Data from: Enlarged multilocus dataset provides surprisingly younger time of origin for the Plethodontidae, the largest family of salamanders

Deep phylogenetic relationships of the largest salamander family Plethodontidae have been difficult to resolve, probably reflecting a rapid diversification early in their evolutionary history. Here, data from 50 independent nuclear markers (total 48,582 bp) are used to reconstruct the phylogeny and divergence times for plethodontid salamanders, using both concatenation and coalescence-based species-tree analyses. Our results robustly resolve the position of the enigmatic eastern North American Four-toed Salamander (Hemidactylium) as the sister taxon of Batrachoseps + Tribe Bolitoglossini, thus settling a longstanding question. Furthermore, we statistically reject sister taxon status of Karsenia and Hydromantes, the only plethodontids to occur outside the Americas, leading us to new biogeographic hypotheses. Contrary to previous longstanding arguments that plethodontid salamanders are an old lineage originating in the Cretaceous (more than 90 Ma), our analyses lead to the hypothesis that these salamanders are much younger, arising close to the K-T boundary (~66 Ma). These time estimates are highly stable using alternative calibration schemes and dating methods. Our data simulation highlights the potential risk of making strong arguments about phylogenetic timing based on inferences from a handful of nuclear genes, a common practice. Based on the newly obtained timetree and ancestral area reconstruction results, we argue that (i) the classic “Out of Appalachia” hypothesis of plethodontid origins is problematic; (ii) the common ancestor of extant plethodontids may have originated in northwestern North America in the early Paleocene; (iii) origins of Eurasian plethodontids likely result from two separate dispersal events from western North America via Beringia in the late Eocene (~ 42 Ma) and the early Miocene (~ 23 Ma), respectively.

最大的蝾螈类群——无肺螈科（Plethodontidae）的深层系统发育关系长期以来难以厘清，这大概率反映了其演化早期曾发生快速辐射分化。本研究利用50个独立核标记（总长度48582 bp），采用串联分析与基于溯祖理论的物种树分析两种方法，重建了无肺螈的系统发育关系并估算了类群的分歧时间。

研究结果稳健地确定了北美东部神秘四趾蝾螈（Four-toed Salamander，Hemidactylium）的系统发育位置：其为肢突蝾螈属（Batrachoseps）与无肺螈族（Bolitoglossini）的姊妹群，从而解决了这一长期悬而未决的学术问题。此外，本研究从统计学上否定了开氏蝾螈属（Karsenia）与洞螈属（Hydromantes）作为姊妹群的分类地位——这二者是仅有的分布于美洲之外的无肺螈类，这一结论为我们提出全新的生物地理假说提供了依据。

与此前长期流行的“无肺螈类是起源于白垩纪（距今超过90 Ma）的古老支系”这一观点相悖，本研究的分析结果表明该类群的起源时间要晚得多，大致形成于白垩纪-古近纪界线（K-T boundary）附近（约66 Ma）。该时间估算结果在采用不同校准方案与定年方法时均表现出极高的稳定性。

我们的数据模拟实验揭示了当前学界的一项潜在风险：以少量核基因的推断为依据构建系统发育时间框架的常见做法，可能会得出过于绝对的结论。基于本研究获得的新的时间校准树与祖先分布区重建结果，我们提出如下论点：（1）经典的“起源于阿巴拉契亚地区”的无肺螈类起源假说存在瑕疵；（2）现生无肺螈类的共同祖先可能起源于古新世早期的北美西北部；（3）欧亚大陆无肺螈类的起源大概率对应两次分别发生于始新世晚期（约42 Ma）与中新世早期（约23 Ma）的、经由白令陆桥（Beringia）从北美西部向外扩散的事件。