PRIMARY RESEARCH PAPER Genetics and stable isotopes reveal non-obvious population structure of bottlenose dolphins (Tursiops truncatus) around the Balearic Islands Jose´ M. Brotons . Valentina Islas-Villanueva . Carme Alomar . Ariadna Tor . Ruth Ferna´ndez . Salud Deudero Received: 18 March 2018 / Revised: 26 July 2019 / Accepted: 29 July 2019 Ó Springer Nature Switzerland AG 2019 Abstract The effective management of wildlife requires that populations are deﬁned in a biological sensible manner. We investigated the population structure of bottlenose dolphins (Tursiops truncatus) in waters around the Balearic archipelago using two complementary techniques; DNA markers (i.e. microsatellites and a portion of the mitochondrial control region) and stable isotopes (d 13 C, d 15 N). We used tissue samples from biopsies (n = 50) and fresh carcasses (n = 7) obtained around the islands of Gimne`sies and Pitiu¨ses, and Comunitat Valenciana (Western Mediterranean Sea). Genetic differentiation between individuals from Gimne´sies and Pitiu¨ses and between individuals from across these two areas and individuals from Comunitat Valenciana was signiﬁ- cant when assessing F ST , but no substructure was found using clustering methods (i.e. DAPC and Bayesian clustering). d 13 C and d 15 N proﬁles were not signiﬁcantly different between dolphins from Gimne´sies and Pitiu¨ses. Dolphins from both areas showed coastal carbon isotopic values and similar trophic niche levels. However, the trophic niche of dolphins from Gimne´sies was broader than the trophic niche of Pitiu¨ ses’ dolphins. These results indicate non- obvious population structure between the mainland and the archipelago, or between islands within the archipelago. The use of combined techniques, which integrate information over different time scales, is applicable to other species and areas. Handling editor: Diego Fontaneto Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10750-019-04038-7) con- tains supplementary material, which is available to authorized users. J. M. Brotons (&) Direccio´ General de Medi Rural i Marı ´, Govern de les Illes Balears, Foners 10, 07006 Palma, Balearic Islands, Spain e-mail: txemabrotons@asociaciontursiops.org J. M. Brotons Asociacio´n Tursiops, c/Pop, 25 1er. 07639, Sa Ra`pita, Balearic Islands, Spain V. Islas-Villanueva Sea Mammal Research Unit, Scottish Oceans Institute, University of St. Andrews, St. Andrews, Fife KY16 8LB, UK V. Islas-Villanueva CONACYT Universidad del Mar, Cd. Universitaria, Puerto A ´ ngel, San Pedro Pochutla, 70902 Oaxaca, Mexico C. Alomar  A. Tor  S. Deudero Instituto Espan˜ol de Oceanografı ´a, Centre Oceanogra`ﬁc de les Balears, Moll de Ponent s/n, 07015 Palma, Balearic Islands, Spain R. Ferna´ndez International Council for the Exploration of the Sea (ICES), HC Andersens Boulevard 44-46, 1553 Copenhagen, Denmark 123 Hydrobiologia https://doi.org/10.1007/s10750-019-04038-7