Speciation models relying on geographic barriers to limit gene flow gather widespread consensus, but are insufficient to explain diversification in highly mobile marine organisms. Adaptation to different environments has been suggested as an alternative driver for differentiation, particularly in cetaceans. In this study, patterns of population structure at neutral and functional markers were investigated for both common (Delphinus delphis) and bottlenose dolphin (Tursiops spp.), chosen due to high levels of morphological and ecological variation within each genus. Candidate functional markers were selected by investigating signals of positive selection in both mammals and cetaceans. \ud No population structure was found in the European common dolphin for neutral microsatellite loci, in contrast to what is observed in other sympatric cetacean species. The previously described differention of the Eastern Mediterranean Sea population, probably results from a recent human-mediated bottleneck. Functional markers showed almost complete uniformity suggesting purifying selection. One non-synonymous mutation in β-casein and the DQβ1 locus were exceptions, with patterns of population differentiation possibly the result of differences in local selective pressures.\ud Additionally, large mitogenomic sequences were used to investigate the worldwide phylogeography of several ecotypes/species within the genus Tursiops, with a recent biogeographical calibration point being used to calculate divergence times. Good node resolution with high statistical support was achieved, with good separation between most ecotypes in their own lineages. However, the results give no support for a monophiletic Tursiops. Divergence times are clustered in specific geological periods characterized by climatic fluctuations from cold to warmer periods. \ud The Common and bottlenose dolphins exhibit contrasting patterns of population structure in an environment containing few geographical barriers. Such difference is speculated to be related with different feeding ecologies and social structures, although data on such are still limited. Although selection can be detected in the genomes of cetaceans both at the species and population level, current patterns of differentiation are thought to occur mainly due to drift. \u
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