Data from: Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders

Incorporation of fossils into biogeographic studies can have a profound effect on the conclusions that result, particularly when fossil ranges are nonoverlapping with extant ranges. This is the case in archaeid spiders, where there are known fossils from the Northern Hemisphere, yet all living members are restricted to the Southern Hemisphere. To better understand the biogeographic patterns of archaeid spiders and their palpimanoid relatives, we estimate a dated phylogeny using a relaxed clock on a combined molecular and morphological data set. Dating information is compared with treating the archaeid fossil taxa as both node calibrations and as noncontemporaneous terminal tips, both with and without additional calibration points. Estimation of ancestral biogeographic ranges is then performed, using likelihood and Bayesian methods to take into account uncertainty in phylogeny and in dating. We find that treating the fossils as terminal tips within a Bayesian framework, as opposed to dating the phylogeny based only on molecular data with the dates coming from node calibrations, removes the subjectivity involved in assigning priors, which has not been possible with previous methods. Our analyses suggest that the diversification of the northern and southern archaeid lineages was congruent with the breakup of Pangaea into Laurasia and Gondwanaland. This analysis provides a rare example, and perhaps the most strongly supported, where a dated phylogeny confirms a biogeographical hypothesis based on vicariance due to the breakup of the ancient continental plates.

将化石纳入生物地理学研究，可对研究结论产生深远影响，尤其当化石分布范围与现生类群的分布范围无重叠时。古蛛科蜘蛛（Archaeid spiders）便是典型案例：北半球已发现其化石记录，但所有现生类群均仅分布于南半球。
为更好地解析古蛛科蜘蛛及其猛蛛总科（Palpimanoidea）近亲类群的生物地理分布格局，本研究基于分子与形态学联合数据集，采用松弛分子钟（relaxed clock）构建定年系统发育树（dated phylogeny）。我们将古蛛科化石类群分别作为节点定标（node calibrations）与非同期末端分类单元（noncontemporaneous terminal tips）进行分析，并设置添加额外定标点与不添加额外定标点的对比实验，以评估不同处理策略的效果。随后采用似然法（likelihood）与贝叶斯方法（Bayesian methods）估算祖先生物地理分布范围，以纳入系统发育重建与定年过程中的不确定性。
研究发现，相较于仅基于分子数据、以节点定标获取定年信息的系统发育定年方法，在贝叶斯框架（Bayesian framework）中将化石作为末端分类单元进行分析，可消除先验分布（priors）赋值过程中的主观性——这是以往研究方法无法实现的。
分析结果显示，南北半球古蛛类支系的分化时间，与盘古大陆（Pangaea）裂解为劳亚大陆（Laurasia）和冈瓦纳大陆（Gondwanaland）的地质事件高度吻合。本研究提供了一个罕见案例，或许是目前支持度最高的案例：定年系统发育树验证了基于古大陆裂解引发的隔离分化（vicariance）所提出的生物地理学假说。