Population genetic and genomic approaches for the management of the blackfoot paua, Haliotis iris Gmelin 1791, within the genus context
Authors:   , Trauzzi Giulia 
Published: August 2023

<p><b>The blackfoot pāua, Haliotis iris Gmelin 1791 is one of three endemic species of abalone (Haliotis spp.) found in New Zealand. This marine gastropod is a taonga (highly prized or treasured) species and a traditional kai moana (seafood) in the Māori culture. The increase in commercial interest around the exploitation of pāua shells and meat in the early 1960s led to the development of fishing restrictions and in 1986/87 and to the pāua fishery management system based on quota management areas (QMAs).</b></p>
<p>In 2016, the Kaikōura earthquake generated a coastal uplift along the Kaikōura region where one of the country’s most productive pāua fisheries is located. Pronounced mortality of seaweed and marine intertidal invertebrates was reported in the affected region. Subsequently, the pāua fishery along approximately 110 km of coastline and encompassing two QMAs (PAU3A and PAU7) was closed for 5 years with substantial losses in annual revenue. It was reopened for 3 months on the 1st December 2021. The fishery was closed again at the end of February 2022 and at the time of writing remains closed. The goals of this thesis are to: 1) identify patterns of global population genetic structure and genetic connectivity within the genus Haliotis by reviewing the published literature to provide context to the findings obtained for the blackfoot pāua from New Zealand; 2) describe the population genetic connectivity, genetic diversity and population genetic structure of pāua populations from the Kaikōura region before and after the 2016 earthquake for the first time through genotyping-by-sequencing (GBS)-derived molecular markers (single nucleotide polymorphisms - SNPs); 3) investigate potential genotypic-environmental associations (GEAs) between the variation at microsatellite markers and environmental variation for pāua populations at the national scale; and 4) identify significant GEAs between neutral genetic variation at SNP loci for pāua at Kaikōura and environmental (i.e., ecological and oceanographic data) data before and after the 2016 earthquake.</p>
<p>Abalone are widely understudied and the literature is strongly biased towards certain species of economic relevance in developed countries where most biological stocks do not correspond to fishing management units. Abalone species worldwide are generally characterised by weak population genetic structure that can be explained by the geomorphology of the coasts (i.e., headlands, bays) and correlated physical oceanography (i.e., ocean currents and upwelling).</p>
<p>For the blackfoot pāua from Kaikōura, weak genetic structure (differentiation from other sites) was found at Cape Campbell, a headland, the northernmost site in the region and a well-known biogeographic boundary in New Zealand. High levels of gene flow and the large effective population sizes (Ne) of all populations in the Kaikōura region may have counterbalanced the effects of the Kaikōura earthquake on this species. Based on the current dataset, no direct effect of the 2016 earthquake was evident for the pāua populations from Kaikōura. Differences in the genetic connectivity patterns between adults and juveniles in PAU3A were detected. This finding could be explained by different scenarios including but not limited to local recruitment, variability in ocean currents and/or cohort effect. Collection of long-term genomic data may further clarify the stability of this pattern and its possible causes. Seascape genetics revealed the association between the genetic differentiation of pāua at Cape Campbell with higher sedimentation levels and higher sea surface temperatures (SST) that may act as barriers to gene flow for pāua to other (regional) sites. Chlorophyll-a and SST were also associated with patterns of genetic connectivity in juveniles in PAU3A and loosely followed a geographic pattern. Multiple estimates of SST, proxies for ocean currents, oceanic fronts and productivity levels of the waters around New Zealand, were significantly associated with variation at microsatellite loci for pāua at the national scale.</p>
<p>This research reports the successful development of high throughput genomic data and its applications to pāua management in New Zealand at regional scales and the use of novel genetic analyses to pāua at the national scale. The overlap between the genetic split detected for pāua at Cape Campbell and the original boundary between the two QMAs (based on the boundary between iwi tribes) denoted how the QMS in New Zealand took into consideration Māori stewardship over marine resources since its beginning. The detection of a genetic break at small spatial scales supports the ongoing shift towards a finer scale fishery management in New Zealand and suggests the implementation of advanced genomic tools to inform management decisions. Seascape genetics analyses carried out in this thesis highlighted a relationship between genetic and environmental variations for pāua at both small and large spatial scales that could inform restoration efforts as well as focus on stocks at potential risk. Increased levels of sedimentation and high SST were recorded in the Marlborough region where pāua stocks are declining. Attention to pāua stocks in areas where these two environmental factors are increasing is suggested especially considering climate global change. The integration of genomic tools into fishery management represents the next big advancement in the long-term sustainable exploitation of pāua stocks in New Zealand.</p>