Genomic analysis of DNA from archived shark jaws

Abstract

During the last century, most species across the globe have experienced the effects of global change and other types of human impact such as exploitation. Genetic analyses of historical collections from museums and other repositories represent a unique resource for tracking demographic and evolutionary effects of climate change and other humaninduced stressors. This research focuses on a large shark, the tiger shark (Galeocerdo cuvier), for which there is a striking lack of genomic resources, despite the strong public and commercial interest in the species, including human shark interactions, conservation and management. The ability of elasmobranchs, as many other species, to react to a rapidly changing environment is still poorly understood. Therefore, the use of genomic data to comprehend present and past evolutionary responses to the environment represents a key to predict the impact of ongoing changes and the resilience of a species to future changes. It is timely we advance our understanding of these events to inform a sustainable use of resources, both in the eye of the economic and social consequences this will have on the future of many communities, but also for protection of global biodiversity as a legacy for future generations. In this study, I have highlighted the importance, and provided an example, of calibrating microsatellite data. I have demonstrated the utility of the resulting genetic database to improve inferences on global population structure by including abundant archival specimens, through identification of basin of origin for samples of unknown provenance ( Manuscript I ). Through genomic scale SNP analyses from contemporary and archived jaw samples I have provided an improved understanding of the spatiotemporal scale of population structuring in tiger sharks. I found clear evidence of temporal genetic changes in tiger sharks from the Australian east coast. The changes were most likely affiliated with the disappearance of a cryptic population, which was likely reduced/extirpated due to local direct and indirect exploitation ( Manuscript II ). By employing SNPs derived from the tiger shark transcriptome, I analysed worldwide contemporary and archived samples in order to elucidate the global population structure of the species. Both SNP and mtDNA data confirmed the deep genetic split between Atlantic and Indo-Pacific populations of tiger sharks and highlighted that it is based on a high number of genome-wide SNPs, suggesting primarily neutral evolutionary processes. However, the presence of loci with very high FST values also suggests adaptive divergence ( Manuscript III ). More importantly, the study showed for the first time extensive population structuring within both the Atlantic and Indo-Pacific oceans, suggesting population structure on a hitherto undetected geographical scale. The findings have large implications for local and global management of tiger sharks as well as other large sharks.