MtDNA-based phylogeography has illuminated the impact of the Pleistocene Ice Age on species distribution dynamics and the build-up of genetic divergence. The well-known shortcomings of mtDNA in biogeographical inference can be compensated by integrating multilocus data and species distribution modelling into phylogeography. We re-visit the phylogeography of the Italian crested newt (Triturus carnifex), a species distributed in two of Europe’s main glacial refugia, the Balkan and Italian Peninsulas. While a new 51 nuclear DNA marker dataset supports the existence of three lineages previously suggested by mtDNA (Balkan, northern Italy and southern Italy), the nuclear DNA dataset also provides improved resolution where these lineages have obtained secondary contact. We observe geographically restricted admixture at the contact between the Balkan and northern Italy gene pools and identify a potential mtDNA ghost lineage here. At the contact between the northern and southern Italy gene pools we find admixture over a broader area, as well as asymmetric mtDNA introgression. Our species distribution model is in agreement with a distribution restricted to distinct refugia during Pleistocene glacial cycles and postglacial expansion with secondary contact. Our study supports: (1) the relevance of the north-western Balkan Peninsula as a discrete glacial refugium; (2) the importance of north-eastern Italy and the northern Apennine as suture zones; and (3) the applicability of a refugia-within-refugia scenario within the Italian Peninsula.

基于MtDNA的系统学已阐明了更新世冰期对物种分布动态和遗传差异的建立的影响。mtDNA在生物地理推断中的众所周知的缺点可以通过将多基因座数据和物种分布模型整合到系统地理学中来弥补。我们再次参观了意大利凤头new（Triturus carnifex），分布在欧洲两个主要的冰川避难所，巴尔干和意大利半岛。新的51核DNA标记数据集支持mtDNA先前建议的三个谱系（巴尔干，意大利北部和意大利南部）的存在，而核DNA数据集在这些谱系获得二级接触的情况下也提供了更高的分辨率。我们在巴尔干和意大利北部的基因库之间的接触处观察到受地域限制的混合物，并在此处确定了潜在的mtDNA幽灵谱系。在意大利北部和南部基因库之间的接触中，我们发现在更广泛的区域存在混合体，以及不对称的mtDNA渗入。我们的物种分布模型与更新世冰川周期和次生接触后冰期扩张期间仅限于不同避难所的分布相一致。我们的研究支持：（1）西北巴尔干半岛作为离散冰川避难所的相关性；（2）意大利东北部和亚平宁北部作为缝合区的重要性；（3）在意大利半岛内实行避难所方案的适用性。