Determining the genetic diversity and differentiation among populations is a critical element of conservation biology, but for many aquatic, data-deficient species with small population sizes, this is not possible. Closely related species may therefore provide a model. For the first time, using over 4000 single-nucleotide polymorphism loci, we characterise the population genetic diversity and structure of one of the world’s rarest marine fish, the spotted handfish (Brachionichthys hirsutus), a species which is also a member of the most threatened marine bony fish family (Brachionichthyidae). Fin clips were taken from 170 live spotted handfish across seven disjunct sites within the only known estuary (in Tasmania, Australia) where multiple populations of the species are found. Spatially discrete populations clustered into three genetic groupings and a significant variance in allele frequencies among populations (overall F_ST = 0.043), even at the small scale of the estuary, was observed. Furthermore, low contemporary migration rate estimates suggest low genetic homogeneity between locations. Because of the low genetic connectivity, population clusters of spotted handfish within the estuary should be considered as separate conservation management units. This insight should be considered for management and conservation strategies of other data-deficient and threatened species in the family.

This technical report is aimed at providing policy makers, fisheries managers, and conservation agencies with information on the population structure of a threatened shark of northern Australia, the Speartooth Shark. The identification of population boundaries is key to determining the appropriate spatial scale for the conservation and management of wildlife. The major river drainages (Wenlock River, Alligator Rivers, Adelaide River) comprising the species’ known range have been shown previously to be distinct genetic populations. Recent surveys have revealed a wider range than previously documented with newly-identified populations in the Daly River of the Northern Territory and the Ord River of Western Australia as well as the species’ rediscovery in Papua New Guinea (PNG). Here we aimed to test the hypothesis that the newly identified rivers (Daly and Ord Rivers), along with the Kikori River in southern PNG, also represent distinct populations given their isolation from known populations. The analysis revealed that the Ord and Kikori Rivers represent distinct populations. Results from the Daly River also suggest that this is a distinct population, although sample size was small and power limited to infer statistical significance. Each river system within the range of the Speartooth Shark should be treated as a separate management unit.

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.