Data from: The Near East as a cradle of biodiversity: a phylogeography of banded newts (genus Ommatotriton) reveals extensive inter- and intraspecific genetic differentiation

The banded newt (genus Ommatotriton) is widely distributed in the Near East (Anatolia, Caucasus and the Levant) – an understudied region from the perspective of phylogeography. The genus is polytypic, but the number of species included and the phylogenetic relationships between them are not settled. We sequenced two mitochondrial and two nuclear DNA markers throughout the range of Ommatotriton. For mtDNA we constructed phylogenetic trees, estimated divergence times using fossil calibration, and investigated changes in effective population size with Bayesian skyline plots and mismatch analyses. For nuDNA we constructed phylogenetic trees and haplotype networks. Species trees were constructed for all markers and nuDNA only. Species distribution models were projected on current and Last Glacial Maximum climate layers. We confirm the presence of three Ommatotriton species: O. nesterovi, O. ophryticus and O. vittatus. These species are genetically distinct and their most recent common ancestor was dated at ∼25 Ma (Oligocene). No evidence of recent gene flow between species was found. The species show deep intraspecific genetic divergence, represented by geographically structured clades, with crown nodes of species dated ∼8-13 Ma (Miocene to Early Quaternary); evidence of long-term in situ evolution and survival in multiple glacial refugia. While a species tree based on nuDNA suggested a sister species relationship between O. vittatus and O. ophryticus, when mtDNA was included, phylogenetic relationships were unresolved, and we refrain from accepting a particular phylogenetic hypothesis at this stage. While species distribution models suggest reduced and fragmented ranges during the Last Glacial Maximum, we found no evidence for strong population bottlenecks. We discuss our results in in the light of other phylogeographic studies from the Near East. Our study underlines the important role of the Near East in generating and sustaining biodiversity.

带纹蝾螈（带纹蝾螈属*Ommatotriton*）广泛分布于近东地区（安纳托利亚、高加索及黎凡特）——从系统地理学（phylogeography）视角来看，该区域长期以来研究程度较低。该属为多型属，但所含物种数量及其间的系统发育关系尚未明确。我们针对带纹蝾螈属的整个分布范围，对2个线粒体DNA（mtDNA）标记与2个核DNA（nuDNA）标记完成了测序。针对线粒体DNA，我们构建了系统发育树，利用化石校准估算了分化时间，并通过贝叶斯天际线图（Bayesian skyline plot）与错配分布分析探究了有效种群大小的变化；针对核DNA，我们构建了系统发育树与单倍型网络（haplotype network）。我们分别基于全部标记数据集、仅核DNA标记数据集构建了物种树（species tree）。将物种分布模型投影至当前气候层与末次盛冰期（Last Glacial Maximum）气候层中。本研究确认带纹蝾螈属存在3个物种：O. nesterovi、O. ophryticus及O. vittatus。这些物种在遗传上彼此分化，其最近共同祖先的分化时间可追溯至约2500万年前（渐新世）。未发现物种间存在近期基因交流的证据。该属物种存在深度的种内遗传分化，表现为具有地理结构的演化支（clade），物种冠节点的分化时间约为800万至1300万年前（中新世至早更新世），这证明了多个冰期避难所中物种的长期原地演化与存续过程。尽管基于核DNA的物种树显示O. vittatus与O. ophryticus为姊妹群关系，但当纳入线粒体DNA数据后，系统发育关系变得无法解析，因此我们现阶段暂不接受某一特定的系统发育假说。虽然物种分布模型显示末次盛冰期时期物种的分布范围曾出现缩减与片段化，但我们未发现存在严重种群瓶颈（population bottleneck）的证据。我们结合近东地区其他系统地理学研究对本研究结果展开了讨论。本研究强调了近东地区在生物多样性的产生与维持中所发挥的重要作用。