Data from: The Carpathians hosted extra-Mediterranean refugia-within-refugia during the Pleistocene Ice Age: genomic evidence from two newt genera

Part of Europe’s temperate species survived the Pleistocene glacial cycles in refugia north of the Mediterranean peninsulas. For one such extra-Mediterranean refugia, the Carpathians, an intricate ‘refugia-within-refugia’ scenario has been suggested, involving species surviving in multiple discrete glacial refugia. We test the Carpathian refugia-within-refugia hypothesis, employing genome-wide multilocus datasets for two newt species (Triturus cristatus and Lissotriton montandoni). We first use Bayesian clustering to delineate intraspecific evolutionary lineages. The number of intraspecific lineages identified, and the allocation of localities to these lineages, were used to construct testable hypotheses on the spatial arrangement of glacial refugia in both newt species. Next we employ approximate Bayesian computation to date whether these lineages are of Holocene (< 12 Ka) or Pleistocene (> 12 Ka) origin. We identify three intraspecific evolutionary lineages for T. cristatus and two for L. montandoni. For both newt species, intraspecific divergence is rooted in the Pleistocene, in line with species survival in distinct range fragments during the last glacial period. Hence, our findings firmly support the Carpathian refugia-within-refugia hypothesis. Furthermore, we show that mitochondrial DNA overestimates the age of intraspecific evolutionary lineages and we urge caution in basing refugia-within-refugia scenarios on mitochondrial DNA alone.欧洲部分温带物种在更新世冰期循环中，于地中海半岛以北的冰期避难所（refugia）中得以存续。针对其中一处地中海以外的冰期避难所——喀尔巴阡山脉，学界已提出复杂的“避难所嵌套避难所（refugia-within-refugia）”情景，即物种在多个独立的冰期避难所中存续。本研究以两种蝾螈（*Triturus cristatus* 与 *Lissotriton montandoni*）的全基因组多位点数据集（genome-wide multilocus datasets）为研究材料，检验喀尔巴阡山脉的“避难所嵌套避难所”假说。首先采用贝叶斯聚类（Bayesian clustering）方法界定种内进化支系；基于鉴定得到的种内支系数量，以及各采样点在支系间的分配情况，我们构建了可检验的假说以阐释两种蝾螈的冰期避难所空间分布格局。随后采用近似贝叶斯计算（approximate Bayesian computation）方法，估算这些支系的起源年代，判断其属于全新世（Holocene，<12 Ka）还是更新世（Pleistocene，>12 Ka）。本研究共鉴定出*Triturus cristatus*存在3个种内进化支系，*Lissotriton montandoni*则存在2个。两种蝾螈的种内分化均起源于更新世，与末次冰期期间物种在不同分布片段中存续的推测相符。因此，本研究结果有力支持了喀尔巴阡山脉“避难所嵌套避难所”假说。此外，本研究发现线粒体DNA会高估种内进化支系的起源年代，呼吁学界在构建“避难所嵌套避难所”情景时，不应仅以线粒体DNA作为依据。