Data from: Phylogeny and temporal diversification of the New World pond turtles (Emydidae)

We present a comprehensive multigene phylogeny and time tree for the turtle family Emydidae. Our phylogenetic analysis, based on 30 nuclear and four mitochondrial genes (23,330 total base pairs) sequenced for two individuals for each of the currently recognized species of the subfamily Emydinae and two species from each of the more species-rich Deirochelyinae genera, yielded a well-supported tree that provides an evolutionary framework for this well-studied clade and a basis for a stable taxonomy. We calibrated an emydid time tree using three well-vetted fossils, modeled uncertainty in fossil ages to reflect their accuracy in node dating, and extracted stem/crown ages of a number of key diversification events. We date the age of crown emydids at a relatively young 44 Ma, and the crown age of both contained subfamilies at roughly 30 Ma. One deirochelyine clade, which includes the genera Graptemys, Malaclemys, Pseudemys, and Trachemys and contains 11% of all turtle species, dates to 21 Ma just prior to the mid-Miocene climatic optimum, suggesting a potential causal link between warm, moist conditions and rapid species accumulation of these highly aquatic turtles. Both nuclear DNA data alone and in combination with mitochondrial DNA support the monophyly of an inclusive genus Emys containing the old world species orbicularis and trinacris and the new world blandingii, marmorata and pallida. Given that all members of this group were originally aligned in the genus Emys and that the age of the clade is roughly equal to other emydine genera, we strongly support a classification that places these five species in a single genus rather than the alternative three-genus scheme (Emys (orbicularis, trinacris), Actinemys (marmorata, pallida), Emydoidea (blandingii). The phylogeny and resulting time tree presented here provides a comprehensive foundation for future comparative analyses of the Emydidae that will shed light on the historical ecology and conservation prioritization of this diverse chelonian clade.我们针对泽龟科（Emydidae）构建了一套全面的多基因系统发育与时间树。本研究基于30个核基因与4个线粒体基因（总碱基对长度达23330 bp）开展系统发育分析，测序样本涵盖泽龟亚科（Emydinae）当前所有已确认物种各2个个体，以及物种更丰富的曲颈龟亚科（Deirochelyinae）各属各2个物种，最终得到一棵支持度良好的系统发育树，为这一被广泛研究的演化支提供了演化框架，同时可为稳定分类体系奠定基础。我们采用3个经过严格验证的化石对泽龟科时间树进行定年校准，并通过模拟化石年代的不确定性来反映节点定年的准确性，同时提取了多个关键分化事件的茎群/冠群分化时间。我们测算得到泽龟科冠群的分化时间约为距今44 Ma，较为年轻；而两个所含亚科的冠群分化时间均约为30 Ma。其中一个曲颈龟亚科演化支包含地图龟属（Graptemys）、菱斑龟属（Malaclemys）、伪龟属（Pseudemys）与彩龟属（Trachemys），涵盖了11%的现存龟类物种，其分化时间为距今21 Ma，恰处于中新世气候适宜期（mid-Miocene climatic optimum）之前，这暗示温暖湿润的环境与这类高度水生的龟类的快速物种形成之间可能存在因果关联。仅基于核DNA数据，以及核DNA与线粒体DNA联合的数据，均支持广义泽龟属（Emys）为单系群，该类群包含旧世界的欧洲泽龟（E. orbicularis）与西西里泽龟（E. trinacris），以及新世界的布氏泽龟（E. blandingii）、大理石泽龟（E. marmorata）与淡色泽龟（E. pallida）。鉴于该类群所有成员最初均被划归泽龟属，且该演化支的分化时间与其他泽龟亚科属群大致相当，我们强烈支持将这5个物种归入单一属的分类体系，而非学界此前采用的三属划分方案：泽龟属（Emys，仅含orbicularis与trinacris）、星点龟属（Actinemys，含marmorata与pallida）以及拟泽龟属（Emydoidea，含blandingii）。本研究构建的系统发育树与配套时间树，为未来针对泽龟科开展的比较分析提供了全面的基础，有望为这一多样的龟类演化支的历史生态学研究与保护优先级制定提供重要启示。