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.

最大的无肺螈科（Plethodontidae）类群的深层系统发育关系长期以来难以解析，这大概率反映了该类群在演化早期经历了快速辐射分化。本研究采集了50个独立核标记（总长度48582 bp）的数据，结合串联法与基于溯祖的物种树分析，重建了无肺螈的系统发育关系与分化时间。研究结果稳健地确定了神秘的北美东部四趾螈（Hemidactylium）的系统发育位置：其为滑趾螈属（Batrachoseps）与褶口螈族（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，本研究通过统计学方法否定了Karsenia属与Hydromantes属作为姊妹群的地位——这两个属是仅有的分布于美洲之外的无肺螈类，该结果为我们提出了全新的生物地理学假说。与此前学界长期持有的“无肺螈起源于白垩纪（距今超90 Ma）的古老类群”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，其起源接近白垩纪-古近纪（K-T）界线（约66 Ma）。采用不同的校准方案与定年方法得到的时间估算结果均具有极高的稳定性。本研究的数据模拟实验凸显了学界常见做法的潜在风险：基于少量核基因推断系统发育时间并得出强结论。基于本次研究获得的全新时间树与祖先分布区重建结果，我们提出以下三点论点：其一，经典的“源自阿巴拉契亚”无肺螈起源假说存在缺陷；其二，现存无肺螈的共同祖先可能起源于古新世早期的北美西北部；其三，欧亚无肺螈类的起源大概率源自两次独立的扩散事件：分别在始新世晚期（约42 Ma）与中新世早期（约23 Ma）通过白令陆桥从北美西部扩散而来。