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.带纹新蝾螈（肋突螈属，Ommatotriton）广泛分布于近东地区（安纳托利亚、高加索以及黎凡特）——从系统生物地理学（phylogeography）视角来看，该区域长期以来研究程度较低。该属为多型属，但所含物种数目及其相互间的系统发育关系尚未达成共识。我们在肋突螈属的整个分布范围内，对2个线粒体DNA（mitochondrial DNA, mtDNA）标记与2个核DNA（nuclear DNA, nuDNA）标记进行了测序。针对线粒体DNA，我们构建了系统发育树，采用化石校准法估算分化时间，并借助贝叶斯天际线图与错配分析探究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。研究人员分别基于全部标记、仅基于核DNA标记构建了物种树。我们将物种分布模型投射于当前气候图层与末次盛冰期（Last Glacial Maximum, LGM）气候图层之上。本研究确认肋突螈属存在3个物种：涅斯特罗夫肋突螈（O. nesterovi）、眼纹肋突螈（O. ophryticus）与带纹肋突螈（O. vittatus）。这些物种在遗传上彼此分化显著，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。这些物种存在显著的种内遗传分化，表现为具有地理结构的支系，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），这一结果为其在多个冰期避难所（glacial refugia）中长期原地演化与存续提供了证据。尽管基于核DNA构建的物种树显示带纹肋突螈与眼纹肋突螈为姐妹种关系，但当纳入线粒体DNA数据后，系统发育关系变得无法明确，因此本研究现阶段暂不采信某一特定的系统发育假说。尽管物种分布模型显示末次盛冰期期间该属的分布范围缩减且碎片化，但我们未发现存在严重种群瓶颈（population bottlenecks）的证据。我们结合近东地区其他系统生物地理学研究，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形成与维持过程中的重要作用。