Testing expectations of connectivity and breeding biology among shark species in a tropical hot spot : the Indo-Pacific

Delineating the extent of connectivity for populations of marine megafauna and understanding the elements driving observed patterns of genetic structure is pivotal for defining the scale of management required. Many species of reef associated sharks have discontinuous distributions separated by vast expanses of unsuitable habitat. The extent of connectivity for many species of sharks throughout the Pacific and Indian Oceans is currently unknown. The Indo-Pacific region is considered a hotspot for tropical sharks, with the majority of all reef shark species found in its waters. Many nations including Indonesia, Australia and Papua New Guinea exploit shark and ray populations as either target or bycatch at varying catch levels. Information on fisheries is better known for Indo-Pacific locations Indonesia and Australia while little is known of their neighbouring nation Papua New Guinea. Genetic markers in the form of mitochondrial DNA (mtDNA), microsatellites (Msats) and Single Nucleotide Polymorphisms (SNPs) can be used to infer a species' biology and ecology. These genetic markers vary in inheritance mode, location within the genome and likelihood of being affected by cellular mechanisms such as recombination. Theoretically, genetic markers have varying capacity to reveal population-level differences and therefore delineate stock structure and connectivity. Such differences mean markers can illuminate processes at different points along the evolutionary trajectory of populations. Often genetic markers are used interchangeably and no formal testing of stock assignment using all three marker types has occurred for any shark species. This thesis draws together diverse genetic approaches to generate novel insights into (i) shark ecology across the Pacific and Indian Oceans, (ii) breeding behaviour of two shark species and (iii)empirical comparisons of genetic diversity and population connectivity using multiple genetic markers. The thesis is composed of a general introduction (Chapter 1), two population genetic studies, each on a commercially important species of shark (Chapter 2-3), a multiple paternity assessment (Chapter 4) and a final discussion and conclusion (Chapter 5). Population genetic studies are reported here for the silvertip shark (Carcharhinus albimarginatus) (Chapter 2) and the scalloped hammerhead shark (Sphyrna lewini) (Chapter 3) to better understand their connectivity throughout the Pacific and Indian Oceans. The genetic differences measured between populations sampled in this study revealed that large body size and ability to cross vast expanses of open ocean was not a consistent predictor of the genetic cohesiveness of the species. The fourth chapter assesses the presence and prevalence of multiple paternity in litters of female grey reef shark (C. amblyrhynchos) and S. lewini individuals captured in Papua New Guinea. Finally, Chapter 5 synthesises these new insights for management purposes and critically compares the variety of genetic markers deployed and identified key considerations for elasmobranch researchers before designing future population genetic studies.