Data from: Genetic isolation between coastal and fishery-impacted, offshore bottlenose dolphin (Tursiops spp.) populations

The identification of species and population boundaries are important in both evolutionary biology and conservation. In recent years, new population genetic and computational methods for estimating population parameters and testing hypotheses in a quantitative manner have emerged. Using a Bayesian framework and a quantitative model-testing approach, we evaluated the species affiliations and genetic connectivity of bottlenose dolphin (Tursiops spp.) populations off remote north-western Australia, with a focus on pelagic ‘offshore’ dolphins subject to incidental capture in a trawl fishery. We analysed 71 dolphin samples from three sites beyond the 50 m depth contour (the inshore boundary of the fishery) and up to 170 km offshore, including incidentally caught and free-ranging individuals associating with trawl vessels; and 273 dolphins sampled at 12 coastal sites within 10 km of the coast. Results from 19 nuclear microsatellite markers showed significant population structure between dolphins from within the fishery and coastal sites, but also among dolphins from coastal sites, identifying three coastal populations. Moreover, we found no current or historic gene flow into the offshore population in the region of the fishery, indicating a complete lack of recruitment from coastal sites. Mitochondrial DNA corroborated our findings of reproductive isolation between dolphins from the offshore population and coastal sites. Most offshore individuals formed a monophyletic clade with common bottlenose dolphins (T. truncatus), while all 273 individuals sampled coastally formed a well-supported clade of Indo-Pacific bottlenose dolphins (T. aduncus). By including a quantitative modelling approach, our study explicitly took evolutionary processes into account for informing the conservation and management of protected species. As such, it may serve as a template for other, similarly inaccessible study populations.

物种与种群边界的鉴定在进化生物学与物种保护领域均具有重要意义。近年来，用于定量估算种群参数、检验假说的新型种群遗传学与计算方法相继涌现。本研究依托贝叶斯框架（Bayesian framework）与定量模型检验方法，对澳大利亚西北部偏远海域的宽吻海豚（*Tursiops* spp.）种群的物种归属与遗传连通性进行了评估，重点关注易被拖网渔业兼捕的远洋离岸型宽吻海豚种群。我们共分析了71份海豚样本，采集自3个位于50米等深线（该拖网渔业的近岸作业边界）以外、离岸最远达170公里的海域，样本包括兼捕个体以及与拖网渔船伴游的自由活动个体；同时采集了12个沿岸站点的273份海豚样本，所有站点均位于距岸10公里范围内。基于19个核微卫星标记（nuclear microsatellite markers）的分析结果显示，渔业作业海域内的海豚种群与沿岸种群之间存在显著的种群结构差异，且沿岸种群内部亦存在分化，共鉴定出3个沿岸种群。此外，本研究未发现当前或历史时期有基因流流入该渔业区域内的远洋种群，表明沿岸种群未向该远洋种群提供任何种群补充。线粒体DNA（mitochondrial DNA）分析结果进一步验证了远洋种群与沿岸种群之间存在生殖隔离的结论：绝大多数远洋个体与普通宽吻海豚（*T. truncatus*）构成单系群，而全部273份沿岸样本均隶属于支持度较高的印太宽吻海豚（*T. aduncus*）单系支系。本研究通过采用定量建模方法，将演化过程明确纳入保护管理的考量范畴，为受保护物种的保护与管理提供了科学依据。该研究可为其他难以开展实地研究的同类种群提供参考范式。