Enhancing Intra‐Specific Population Genetic Studies of Bottlenose Dolphins ( Tursiops truncatus ) in Irish Waters by Integrating Least Invasive Samp

ABSTRACT

Population genetic studies provide important data for evidence‐based conservation and management of marine mammal species. Obtaining tissue and genetic material from marine mammals is challenging, often leading to limited sample sizes, however emerging least‐invasive sampling methods, such as extra‐organismal DNA (e.g., blows) and environmental DNA (eDNA) (e.g., water), have the potential to provide additional samples for intra‐specific genetic studies. Thus, this study aimed at further investigating population genetic structure of Irish bottlenose dolphins ( Tursiops truncatus ) by corroborating samples sourced with direct methods (e.g., biopsies of free‐ranging dolphins and tissue from dead dolphins) ( n  = 67) with samples collected using least invasive indirect methods (eDNA isolated from water, or extraorganismal DNA from blows, faeces, and sloughed skin, collected opportunistically in proximity to individuals) ( n  = 52). Using 15 microsatellite markers, a 540 bp portion of mitochondrial DNA (mtDNA) control region and nuclear sex markers, intra‐specific genetic information was obtained from samples sourced with indirect methods, including previously‐known mtDNA haplotypes recovered from 11 samples (21% success rate) and consistent microsatellite genotypes from 5 of 15 markers, sufficient for assigning individuals to population of origin. This work led to the most comprehensive population genetic study of Irish bottlenose dolphins to date (140 individuals), confirming the presence of three genetically distinct populations, namely an offshore ecotype and two coastal resident populations (the Shannon Estuary and the Connemara‐Mayo‐Donegal population). Importantly, findings from this study provide corroborative evidence that Shannon dolphins use Brandon Bay (Co. Kerry) as a key foraging area, which is outside the current Shannon Estuary Special Area of Conservation (SAC) boundary, hence advocating a revision of such boundaries. Additionally, this study included samples from a number of Irish “solitary” dolphins, which were genetically assigned to the offshore ecotype, further showcasing least‐invasive sampling methods, including eDNA, as a promising tools for the study of intra‐specific genetic variation.