With recent advances in sequencing technology, genomic data are changing how important conservation management decisions are made. Applications such as Close‐Kin Mark‐Recapture demand large amounts of data to estimate population size and structure, and their full potential can only be realised through ongoing improvements in genotyping strategies. Here we introduce DArTcap, a cost‐efficient method that combines DArTseq and sequence capture, and illustrate its use in a high resolution population analysis of Glyphis garricki, a rare, poorly known and threatened euryhaline shark. Clustering analyses and spatial distribution of kin pairs from four different regions across northern Australia and one in Papua New Guinea, representing its entire known range, revealed that each region hosts at least one distinct population. Further structuring is likely within Van Diemen Gulf, the region that included the most rivers sampled, suggesting additional population structuring would be found if other rivers were sampled. Coalescent analyses and spatially explicit modelling suggest that G. garricki experienced a recent range expansion during the opening of the Gulf of Carpentaria following the conclusion of the Last Glacial Maximum. The low migration rates between neighbouring populations of a species that is found only in restricted coastal and riverine habitats show the importance of managing each population separately, including careful monitoring of local and remote anthropogenic activities that may affect their environments. Overall we demonstrated how a carefully chosen SNP panel combined with DArTcap can provide highly accurate kinship inference and also support population structure and historical demography analyses, therefore maximising cost‐effectiveness.

A poster providing a summary of the Marine Biodiversity Hub research on the Northern River Shark.

A decade of Marine Biodiversity Hub Research led by Charles Darwin University shows the Northern River Shark to be more wide-ranging than previously thought, with new populations documented in several northern rivers. In 2010, the species was known from only 32 records in six rivers/estuaries; now more than 600 individuals have been recorded in 12 rivers/estuaries. Five genetically distinct populations were identified: four in Australia and one in Papua New Guinea. CSIRO close-kin mark-recapture analyses enabled the first population size estimates for one of these populations: the Northern Territory’s Van Diemen Gulf population size was estimated to be only ~600–1100 adults. The research provides monitoring and population assessment capability directly relevant to managing the recovery of the Northern River Shark and underpins environmental assessments under the EPBC Act in the context of northern Australia’s development.