In elasmobranchs, evolutionary rates of mitochondrial genes are low and variation between distinct populations can be hard to detect with the commonly used single mitochondrial gene approach. In this study, we explored the potential of whole mitogenome sequencing for phylogeographic studies in elasmobranchs by focusing on Glyphis glyphis, a rare and Critically Endangered euryhaline shark with presumably low population size and low genetic diversity.

Highly reliable mitogenomic sequences were obtained from 93 sharks sampled in three different rivers using long range PCR and amplicons sequencing with Illumina Miseq. The genetic diversity in G. glyphis was extremely low. Only 19 variable sites were found, distributed across 12 haplotypes. However, this small amount of genetic variation was enough to demonstrate the existence of barriers to gene flows between each population. We will discuss how this approach performed compared to single gene approaches, demonstrating the high potential of mitogenomics for population structure analysis in species with low genetic diversity. We will also briefly comment on the cost-efficiency of our sequencing approach and how it compares to traditional Sanger sequencing.