The molecular ecology of an understudied endemic marine isopod - Isocladus armatus : a thesis presented in partial fulfilment of the requirements for the degree of Master of Natural Science at Massey University, Albany, New Zealand

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Massey University
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The study of populations and the adaptive significance of traits is a major theme in molecular ecology literature. In this thesis I present three lines of research that contribute to the understanding the molecular ecology of a species of New Zealand endemic marine isopod - Isocladus armatus (family: Sphaeromatidae). The goal of this thesis is to develop and utilize a framework to better understand the genomics of marine isopods from a range of genomic perspectives. The first primary chapter aims to assess two ways of enriching mitochondrial DNA from whole genome DNA, and to assemble this species mitochondrial genome. My research indicates that an atypical mitochondrial genome structure, widespread across Isopoda - but previously thought absent within Sphaeromatidae, is present within I. armatus suggesting that this trait has been maintained for an order of magnitude longer than previous estimates. The second primary chapter aims to describe and understand the genetic structure of populations for 8 locations around New Zealand, to understand connectivity and dispersal for I. armatus. Using a panel of 8,020 loci, I find high gene flow on a small spatial scale, while populations on a larger spatial scale exhibit a pattern of Isolation-By-Distance. Additionally, gene flow over one well known biogeographic barrier was much higher than between any other populations on a similar spatial scale, suggesting this barrier may not exhibit a strong effect on this species. Thus, my research indicates a need to revisit and study the way biogeographic barriers affect species with different life histories. The final primary chapter aims to understand the genetic basis for colour polymorphism in I. armatus, with the intention of understanding the adaptive significance and selective mechanism behind this trait. I use genome wide association approaches with a panel of 20,000 loci to answer these questions. I found that loci associated with Colour Polymorphism exhibited signatures of disruptive selection, contrary to initial hypothesis where I expected balancing selection to main colour polymorphism. I propose that substrate heterogeneity in Isocladus armatus’ habitat results in microhabitats, each of which imposes a selective pressure benefiting a specific morph type. The size of these microhabitats is so small that high levels of interbreeding between these microhabitats, and thus between morphs, results in the maintenance of polymorphism across the population.
Sphaeromidae, New Zealand, Molecular genetics, Isopoda, Color, Mitochondrial DNA