The application of molecular genetic tools to examine diet and population structure in the New Zealand scampi, Metanephrops challengeri

Abstract

The New Zealand scampi, Metanephrops challengeri, is an endemic commercially-prized deep sea lobster that is usually bottom trawled from water of 100 - 500 m deep. These lobsters are typically the dominant mobile megafaunal species in their deep sea benthic habitat with their burrowing behaviour playing an important role in bioturbation of the seafloor habitat. They have limited dispersal capabilities, possessing larvae with weak swimming abilities and a short pelagic duration, while the reptant juvenile/adult stages of the lifecycle are obligate burrow dwellers with limited movements, making them vulnerable to overexploitation. Despite their economic significance, relatively little is known about their ecology or the environment in which they live. The aim of this thesis was to use recent advances in next-generation sequencing and computational methods to deliver powerful new insights into the diet and population structure of the New Zealand scampi. DNA metabarcoding was used to identify taxa from gut content of 66 scampi from four fishery management areas (FMAs). An optimized DNA metabarcoding protocol revealed more than 150 species in the gut content of this lobster species; their diet was taxonomically diverse and dominated by crabs, prawns and fish. There was a strong indication that discarded bycatch formed an important component of the diet of scampi. The dietary taxa identified can be used to guide the development of attractive baits that can be tested in baited pots and further explored for aquaculture feed development. To investigate the population structure of the scampi around New Zealand, a combination of genotyping-by-sequencing and hydrodynamic particle modelling were used. The analyses of 91 scampi samples from five FMAs identified three genetically distinct groups that were geographically isolated around New Zealand. Hydrodynamic modelling of larval dispersal indicated directional gene flow around New Zealand, which was largely concordant with the gene flow inferred from the genomic data. The results highlight the importance of ensuring the stock sustainability of source populations. The genetic variation among FMAs provides aquaculture development a rigorous basis for selecting a genetically diverse set of wild broodstock to form the foundation of a domesticated population. Overall, the research presented in this thesis demonstrates the effectiveness of applying emerging molecular genetic methods to revealing the biology and ecology of economically important species in otherwise difficult to study deep sea habitats.