Data from: Mito-nuclear phylogeography of the cyprinid fish Gymnodiptychus dybowskii: long-term vicariance and distinct demographic histories in the arid Tien Shan region of Central Asia

We evaluated the phylogeography and historical demography of the cyprinid fish Gymnodiptychus dybowskii (subfamily Schizothoracinae) across three Northern Qinghai-Tibetan Plateau (QTP) river systems in the Tien Shan range: the Kaidu River, Ili River and Junggar Basin. Results from both mtDNA (16S rRNA and Cyt b) and nuDNA (RAG-2) resolved three reciprocally monophyletic clades, one in each of the three river basins. Estimated divergence times (HPD 2.4-3.7 Mya) are consistent with the hypothesis that these three clades are products of vicariance resulting from the intensive uplift of QTP and Tien Shan, and resulting expansion of the Taklimakan and Gurbantunggut deserts. Several lines of evidence indicate dynamic demographic histories for the three clades, with late Quaternary population bottlenecks and expansions in the Kaidu and Ili rivers and, possibly, a Holocene decline in the Junggar Basin. For conservation purposes, the three clades should be treated as species or minimally, as evolutionarily significant units. They have experienced decades of anthropogenic disturbance and preservation of the three species/ESUs will require more sustainable management of the aquatic resources.我们针对天山山脉范围内青藏高原（Qinghai-Tibetan Plateau, QTP）北部三大河流水系（开都河、伊犁河及准噶尔盆地流域）中的鲤科（Cyprinidae）鱼类裸腹重唇鱼（Gymnodiptychus dybowskii，裂腹鱼亚科Schizothoracinae）的系统地理学（phylogeography）与历史种群动态（historical demography）开展了评估。基于线粒体DNA（mtDNA，包含16S核糖体RNA（16S rRNA）与细胞色素b（Cyt b）基因）及核DNA（nuDNA，重组激活基因2（RAG-2））的分析结果均显示，存在三个相互单系的演化支，且三者分别对应上述三大流域。估算得到的分化时间（最高后验密度（Highest Posterior Density, HPD）区间为2.4~3.7百万年前（Mya））与以下假说相符：这三个演化支是由青藏高原与天山的强烈隆升、以及塔克拉玛干沙漠和古尔班通古特沙漠扩张所引发的地理隔离分化所形成的产物。多项证据表明这三个演化支均经历了动态的种群历史：开都河与伊犁河流域的种群在晚第四纪时期出现了种群瓶颈与扩张事件，而准噶尔盆地种群可能在全新世出现了种群衰退。从保护生物学角度而言，这三个演化支应被划分为独立物种，至少应作为进化显著单元（evolutionarily significant units, ESUs）进行管理。该类群已遭受数十年的人为干扰，因此对这三个物种/进化显著单元的保护，需要对水生生物资源实施更可持续的管理措施。