Population genetic analyses enable the study of distribution and connectivity of reproductive units, generating evidence-based advice to effectively guide wildlife management and conservation efforts. In this study, 68 tissue samples from bottlenose dolphins (Tursiops truncatus) from Irish waters were analysed using mitochondrial DNA (mtDNA) control region sequences and combined with previously published data (total n = 122). Overall, 15 distinct haplotypes were discovered in Irish waters, encompassing the three putative populations (offshore, Shannon, coastal) known to occur in Irish waters, which also showed significant mtDNA differentiation, confirming previous findings using nuclear microsatellite data. While testing alternative and novel approaches, such differentiation was not found when using a set of 24 Single Nucleotide Polymorphism (SNP) markers, which were originally developed to resolve population structure of the same species but in the Gulf of Mexico. However, in silico testing of an alternative set of SNP markers (previously designed to differentiate between offshore and costal ecotypes) show higher potential to be applied to Irish populations. This study increased sample size and effort in delineating levels of genetic diversity and population structure of Irish bottlenose dolphins, as well as provided novel insights on future molecular tools to guide protection and ensure survival of this marine top predator.
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