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Declines in global marine finfish catches, which accounts for ~15% of the animal protein consumed by humans, has caused a 6-fold increase in total reported catch of invertebrates since 1950. This has led to the over-exploitation and decline of many marine invertebrate fisheries. The red rock lobster (Jasus edwardsii) fishery is New Zealand’s most economically valuable inshore fishery. The current management strategy relies on the assumption that the stock is comprised of a single panmictic population. However, more recent studies have challenged the genetic homogeneity of Jasus edwardsii across the Tasman sea and described high levels of self-recruitment in a Stewart Island subpopulation. A disregard for the underlying genetic structure in the management of a fishery can lead to excessive removal of individuals from populations contributing to the overall genetic diversity of the stock and thus reduce the species adaptability. The ability to adapt to new environments is particularly important in the context of global climate change and can significantly affect the long-term sustainability of the stock. Thus, the goal of this study was to identify specific patterns of genetic diversity of Jasus edwardsii population and provide an interpretation and assessment of the impact on the NZ fishery. The first objective was to optimize and validate molecular and bioinformatic protocols of Single Nucleotide Polymorphism (SNP) discovery for the red rock lobster Jasus edwardsii. The double digest restriction-site associated DNA (ddRADseq) protocol was optimized for the relatively large red rock lobster genome, which also has a high paralog content. The impact of bioinformatic processing on the population genetic inferences was then assessed by testing three different SNP discovery pipelines with the Rad-loci pipeline producing the most optimal marker discovery rate with a low level of missing data and a low SNP error rate. An analysis of technical replicates confirmed the reproducibility of both the molecular and bioinformatic protocols and also the validated the data generation process suitable for population genetic analyses. The second objective of my thesis was to investigate the genetic structure and population connectivity of adult red rock lobsters. The SNPs discovered were characterised as selectively neutral or under divergent selection (outlier) and both types of markers were analysed using Bayesian model-based clustering (STRUCTURE), non model-based multivariate analysis (Discriminant Analysis of Principal Components (DAPC)) and F-statistics. A lack of population differentiation using neutral genetic markers indicated a high level of gene flow and connectivity between populations. In contrast, there was evidence for selective pressure as a result of the analysis of outlier markers. Three main regions were identified: North-East NZ, North-West NZ and South NZ sub-populations, as part of a larger NZ metapopulation (FST ranged from 0.025 to 0.049, P

Genome-wide SNP analysis reveals patterns of population differentiation and adaptation of red rock lobster Jasus edwardsii