Connecting Populations Across Ocean Basins: Genomics of Short-finned Pilot Whales (Globicephala macrorhynchus) in the Western North Atlantic

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Short-finned pilot whales (Globicephala macrorhynchus) are widely-distributed throughout the Atlantic Ocean. These whales are capable of traveling large distances, yet their regional movement patterns and population structure are poorly defined, making stock identification and species management challenging. To understand the population structure of these whales, I analyzed genetic relatedness across 56 distinct individuals in three geographic locations: the Caribbean nation of St. Vincent & the Grenadines (n = 17), Florida, USA (n = 7), and North Carolina, USA (n = 36). I generated genetic sequences from tissue samples using double digest restriction site associated DNA sequencing (ddRAD-Seq). I then derived 3,227 single nucleotide polymorphisms (SNPs) from the Freebayes bioinformatics pipeline. To infer population structure, I used a Bayesian clustering analysis implemented in STRUCTURE software. The results indicate that individuals from all of the three sampling locations are genetically similar. This supports the hypothesis that there is substantial gene flow between the eastern Caribbean and southeast United States. It is likely that the Gulf Stream and extensive continental shelf facilitate long-ranging individual or group movement, and thus connectivity. Interestingly, results also indicate a second, genetically-distinct population comprised of three individuals (two from St. Vincent and one from North Carolina). While more sampling is needed to confirm this second population, it is possible that there is a larger oceanic stock in the western North Atlantic. Together, these findings can be used to better inform the management of short-finned pilot whales, which is imperative considering rising anthropogenic pressures, mass-strandings, and the species’ cultural importance in artisanal whaling.






Hanson, Sophie (2022). Connecting Populations Across Ocean Basins: Genomics of Short-finned Pilot Whales (Globicephala macrorhynchus) in the Western North Atlantic. Honors thesis, Duke University. Retrieved from

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