Open Access Te Herenga Waka-Victoria University of Wellington
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Population genetics and connectivity in Paphies subtriangulata and Paphies australis (Bivalvia: Mesodesmatidae)

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posted on 2021-11-14, 03:07 authored by Hannan, Danielle Amelia

Understanding the different types of genetic population structure that characterise marine species, and the processes driving such patterns, is crucial for establishing links between the ecology and evolution of a species. This knowledge is vital for management and conservation of marine species. Genetic approaches are a powerful tool for revealing ecologically relevant insights to marine population dynamics. Geographic patterns of genetic population structure are largely determined by the rate at which individuals are exchanged among populations (termed ‘population connectivity’), which in turn is influenced by conditions in the physical environment. The complexity of the New Zealand marine environment makes it difficult to predict how physical oceanographic and environmental processes will influence connectivity in coastal marine organisms and hence the type of genetic structure that will form. This complexity presents a challenge for management of marine resources but also makes the New Zealand region an interesting model system to investigate how and why population structure develops and evolves over time. Paphies subtriangulata (tuatua) and P. australis (pipi) are endemic bivalve ‘surf clams’ commonly found on New Zealand surf beaches and harbour/estuary environments, respectively. They form important recreational, customary and commercial fisheries, yet little is known about the stock structure of these species. This study aimed to use genetic techniques to determine population structure, levels of connectivity and ‘seascape’ genetic patterns in P. subtriangulata and P. australis, and to gain further knowledge of common population genetic processes operating in the New Zealand coastal marine environment. Eleven and 14 novel microsatellite markers were developed for P. subtriangulata and P. australis, respectively. Samples were collected from 10 locations for P. subtriangulata and 13 locations for P. australis (35-57 samples per location; total sample size of 517 for P. subtriangulata and 674 for P. australis). Geographic patterns of genetic variation were measured and rates of migration among locations were estimated on recent and historic time scales. Both species were characterised by genetic population structure that was consistent with their habitat. For P. subtriangulata, the Chatham Island population was strongly differentiated from the rest of the sampled locations. The majority of mainland locations were undifferentiated and estimated rates of migration among locations were high on both time scales investigated, although differentiation among some populations was observed. For P. australis, an overall isolation by distance (IBD) pattern was likely to be driven by distance between discrete estuary habitats. However, it was difficult to distinguish IBD from hierarchical structure as populations could be further subdivided into three significantly differentiated groups (Northern, South Eastern and South Western), providing evidence for barriers to dispersal. Further small scale patterns of genetic differentiation were observed in some locations, suggesting that complex current patterns and high self-recruitment drive small scale genetic population structure in both P. subtriangulata and P. australis. These patterns of genetic variation were used in seascape genetic analyses to test for associations with environmental variables, with the purpose of understanding the processes that might shape genetic population structure in these two species. Although genetic population structure varied between the two species, common physical and environmental variables (geographic distance, sea surface temperature, bed slope, tidal currents) are likely to be involved in the structuring of populations. Results suggest that local adaptation, in combination with restricted dispersal, could play a role in driving the small scale patterns of genetic differentiation seen among some localities. Overall, the outcomes of this research fill a gap in our knowledge about the rates and routes by which populations are connected and the environmental factors influencing such patterns in the New Zealand marine environment. Other studies have highlighted the importance of using multi-faceted approaches to understand complex processes operating in the marine environment. The present study is an important first step in this direction as these methods are yet to be widely applied to New Zealand marine species. Importantly, this study used a comparative approach, applying standardised methodology to compare genetic population structure and migration across species. Such an approach is necessary if we wish to build a robust understanding of the spatial and temporal complexities of population dynamics in the New Zealand coastal marine environment, and to develop effective management strategies for our unique marine species.


Copyright Date


Date of Award



Te Herenga Waka—Victoria University of Wellington

Rights License

Author Retains Copyright

Degree Discipline

Marine Biology

Degree Grantor

Te Herenga Waka—Victoria University of Wellington

Degree Level


Degree Name

Doctor of Philosophy

ANZSRC Type Of Activity code

970106 Expanding Knowledge in the Biological Sciences

Victoria University of Wellington Item Type

Awarded Doctoral Thesis



Victoria University of Wellington School

School of Biological Sciences


Ritchie, Peter; Gardner, Jonathan; Bell, James