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Open Access Publications from the University of California

Phylogenetic and Phylogeographic Analysis of Beaked Whales in the Northern Bahamas: Implications for Conservation


Little is known about Ziphiidae, elusive deep-diving beaked whales that spend little time at the surface and occur exclusively in deep waters off the continental shelf. Mass strandings of Blainville’s (Mesoplodon densirostris) and Cuvier’s (Ziphius cavirostris) beaked whales have been correlated with sonar exercises conducted by the United States Navy at their sonar-testing facilities in the northern Bahamas. It is not known how naval sonar may be affecting local populations of M. densirostris and Z. cavirostris that inhabit the waters surrounding the testing site. Current regulations and conservation measures established to protect the whales are limited due to an overall lack of understanding in the distribution, abundance, and population structure of beaked whales in the region and globally. To better understand the population structure of these animals, full mitochondrial genomes of both species were generated from 41 stranded and live animals across global ocean basins to analyze the mitogenomic diversity and phylogeographic patterns both around the Bahamas and globally. Within M. densirostris¸ haplotypes were found to be divided into two distinct geographic clades representing possible Atlantic and Pacific sub species or species. In Z. cavirostris, 3 major clades were discovered, however, in two clades both Atlantic and Pacific animals were found, indicating that inter-ocean migration events have occurred relatively recently, or that there is ongoing gene flow for this species between ocean basins. Further sampling of both species and additional data from nuclear DNA will be required to fully resolve this and to better understand and mitigate the effects of naval activities on beaked whale populations within the northern Bahamas and elsewhere.

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