Evaluating the extinction risk of the endangered Maugean skate (Zearaja maugeana), Macquarie Harbour, Tasmania

Rare species, with low population sizes, restricted ranges and specialized habitat requirements, are particularly vulnerable to extinction. A small population generally has a low genetic effective population size (Ne) and can be susceptible to genetic effects (i.e. genetic drift and inbreeding), resulting in the loss of population fitness and a reduced evolutionary potential to adapt to changes occurring in the environment. Species that have a restricted range generally have less ecological flexibility, resulting in highly specialized diet and habitat requirements, which, should these become compromised, can increase the risk of extinction. In the marine environment, many fish species are currently threatened by one or more anthropogenic pressures, such as by-catch, overexploitation or habitat loss. Elasmobranchs, including sharks, rays and skates, are among some of the most threatened species, with slow growth, late maturity and relatively low fecundity preventing a fast recovery after population declines. Given that elasmobranch species are generally highly mobile, only a few examples exist of rare species that are range-restricted. The endangered Maugean skate (Zearaja maugeana) is a rare skate species that has only been recorded in two estuarine embayments, Bathurst Harbour (BH) and Macquarie Harbour (MH), on the west coast of Tasmania, Australia. Despite various diving and fishing surveys, this species has not been sighted in BH for 25 years, suggesting that it may now be restricted to MH. In MH, the small population (~3200 individuals) is threatened by a variety of anthropogenic pressures, including historical mining pollution and being caught as by-catch in gillnets. Presently, however, the main threat to the species is a change in environmental conditions (i.e. a decline in dissolved oxygen (DO) levels at depth) associated with the expansion of salmonid aquaculture farms operating in the harbour. Low DO has the potential to impact the preferred habitat and prey availability of the Maugean skate, which has a poor tolerance for low DO and a highly specialized diet of benthic prey. With little knowledge available on the evolutionary potential of the species, the aim of this study was to investigate the genetics and ecology of the population in MH, thereby assessing the risk of local, and likely global, extinction. The first aim of this study was to use population genetics to investigate the genetic diversity, relatedness among individuals (i.e. inbreeding), population structure and effective population size (Ne) of the Maugean skate population in MH. Mitochondrial and nuclear DNA markers showed that the population has very low genetic diversity (likely as a result of a recent historical founder event), a low Ne and could be experiencing restriction gene flow in the harbour. Although results suggest that the Maugean skate has likely existed with low genetic diversity for many generations, low diversity can lead to a reduced evolutionary potential. This decreases the ability of the species to adapt to current and future environmental changes, thereby increasing the risk of extinction. Using an alternative genetic technique, this thesis trialed a method for detecting the presence of rare, marine elasmobranch species in the wild. Species-specific genetic primers and probes were designed to detect environmental DNA (eDNA) (i.e. DNA that is deposited in the environment through a variety of bodily processes, such as the shedding of skin) of the Maugean skate in MH by collecting water samples at depth (10 – 15m). Results confirmed that eDNA can be used as a tool for detecting rare, marine elasmobranch species from 1L of water collected in the wild. This technique can be used to monitor the presence of the Maugean skate in MH and to determine whether the species still occurs in BH. By confirming the entire distributional range of the species, effective conservation management strategies can be developed. The second aim of the study was to investigate long-term specialized dietary requirements (trophic position and diet composition) of the species in MH using stable isotope analysis (SIA). Results showed that this species is a tertiary consumer occupying a relatively high trophic position in the food web, thereby increasing the susceptibility to changes occurring in prey availability at lower trophic levels. A full Bayesian mixing model confirmed previous stomach content analysis (SCA) findings of a highly specialized diet, consisting primarily of crustaceans. Importantly, with further investigation, SIA results showed evidence of an ontogenetic dietary shift with maturity, with smaller invertebrates (i.e. polychaetes) only being important for the diet of immature individuals and negligible for mature individuals. A decline in the abundance of smaller invertebrates could impact the foraging success and survival of immature Maugean skates, influencing overall recruitment success and population fitness of the species. Therefore, further reductions in the abundance of primary prey species may have significant implications for the foraging success and persistence of the species. Overall, the results of this study have shown that the rare and restricted Maugean skate, with low evolutionary adaptive potential and specialized ecological requirements, has a high risk of extinction. Therefore, any additional anthropogenic threats, resulting in reduced population fitness, have the potential to increase the extinction risk of the population in MH. Given the apparent disappearance of individuals from BH, local extinction from MH could have devastating consequences for the species overall. Management agencies are urged to minimize future changes occurring in the benthic environment of MH and investigate genetic management options for the species. Importantly, future work should use the eDNA assay developed in this study in combination with other techniques (fishing and underwater surveys) to determine whether the species still exists in BH. Finally, it is strongly recommended that the conservation status of this species be reviewed in light of the results of this thesis