Since the first investigation 25 years ago, the application of genetic tools to address ecological and evolutionary questions in elasmobranch studies has greatly expanded. Major developments in genetic theory as well as in the availability, cost effectiveness and resolution of genetic markers were instrumental for particularly rapid progress over the last 10 years. Genetic studies of elasmobranchs are of direct importance and have application to fisheries management and conservation issues such as the definition of management units and identification of species from fins. In the future, increased application of the most recent and emerging technologies will enable accelerated genetic data production and the development of new markers at reduced costs, paving the way for a paradigm shift from gene to genome-scale research, and more focus on adaptive rather than just neutral variation. Current literature is reviewed in six fields of elasmobranch molecular genetics relevant to fisheries and conservation management (species identification, phylogeography, philopatry, genetic effective population size, molecular evolutionary rate and emerging methods). Where possible, examples from the Indo-Pacific region, which has been underrepresented in previous reviews, are emphasized within a global perspective.

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Background: The territorial fishing zones of Australia and Indonesia are contiguous to the north of Australia in the Timor and Arafura Seas and in the Indian Ocean to the north of Christmas Island. The area surrounding the shared boundary consists of a variety of bio-diverse marine habitats including shallow continental shelf waters, oceanic trenches and numerous offshore islands. Both countries exploit a variety of fisheries species, including whaler (Carcharhinus spp.) and hammerhead sharks (Sphyrna spp.). Despite their differences in social and financial arrangements, the two countries are motivated to develop complementary co-management practices to achieve resource sustainability. An essential starting point is knowledge of the degree of population subdivision, and hence fisheries stock status, in exploited species.

Rhynchobatus spp. (wedgefishes) are large benthopelagic shark-like rays with fins that are highly prized in the international shark fin trade. They are among the most threatened groups of sharks and rays globally. While Rhynchobatus spp. are known to be under considerable fishing pressure as a group, taxonomic confusion among species within the genus has compromised species-specific fishery and demographic data that are urgently needed for developing effective management strategies. Rhynchobatus australiae (Whitley, 1939) is a large Indo-West Pacific species reaching 2 to 3 m that is classified as Vulnerable on the IUCN Red List. This study combines new empirical data from field surveys with data obtained from verified reference specimens to investigate genetic and phenotypic variation in R. australiae and its relative incidence in fisheries. R. australiae dominated Rhynchobatus catch in fisheries surveys across Southeast Asia, and was the most commonly recorded species of the genus in Australia (94% and 58% of captures respectively, n = 207). Study specimens were consistent with a single species with moderate spatial mtDNA variation (Φ ST = 0.198, p < 0.0001). We show that R. australiae can be reliably differentiated from other Indo-Pacific species with nadh2 (1044bp), and a section of the control region (456bp) short enough to amplify DNA from processed fins in international trade. We document aspects of morphological variability to assist in the description of external characters that differentiate this species. This is the first range-wide intraspecific study on any wedgefish species, and provides the most complete synthesis of mtDNA data to date for identifying Rhynchobatus fins in the global shark fin trade.