Population Structure of Riverine and Coastal Dolphins Sotalia fluviatilis and Sotalia guianensis: Patterns of Nuclear and Mitochondrial Diversity and Implications for Conservation

Mitochondrial Genetic Diversity, Population Structure and Detection of Antillean and Amazonian Manatees in Colombia: New Areas and New Techniques

The Antillean manatee (Trichechus manatus) and the Amazonian manatee (Trichechus inunguis) are distributed in rivers in the Caribbean and Amazonian region of Colombia respectively. For 30 years, genetic information has been obtained from these populations in order to inform conservation programs for these endangered species and decide on the location to release them back to the wild. However, in previous studies, samples from rivers in some areas of the country were not included, given the difficulties to access these regions due to either logistic or safety issues. In this study, we analyzed mitochondrial DNA (mtDNA) control region (CR) sequences of from samples of T. manatus (n = 37) and T. inunguis (n = 4) (410 and 361 bp, respectively), obtained in new and previously unexplored rivers and bays in the country, including Santa Marta, Urabá Gulf, Ayapel Marsh (San Jorge River Basin), Meta River and Magdalena Medio and the low Magdalena River (Cesar Province and Canal del Dique) as well as additional samples from Puerto Nariño in the Colombian Amazon. Our results included the discovery of two newly described mtDNA CR haplotypes for T. manatus. In addition, we confirmed significant population differentiation at the mitochondrial level between the Magdalena and Sinú rivers and differentiation among areas of the same river, including the middle and low Magdalena River. This differentiation may be related to anthropic changes in the river since construction of the Canal del Dique in the XVI century. We also tested environmental DNA sampling and analyses techniques to evaluate its potential use for manatee detection and monitoring in bodies of water in Colombia, in order to evaluate new areas for future manatee conservation initiatives. We emphasize the need to continue using genetic information to provide evidence on the potential best locations to undertake animal release to prevent outbreeding depression.

Low mitochondrial genetic diversity in the Indian Ocean humpback dolphin Sousa plumbea in South African waters

The Indian Ocean humpback dolphin Sousa plumbea has been described as South Africa’s most endangered marine mammal due to its low abundance, reliance on coastal habitats with increasing anthropogenic threats and high rates of mortality from bycatch in bather protection nets (BPNs). Although the species has been well studied in South Africa, only a single study has examined its molecular ecology to date, and its population structure remains poorly understood. However, understanding population structure is vital for the conservation and management of a species. To address these research gaps for S. plumbea in South African waters, we analysed the mitochondrial D-loop of 157 museum skin and tooth samples collected between 1963 and 2017 from across the species’ geographic range in South Africa. Our data show that the humpback dolphin has extremely low mitochondrial diversity (haplotype diversity, HD = 0.47; nucleotide diversity, π = 0.2%) with only 3 haplotypes identified, which is comparable to the Critically Endangered Māui dolphin Cephalorhynchus hectori maui and the Critically Endangered Mekong population of Irrawaddy dolphin Orcaella brevirostris. Mitochondrial genetic diversity has not changed significantly in the last 50 yr, despite the high levels of bycatch in BPNs over this time period. Furthermore, we found no evidence of differentiation between dolphins from the KwaZulu-Natal Coast and the Cape South Coast (Western Cape and Eastern Cape). The extremely low mitochondrial diversity we found adds to the growing body of evidence that the humpback dolphin is becoming increasingly vulnerable and that urgent conservation efforts are required for the survival of the species.