1 SC/61/SM11 Do not cite without permission from the authors Worldwide Phylogeography of the genus Delphinus revisited Ana R. Amaral 1,2,* , Luciano B. Beheregaray 2,6 , Marina Sequeira 3 , Kelly M. Robertson 4 , M. Manuela Coelho 1 and Luciana M. Möller 5,6 1 Universidade de Lisboa, Faculdade de Ciências, Centro de Biologia Ambiental, Campo Grande, 1749-016 Lisbon, Portugal 2 Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia 3 Instituto de Conservação da Natureza e Biodiversidade, Reserva Natural do Estuário do Sado, Praça da República, 2900-587 Setúbal, Portugal 4 National Marine Fisheries Service, Southwest Fisheries Science Center, 3333 N. Torrey Pines Ct., La Jolla, CA 92037, USA 5 Graduate School of the Environment, Macquarie University, Sydney, NSW, 2109, Australia 6 School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia *Contact e-mail: aramaral@fc.ul.pt ; aamaral@bio.mq.edu.au ABSTRACT The genus Delphinus comprises two species and one subspecies: the short-beaked common dolphin, Delphinus delphis (Linnaeus, 1758), distributed in continental shelf and pelagic waters of the Atlantic and Pacific Oceans, the long-beaked common dolphin, D. capensis (Gray, 1828), distributed in nearshore tropical and temperate waters of the Pacific and Southern Atlantic Oceans, and the Arabian long-beaked common dolphin, D. capensis tropicalis van Bree, 1971, which occurs in the Indian Ocean. Here we present a worldwide phylogeographic study based on sequences of the mitochondrial DNA cytochrome b gene. A total of 279 individuals were analysed: 211 D. delphis from the Northeast (82) and Northwest (27) Atlantic, and Northeast (28) and Southwest (74) Pacific; 26 D. capensis from the Northeast Pacific, 18 D. capensis from the Southeast Atlantic, and 24 D. capensis tropicalis from the Indian Ocean. Haplotype and nucleotide diversities of most populations were high when compared with other cetacean species, which is possibly a signature of large, long-term effective population size. Shared haplotypes between the two common dolphin species and subspecies were found, as well as between all oceans sampled. Fixation indices (φ ST and F ST ) show that the tropicalis and D. capensis samples from the NE Pacific are differentiated from samples from all other regions. D. delphis from the Northeast and Southwest Pacific also show some differentiation from samples from other regions, but with relatively low values of fixation indices. In contrast, the median-joining network reveals clusters of haplotypes without a clear geographical or taxonomic correspondence. Overall, these results suggest that relatively high levels of gene flow occur between regions and possibly among recognized species, questioning current taxonomy, confounding population history and making the establishment of population boundaries very difficult. Several phylogeographical hypotheses for the observed patterns are currently being tested with recently developed methods that use coalescent models for estimating demographic parameters. Additionally, data on a powerful set of microsatellite markers are being obtained in order to document the direction and magnitude of events of recent gene flow between populations and oceanic regions. KEYWORDS: common dolphins; short-beaked; long-beaked; Atlantic Ocean; Pacific Ocean; Indian Ocean; taxonomy; gene flow Colour copies of pages 8 and 9 available on request