Population Genomics of New Zealand Kaimoana Species at Various Spatial Scales

<p dir="ltr"><b>Understanding the genetic connectivity and genetic structure of valuable New Zealand kaimoana (seafood) species, such as the green-lipped mussel (Perna canaliculus) and southern rock lobster (Jasus edwardsii), is crucial for designing conservation strategies and implementing effective management options for these fisheries resources. However, for many species (in particular, those with long pelagic larval durations), identifying connectivity patterns and resolving genetic structure at various spatial scales remains a challenge. This is particularly true for P. canaliculus, which exhibits interesting life history characteristics involving primary and secondary settlement that may prolong its pelagic larval duration (PLD; 3-6 weeks), as well as for J. edwardsii, which possibly has the longest PLD of any crustacean, with pelagic stages remaining in the water column for 1-2 years. This study employed genomic tools to characterise genetic connectivity and genetic structure for these two economically and culturally important seafood species at the national and regional scales.</b></p><p dir="ltr">Using single nucleotide polymorphism (SNP) markers, in Chapter 2 I report the pronounced genetic differentiation of the northern and southern groups of P. canaliculus at a genetic break, which was reported by earlier studies using a range of population genetic markers (e.g. SSCPs, mtDNA, microsatellites). However, this study reported for the first time the presence of this differentiation in both neutral and outlier loci, and that the genetic split is attributed to the influence of oceanographic distance and environmental differences such as bottom temperature and phosphate concentration across regions. Additionally, the chapter highlighted further genetic divergence of Christchurch mussels from the southern group, likely due to the impact of genetic drift, indicated by a low effective population size estimate.</p><p dir="ltr">In Chapter 3, I identify region-wide genetic connectivity of P. canaliculus in the Bay of Plenty (BoP) using neutral markers, due to the mussel’s relatively long PLD of up to 3-6 weeks. Interestingly, regional genetic differentiation was observed amongst the outlier loci, consistent with other recent findings on region-scale variations in oceanographic processes and microchemical signatures in the area. The analysis of both neutral and outlier datasets suggests that Tirohanga (central BoP) could potentially serve as a source population for mussel spat in the region. Moreover, this study highlights the possibility of introgression of Kaitaia spat genes into the local gene pool of BoP mussels. These findings lead to recommendations for Whakatōhea (the local iwi that solely owned the Ōpotiki mussel farm) to protect the source of mussel spat in the region and monitor the potential effect of genetic introgression into the local mussels of BoP.</p><p dir="ltr">In Chapter 4, I report pronounced differentiation of J. edwardsii between Australia (Tasmania) and New Zealand samples. In New Zealand, substantial gene flow was observed across its species range, consistent with its 1-2 year pelagic larval duration (PLD). Subtle genetic differentiation was observed at site 902 at CRA1 (the northernmost part of New Zealand) at the neutral loci, attributed to variations in habitat (roughness and depth) and physical properties of the ocean (temperature and tidal speed). Additionally, three genetic groups were delineated using the outlier markers, separating the northeast (NE), northwest (NW), and south (S). Migration models indicated an asymmetric pattern of gene flow (S→NW→NE), which is consistent with previous larval dispersal and settlement models. Patterns of genetic structure at the outlier loci were strongly correlated with environmental variables across New Zealand, such as roughness at the seafloor and sea surface temperature, which may be associated to settlement, post-settlement, and survival of J. edwardsii. These findings highlight complex connectivity patterns and the impact of oceanographic processes and environment factors on the genetic structure and local adaptation of J. edwardsii, despite its high dispersive potential.</p><p dir="ltr">Overall, this research provides significant support for devising spatially explicit management and conservation strategies for these two economically and culturally important seafood species in New Zealand. The study highlights the utility of SNP markers - both neutral and outlier loci - for understanding the genetic connectivity and genetic structure of the green-lipped mussel (P. canaliculus) and rock lobster (J. edwardsii) at various spatial scales. For both species, several important genetic groupings were identified at the international scale (rock lobsters) and the national scale (rock lobsters and green-lipped mussels), including the detection of potential source populations, along with the identification of environmental and evolutionary forces shaping these species-specific patterns. The research also emphasises that while empirical genetic data can offer substantial evidence or support for decision-making, a multidisciplinary approach can provide even more valuable information to support the development of spatially explicit management and conservation strategies for these important species in New Zealand.</p>