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

The identification of species and population boundaries is important in both evolutionary and conservation biology. 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 status and genetic connectedness of bottlenose dolphin (Tursiops spp.) populations off remote northwestern 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 inshore of the 50 m depth contour and 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 genetic 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.,Allen_et_al_IBDIBD analysis using microsatellite data and geographic distancesAllen_et_al_Microsat_DataMicrosatellite data (recoded). For original scores please contact Michael Krützen ([e-mail])Allen_et_al_infile_migrate-n_analysisInput_file_migrate_analysisAllen_et_al_mtDNA_treeNexus mtDNA input file. Identical haplotypes are collapsed.,

物种与种群界限的鉴定，在进化生物学与保护生物学领域均具有重要意义。近年来，一批可定量估算种群参数、检验科学假说的新型种群遗传学与计算方法应运而生。本研究依托贝叶斯框架（Bayesian framework）与定量模型检验思路，对澳大利亚西北偏远海域的宽吻海豚（*Tursiops* spp.）种群的物种地位与遗传连通性展开评估，重点关注易被拖网渔业兼捕的远洋“近海”（offshore）海豚类群。
本研究共分析71份海豚样本，采样点均位于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3处区域，样本涵盖兼捕个体及与拖网渔船伴游的自由活动个体；此外还分析了12处近岸采样点的273份海豚样本，这些采样点均处于50米等深线以内且距海岸不足10公里。
基于19个核微卫星（microsatellite）标记的分析结果显示，渔业作业海域内的海豚与近岸采样点的海豚之间存在显著的种群遗传结构，且近岸采样点的海豚类群内部同样存在遗传分化，共鉴定出3个近岸种群。此外，研究未发现当前或历史上存在基因流进入该渔业区域的近海种群，表明近岸种群未向该近海种群提供任何补充群体。线粒体DNA（mitochondrial DNA）分析结果进一步佐证了近海种群与近岸种群间的遗传隔离：绝大多数近海个体与普通宽吻海豚（*T. truncatus*）构成单系群，而全部273份近岸采样个体均属于支持度较高的印度-太平洋宽吻海豚（*T. aduncus*）支系。
本研究通过引入定量建模方法，将进化过程明确纳入分析框架，为保护物种的保护与管理提供科学依据。因此，本研究可为其他难以开展研究的种群提供可借鉴的研究范式。
附数据文件说明：
1. Allen_et_al_IBD：基于微卫星数据与地理距离的IBD（隔离距离，Isolation by Distance）分析
2. Allen_et_al_Microsat_Data：已重新编码的微卫星数据。如需获取原始得分，请联系Michael Krützen（邮箱：[e-mail]）
3. Allen_et_al_infile_migrate-n_analysis：migrate-n分析输入文件
4. Allen_et_al_mtDNA_tree：Nexus格式线粒体DNA输入文件，相同单倍型已进行合并。