate individual-level haplotyping from seawater eDNA. When DNA from one individual clearly dominates each eDNA sample, it provides many of the same opportunities for population genetic analyses as a tissue sample, potentially removing the need for tissue sampling. Our results show that eDNA approaches for population-level analyses have the potential to supply critical demographic data for the conservation and management of marine megafauna.

Original languageEnglish
JournalMolecular Ecology Resources
Pages (from-to)56-65
Number of pages10
Publication statusPublished - Jan 2022

    Research areas

  • eDNA, elasmobranchs, environmental DNA, haplotype, intraspecific diversity, mtDNA, population genetics, PATTERNS, GENETIC-STRUCTURE, RHINCODON-TYPUS, R PACKAGE, SOUTH, LARGEST FISH, Haplotypes, DNA, Environmental, Animals, Sharks/genetics, Australia, Seawater

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