Population Genomic Studies Of The New Zealand Green-Lipped Mussel, Perna Canaliculus Gmelin, 1791
Authors:   , Parada Roberto 
Published: February 2025

<p dir="ltr"><b>Population connectivity significantly influences the spatial structure and dynamics of marine populations. Marine species, particularly those with pelagic larval stages, depend on larval dispersal for connectivity, which is driven by complex interactions between biological traits and oceanographic conditions. Understanding larval dispersal is crucial for conservation, yet challenging due to the difficulties in tracking larvae and identifying their origins. Recent advancements in genetic markers, especially single nucleotide polymorphisms (SNPs), and high-throughput sequencing technologies have enhanced our understanding of population genomics, providing detailed insights into the evolutionary processes shaping genetic variation. Integrating these genetic data with oceanographic models provides insights into larval connectivity, often highlighting the importance of local retention and recruitment for population stability. The emerging field of seascape genomics further enhances our understanding of marine population dynamics by linking genetic variation to environmental factors, revealing how oceanographic features and environmental gradients may shape genetic diversity and connectivity. This knowledge is pivotal in predicting the impacts of climate change on marine populations and in designing effective marine protected areas and conservation strategies to ensure the resilience and connectivity of marine ecosystems.</b></p><p dir="ltr">This thesis explores the population genetic connectivity of a marine species, <i>Perna canaliculus</i>, the green-lipped mussel. This is an endemic species in New Zealand/Aotearoa found on rocky reefs and soft sediment beds across the subtidal and intertidal environments of the three main islands in the country. It is a highly valued food source for Māori and the mainstay of the aquaculture industry, where it represents the most important export species by both tonnage and dollar value. Most mussel seed used in farming comes from one site, Te Oneroa-a-Tōhe – Ninety Mile Beach (NMB), in the far north of the country, representing ~80% of the seed used (commonly known as Kaitaia spat, KS). Many attempts have been made to identify the source of KS and to describe the genetic structure of the species at both regional and national scales. Previous studies have divided the green-lipped mussel populations into northern and southern regions, separated by a pronounced genetic break located below the Cook Strait/Raukawa Moana region, at ~42⁰ S on both the east and west coasts of the northern South Island/Te Waipounamu. The low-resolution power of the genetic markers employed prevented previous research from detecting further division within these two regions, and also to locating the specific sites supplying KS to NMB.</p><p dir="ltr">In this thesis, 37 sampling sites (1862 mussels) distributed across New Zealand/Aotearoa were used to obtain SNP markers from Next Generation Sequencing in an attempt to study the population genetic structure of the green-lipped mussel at greater resolution than previous studies. The panel of SNPs was divided into neutral (185 loci) and outlier (28 loci) to investigate the different processes influencing genetic variation in this species.</p><p dir="ltr">At the national scale (chapter 2), the two previously characterised regions were detected, but the genetic break on the east coast was not identified due to sampling limitations and therefore the only sampling site in this coast (Christchurch/Ōtautahi, CH) was considered to be part of the major Northern mussel region. The west coast genetic break was detected, and it matched the location described for the green-lipped mussel and other marine benthic species. In addition, the inclusion of geospatial analysis enabled the identification of six genetic clusters, with five of them being a subdivision of the Northern mussel region. This new subgrouping allowed the distinction of six different regional clusters, termed: West Coast of the North Island (WCN, 13 sampling sites); Bay of Plenty (BOP, 7 sites); Wellington Harbour (WH, 1 site); North Coast of the South Island (NCS, 8 sites); West Coast of the South Island (WCS, 2 sites); and Christchurch (CH, 1 site). The patterns of genetic variation were subsequently used in seascape genomic analyses to test for associations with environmental variables. Sea surface temperature (SST), chlorophyll A concentration (ChlA), bathymetric position index broad (BPI_broad), gravel, sand and photosynthetic active radiation (PAR) were significantly correlated with genetic variation across sampling sites, suggesting that food-related variables plus temperature and current-associated habitat composition play key roles shaping the genetic diversity of the green-lipped mussel in New Zealand/Aotearoa.</p><p dir="ltr">SNP-based analyses revealed that a representative sample of KS was part of the WCN genetic cluster, and further analyses were performed to find statistically significant differences between this sample and the rest of the genetic clusters (chapter 3). Pairwise F<sub>ST</sub> estimates using both neutral and outlier SNPs revealed significant differences in allele frequencies between KS and all genetic clusters with the exception of WCN. Individual genetic assignment tests and relative migration networks further confirmed the WCN genetic cluster as the source for KS. Additional genetic tests (DAPC, Geneland, pairwise F<sub>ST</sub>) were used to detect any discernible genetic structure within the WCN genetic cluster that would differentiate amongst its sampling sites to help narrow down the sources for KS. As a result, a location situated inside an estuary, Opononi Dock (OD) was discarded as potential source for KS. An additional statistical comparison between the genetic connectivity and larval connectivity output from an oceanographic model ruled out the most distant sampling site from within the WCN genetic cluster, Raglan/Whāingaroa (RG) as a relevant demographic source for KS. The KS sample is therefore most closely related to, and derived from, mussel sampling sites within the immediate region of NMB itself.</p><p dir="ltr">The genetic break on the west coast of the South Island/Te Waipounamu was more precisely located between the NCS and WCS genetic clusters (chapter 4). A hybrid zone characterised by low interbreeding between the two mussel lineages was previously described for the green-lipped mussel, but the mechanisms and patterns of allele introgression remained elusive. In this thesis, I analysed the hybrid zone using a genomic cline approach, estimating the change of allele frequencies using a hybrid index, to elucidate patterns of introgression. The analysis suggests that the hybrid zone is situated in a context that promotes the preference of South-Western allele polymorphisms, as most of the loci exhibited a pattern of South-West to North-East introgression. In addition, the presence of F1 individuals was not detected, however F2 and backcrosses were found in up to ~45% of the mussels at some of the sites within the hybrid zone, suggesting a bottleneck in the formation of first-generation hybrid mussels. The mechanisms and factors influencing the genetic variation across the hybrid zone could not been identified, as the environmental variation obtained for the sites involved was negligible.</p><p dir="ltr">This research represents an application of NGS-derived markers in the identification of genetic structure of one of the most important economic marine species in New Zealand/Aotearoa. The findings of high resolution spatial genetic structure can help in the delineation of management units for the green-lipped mussel and inform further sampling to locate more genetic clusters for the species. The combined multidisciplinary approach comparing genetic connectivity with oceanographic connectivity data proved to be useful in the identification, for the very first time ever, of relevant sites acting as the sources of KS. This information will be important for the New Zealand/Aotearoa government (Fisheries NZ) because it provides key scientific evidence to help develop guidelines to design effective management measures preserving these source sites against human impact and other threats. Finally, the analysis of the genetic break and hybrid zone has provided further information about its location and extent, and has shed light on the genetic composition of the mussel populations inhabiting this region.</p>