Genetic structure of Sydney Cockle Anadara trapezia: Implications for stock assessment and restoration of extirpated populations

Abstract

Sydney Cockle (Anadara trapezia) is distributed throughout south-eastern Australian estuaries, and subject to increasing fisheries interest. Population structure for the species is uncertain, but there is mounting evidence of both harvest and environmental conditions impacting populations. Aquaculture-aided enhancement (AAE) is being considered as a tool to support ongoing management of the species. This study developed a novel single nucleotide polymorphism (SNP) marker panel for Sydney Cockle, and applied this to evaluate population structure across south-eastern Australia and inform future AAE. Sample collection targeted locations where the species had previously been found and spanned > 1100 km of coastline, but sampling efforts also revealed the potential extirpation of Sydney Cockle across a large swath of coastline. Analyses did not provide evidence for genetic structure across the region investigated. Overall F_ST was low (0.004), and the pairwise comparisons suggested only minor genetic distances among locations (F_ST ≤ 0.037). Furthermore, discriminant analysis and a likelihood-based clustering analysis did not indicate that any population subdivision was present. The SNP data revealed little evidence for any intra-estuarine structure or discontinuous stock structure across the sampled area, and there was no relationship between genetic distance and geographic distance. Similar results were obtained when stringent filters used to remove any bias in the data were removed. The south-eastern Australian estuaries supporting Sydney Cockle can be considered as connected units within minimal genetic differentiation, however the management of persistent local populations may require considerations broader than genetic structure. The genetic markers developed, and associated population analysis, provide a solid foundation for genetic resource management of any future AAE efforts for the species.