Standard Presentation Australian Marine Sciences Association 2026 Conference

Dugong Population Genomics in Australia (140002)

Eva Paulus 1 , Ira Cooke 2 3 , Holly Raudino 4 , Ana Sequeira 5 6 , Malgana Sea Rangers 7 , Kimberley Indigenous Saltwater Advisory Group 8 , Rachel Groom 9 10 11 , li-Anthawirriyarra Sea Rangers 12 , Wellesley Islands Land & Sea Rangers 13 , Gangalidda Garawa Rangers 14 , Normanton Rangers 14 , Helen Penrose 1 , Damien Stanioch 15 , Helene Marsh 1 , Jan Strugnell 1 , Christophe Cleguer 16
  1. College of Science and Engineering, James Cook University, Townsville, QLD, Australia
  2. Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
  3. College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia
  4. Marine Science Program, Department of Biodiversity, Conservation and Attractions, Perth, WA, Australia
  5. School of Biological Science and UWA Oceans Institute, University of Western Australia, Crawley, WA, Australia
  6. Australian National University, Canberra, ACT, Australia
  7. Malgana Aboriginal Corporation, Denham, WA, Australia
  8. Kimberley Indigenous Saltwater Advisory Group, Broome, WA, Australia
  9. Northern Institute, Darwin, NT, Australia
  10. ARC Centre of Excellence for Indigenous and Environmental Histories and Futures, James Cook University, Cairns, QLD, Australia
  11. Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
  12. Li-Anthawirriyarra Sea Rangers Unit, Borroloola, NT, Australia
  13. Wellesley Islands Land Sea Social Economic Development Pty Ltd, Gununa, QLD, Australia
  14. Carpentaria Land Council Aboriginal Corporation, Cairns, QLD, Australia
  15. Darwin River Natural History Museum, Darwin, NT, Australia
  16. Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER), James Cook University, Townsville, QLD, Australia

Australia supports the world’s largest remaining dugong (Dugong dugon) population, yet continental-scale connectivity and demographic history remain poorly resolved. Here, we present the first continent-wide population genomic assessment of dugongs using whole-genome sequencing from 210 individuals. We analysed samples collected across the entire Australian range to investigate population structure, inbreeding, and historical demography.

We identified three distinct genetic populations, likely shaped by historical sea-level fluctuations and changes in seagrass habitat availability. Demographic reconstructions indicate that dugongs were restricted to small refugia during the Last Glacial Maximum (20,000 years ago), followed by post-glacial population expansion.

Genome-wide patterns of diversity suggest that Australian dugong populations remain relatively healthy overall, although elevated runs of homozygosity indicate increased inbreeding at the edges of their range. Admixture analyses further highlight varying levels of connectivity among regions, reflecting both historical isolation and contemporary gene flow.

This study offers important insights into how past environmental change has shaped present-day dugong populations. These findings redefine dugong management units at a continental scale, providing a strong evidence base to inform spatial management and the protection of a seagrass-dependent species vulnerable to accelerating coastal change and anthropogenic pressures.