Fine-scale genetic structure in Lahille’s bottlenose dolphins (Tursiops truncatus gephyreus) is associated with social structure and feeding ecology

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Varying levels of population structure may arise from interactions between intrinsic behavioral and demographic factors and extrinsic environmental factors. Social organization, habitat use, resource partitioning, or even individual preferences are putative drivers of population genetic differentiation over fine spatial scales. Here, genome-wide data from single-nucleotide polymorphisms (SNPs) and carbon and nitrogen stable isotope data were used to examine population structure and niche partitioning among three social units of bottlenose dolphins with strong home range overlap in a relatively small geographic area in southern Brazil. Results from model-based and model-free analyses of population structure supported the delineation of two populations, one with preferences for estuarine waters and another strictly coastal, consistent with isotopic niche differentiation. These findings suggest that genetic and ecological structuring is mainly driven by habitat use. At finer scale, we also detected low but significant genetic differentiation among the three social units. The outcomes of this study provide new insights into population structure of Lahille’s bottlenose dolphins in the Patos Lagoon estuary and its adjacent coastal waters, which are exposed to increasing levels of anthropogenic disturbances, such as intensive artisanal fisheries, pollution, and boat traffic. Although for demographic studies, the estuary and the coastal dolphins should be treated separately, for conservation purposes, we recommend that the three social units be regarded as different entities.