The current taxonomic status of Sotalia species is uncertain. The genus once comprised five species, but in the twentieth century they were grouped into two (riverine Sotalia fluviatilis and marine Sotalia guianensis) that later were further lumped into a single species (S. fluviatilis), with marine and riverine ecotypes. This uncertainty hampers the assessment of potential impacts on populations and the design of effective conservation measures. We used mitochondrial DNA control region and cytochrome b sequence data to investigate the specific status of S. fluviatilis ecotypes and their population structure along the Brazilian coast. Nested-clade (NCA), phylogenetic analyses and analysis of molecular variance of control region sequences showed that marine and riverine ecotypes form very divergent monophyletic groups (2.5% sequence divergence; 75% of total molecular variance found between them), which have been evolving independently since an old allopatric fragmentation event. This result is also corroborated by cytochrome b sequence data, for which marine and riverine specimens are fixed for haplotypes that differ by 28 (out of 1,140) nucleotides. According to various species definition methods, we conclude that marine and riverine Sotalia are different species. Based on priority criteria, we recommend the revalidation of Sotalia guianensis (Van Bénéden 1864) for the marine animals, while riverine dolphins should retain the species name Sotalia fluviatilis (Gervais 1853), thus becoming the first exclusively riverine delphinid. The populations of S. guianensis show a strong subdivision (ΦST=0.628) along the Brazilian coast, with at least three evolutionarily significant units: north, northeastern and south/southeastern. © Springer-Verlag 2005.
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