Population Genetics of New Zealand Scampi (Metanephrops challengeri)

A fundamental goal of fisheries management is sustainable harvesting and the preservation of properly functioning populations. Therefore, an important aspect of management is the identification of demographically independent populations (stocks), which is achieved by estimating the movement of individuals between areas. A range of methods have been developed to determine the level of connectivity among populations; some measure this directly (e.g. mark-recapture) while others use indirect measures (e.g. population genetics). Each species presents a different set of challenges for methods that estimate levels of connectivity. Metanephrops challengeri is a species of nephropid lobster that supports a commercial fishery and inhabits the continental shelf and slope of New Zealand. Very little research on population structure has been reported for this species and it presents a unique set of challenges compared to finfish species. M. challengeri have a short pelagic larval duration lasting up to five days which limits the dispersal potential of larvae, potentially leading to low levels of connectivity among populations. The aim of this study was to examine the genetic population structure of the New Zealand M. challengeri fishery. DNA was extracted from M. challengeri samples collected from the eastern coast of the North Island (from the Bay of Plenty to the Wairarapa), the Chatham Rise, and near the Auckland Islands. DNA from the mitochondrial CO1 gene and nuclear ITS-1 region was amplified and sequenced. The aligned dataset of DNA sequences was then used to estimate levels of both genetic diversity and differentiation, and examine demographic history. Analyses of population structure indicate that M. challengeri from the Auckland Islands region are genetically distinct from M. challengeri inhabiting the Chatham Rise, and those collected from waters off the eastern coast of the North Island. There appears to be gene flow among the sampling sites off the eastern coast of the North Island and on the Chatham Rise, but some isolation by distance was detected. These results indicate that some of these populations may be demographically uncoupled. Genetic diversity estimates combined with Bayesian skyline plots and demographic history parameters suggest that M. challengeri populations have recently undergone a size expansion. The genetic structuring between the Auckland Islands site and all others may be due to a putative habitat disjunction off the Otago shelf. In contrast, a largely continuously distributed population along the eastern coast of the North Island and the Chatham Rise most likely promotes gene flow as larvae can be transported limited distances by oceanic currents. Historical changes in climate may have influenced the patterns of present-day structure and genetic diversity of M. challengeri, by altering habitat availability and other characteristics of their environment. This study provides evidence that species which appear to have limited dispersal potential can still maintain connected populations, but there are situations where large breaks in suitable habitat appear to limit gene flow. The results of this study will help inform stock structure of the M. challengeri fishery, which will enable stock assessments to be more precisely aligned to natural population boundaries.