Population structure, temporal stability and seascape genetics of two endemic New Zealand Pleuronectiformes, Rhombosolea plebeia (sand flounder) and R. leporina (yellowbelly flounder)

New Zealand’s coastal waters are an integral part of the social, economic and environmental heritage of this Pacific archipelago. Evolving in isolation for 82 million years under volatile tectonic action and volcanism, the marine biogeography of New Zealand is complex and diverse. Many hypotheses have been proposed to explain the subdivisions of biogeographic areas based on species distributions, habitat and population genetics. In this study, I test whether there is differentiation in coastal population connectivity between northern and southern provinces, the location of the break and what environmental factors may explain the patterns observed.  Sandy, soft bottom and estuarine ecosystems make up a large proportion of the coastline, but are not well-represented in population genetic studies in New Zealand and internationally. I chose Rhombosolea leporina (sand flounder) and Rhombosolea plebeia (yellowbelly flounder) as endemic, commercially and traditionally important inhabitants of the shallow coastal waters and estuaries to explore levels of gene flow among most of the marine biogeographic regions of the New Zealand mainland.  The goal of this thesis research was to (1) develop polymorphic DNA microsatellite markers and (2) investigate the population genetic patterns at multiple spatial scales. Although these species have a relatively long pelagic larval duration (PLD) of ~70 days, I found a significant level of population structure for both species. There was a pattern of isolation by distance and a north to south break in connectivity on the east coast for R. plebeia, but an east to west disjunction in R. leporina. There was no evidence of a north to south genetic break in R. leporina, however populations on the south east coast of the South Island were significantly differentiated in both species.  A test for temporal effects (3) of genetic variation was conducted to determine whether spatial patterns of differentiation were consistent across multiple sampling seasons and age classes. Aspects of the sweepstakes recruitment success (SRS) hypothesis were tested by examining differences in allele frequencies and levels of genetic diversity as a function of time. The analyses found evidence of temporal stability between years and between juveniles and adults.  Lastly, (4) the coastal and estuarine environmental variables were modelled using information from two public GIS datasets and several measures of genetic differentiation. The aim of this chapter was to determine which environmental and geospatial factors showed a significant level of correlation with the spatial genetic patterns reported in the earlier studies. For R. leporina, latitude, sediment and current speeds were significantly correlated with the genetic estimates of FST, F’ST and Jost’s D. In R. plebeia, a correlation was found between latitude, longitude, sediment, current speeds, sea surface temperature and width of the estuary mouth. The results of the modelling study suggest avenues for further research using candidate genes, such as heat shock proteins and rhodopsin.  This was the first study of New Zealand pleuronectids using a multidisciplinary approach with microsatellite DNA markers, GIS, and an array of bioinformatics software to study coastal connectivity on multiple spatial and temporal scales. Significant genetic structuring was found among populations of animals that are potentially well connected through continuous sandy, soft bottom environments and a long PLD. Despite similar life histories and ecologies, the two species were quite divergent in that there was little cross amplification of markers, different patterns of genetic structure and separate outcomes from environmental modelling. These results suggest that managing several species under one management plan may be an oversimplification of the complexities of the population dynamics and evolutionary histories of these species. Conservation and management options for coastal fisheries and possible avenues for future research are proposed.