Unveiling the Genetic Structure of New Caledonian Dugongs Using a Multiscale Genetic Approach: Conservation Challenges for an Isolated Population

Coastal marine megafauna faces increasing threats from habitat degradation, climate change, and human activities, making conservation efforts crucial for their survival. The New Caledonian dugong population was reclassified as Endangered on the IUCN Red List in 2021, following research on its abundance and genetic diversity. With fewer than 800 individuals estimated between 2008 and 2012, urgent conservation measures are needed to prevent further decline. Modern genetic tools provide critical insights into spatial genetic differentiation and gene flow across New Caledonia's extensive lagoon habitats. In this study, we analyzed 66 skin samples from live and stranded dugongs collected between 2003 and 2023, using a multiscale genetic approach. We examined mitochondrial DNA control region sequences at the Indo-Pacific level, 13 microsatellite loci to compare New Caledonian and Australian populations, and 2499 single nucleotide polymorphisms (SNPs) to assess fine-scale structure within New Caledonia. Our findings confirm that the New Caledonian dugong population has extremely low genetic diversity and is highly differentiated from its Australian counterpart. The effective population size (<i>N</i> _<i>e</i> ) was critically low, ranging between 95 and 160 individuals, depending on the analytical approach. Within New Caledonia, we identified two genetically distinct clusters along the west coast, north and south of Bourail, a division consistent with previous satellite tracking studies showing no movement across this natural boundary. These findings highlight the urgency of conservation action and suggest that the population's isolation and low genetic diversity may warrant an upgrade to Critically Endangered status.