Population connectivity of the Southern rock lobster, Jasus edwardsii

Understanding the mechanisms driving larval dispersal and connectivity is of ecological relevance and is beneficial in fisheries management. Defining population structure and stock boundaries helps in management of spawning stock biomass and annual harvests. Moreover, determining if there are patterns in dispersal can help identifying source populations that need management strategies directed towards maintaining appropriate levels of egg production. The Southern rock lobster, Jasus edwardsii, extends around southeast Australia and New Zealand and supports valuable fisheries in both countries. Adults J. edwardsii do not migrate and their phyllosoma larvae, the dispersal stage, are adapted for drifting for approximately 12 to 24 months of pelagic larval duration. Consequently there has been an assumption of genetic homogeneity within the population throughout Australia. The assumption of panmixia has been supported by larval transport simulations and previous studies on genetic connectivity. The general eastward flow of currents in southeast Australia has been identified as the likely main dispersal mechanism. South Australia is a highly productive area, and is predicted by oceanographic models to be a source of larvae to the Tasmanian fishery. A second prediction from larval transport simulations is that regional self-recruitment varies markedly across the species range in Australia. Long-term monitoring of recruitment throughout the fishery shows high year-to-year variability in recruitment, as well as regional fluctuations. This has been linked to changes in environmental conditions. Fluctuations in recruitment magnitude can reduce the accuracy of population modeling of the stock, which is used to determine harvest strategies. In this thesis I assessed variability in genetic identity of Southern rock lobster at different spatio-temporal scales to evaluate drivers of population structure. I reviewed possible biological, environmental (e.g., dispersal history) or adaptive drivers (e.g., natural selection) by analyzing single nucleotide polymorphisms (SNPs) markers generated using double digest restriction site-associated DNA sequencing (ddRADseq). I measured genetic variability in J. edwardsii across three spatial scales, broad (1,000’s km), medium (100’s km) and fine-scale (10’s km), as well as two temporal scales, within a year and between years. In chapter 2, large-scale connectivity and potential for local adaptation between adult J. edwardsii from Australia and New Zealand was investigated using neutral and outlier markers. There was large-scale genetic divergence between Australia and New Zealand, two countries thousands of kilometres apart, at neutral regions of the genome (F\(_{ST}\) = 0.022), supporting previous findings of limited larval dispersal across the Tasman Sea. A much larger genetic differentiation was detected (F\(_{ST}\) = 0.134), using regions of the genome under putative selection suggesting local adaptation and post-settlement mortality of unfit genotypes. In chapter 3 I assessed the extent and patterns of genetic variability in new recruits through time on a medium spatial scale. To determine the role of genetics in the observed interannual variability and how post-settlement selection acts to modify the observed structure in recruits, pueruli and post-pueruli settling during four consecutive years were analyzed. Interannual genetic variability of recruits within and between two sites located 100’s of kilometres apart in South Australia and Tasmania provided support for chaotic genetic patchiness. Lower genetic diversity was observed during years of low puerulus catch rates at the Tasmanian site, suggesting regional genetic differences in recruitment. Additionally, the magnitude and strength of genetic divergence detected in the markers under putative positive selection also exhibited temporal and spatial variability. Both locations exhibited a single marker under putative positive selection in common across years, providing weak evidence for post-settlement selection. In chapter 4 I assessed fine-scale temporal and spatial genetic and phenotypic divergence in recruits across a latitudinal gradient. This was done using new recruits within one recruitment season in Tasmania from sites 10’s of kilometres apart. There was a lack of overall population structure identified between three sites along a latitudinal gradient, but genetic divergence at a small spatial scale suggested chaotic genetic patchiness. Individuals sampled from the southernmost site during three consecutive monthly collections were genetically divergent from each other. There were also phenotypic differences of pueruli between sites and months of settlement; individuals at the northernmost site were consistently smaller at settlement. Collective dispersal is a possible mechanism of larval J. edwardsii, based on significant phenotypic differences between sites that were persistent through time. This implied that larvae released during the same spawning event could maintain cohesiveness until settlement, leading to genetic patchiness among individuals recruiting during the same year. In chapter 5 I tested a number of the dispersal pathways projected by a larval transport simulation model for J. edwardsii. The predicted population of origin of pueruli caught in collectors in South Australia and Tasmania was then tested using genetic assignment to determine if they were the likely point of origin. All three adult lobster sampling sites were assigned as equally likely source for recruits in both South Australia and Tasmania. These results further evidenced the high level of genetic exchange in the Australian J. edwardsii population. In general, the findings of this thesis provide new evidence on the dispersal mechanisms used by larval J. edwardsii driving the observed genetic variation in recruits. The high level of genetic admixture found herein highlights the need of a coordinated fisheries management strategy between states in order to protect subpopulations that constitute important source of recruits