| Summary: | Bottlenose dolphins (Tursiops truncatus) are widely accepted as belonging to one of two ecotypes: offshore or inshore. These ecotypes exhibit remarkable differences in ecology, morphology, and genetic diversity. However, regional patterns of genetic differentiation and stock delineation remain poorly defined for both ecotypes. To improve our understanding of the population structures among these groups we investigated genome-wide genetic variation from 96 biopsy samples collected from bottlenose dolphins in inshore and offshore waters of the northwest Atlantic from North Carolina to Florida using restriction site associated DNA sequencing to infer population structure. Analysis of 14,783 single nucleotide polymorphisms revealed at least three genetically differentiated populations. Our results suggest an inshore population along North Carolina’s Outer Banks (n=32), an offshore population off the continental shelf break from North Carolina to Jacksonville, Florida (n= 38), and a shelf population off Jacksonville, Florida (n=26). Bayesian clustering showed significant admixture between the North Carolina and Jacksonville populations, providing potential evidence of historical or current gene flow. Most of the offshore samples were collected off Cape Hatteras, but this population also includes four individuals sampled beyond the continental shelf break off Jacksonville, FL, in close spatial proximity to shelf animals. This suggests a sharp distinction between shelf and offshore individuals structured by the shelf break itself. Such habitat heterogeneity is likely a driver in diversifying populations through influences on social behavior and foraging strategies. Our analyses provide fine-scale genetic resolution of bottlenose dolphin population differentiation in the Western North Atlantic. These results help inform conservation management and advance our understanding of processes that may drive the evolution of population genetic structure.
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