Data from: Mito-nuclear phylogeography of the cyprinid fish Gymnodiptychus dybowskii 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 (highest posterior density (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 (ESUs). They
have experienced decades of anthropogenic disturbance and preservation of
the three species/ESUs will require more sustainable management of the
aquatic resources.