Data from: Interaction of sequence data and paleogeographic priors in biogeographic dating: How could biological data inform time-constrained geological models?

Biological and geographic patterns and processes are linked such that
biological data hold information on paleogeographical patterns and
processes. Here, we aimed to test Biogeographic dating as a methodological
framework for the integration of biological, paleontological, and
geological data to test paleogeographic hypotheses. In Biogeographic
dating, both forms of data are specified and analyzed simultaneously. We
evaluate how uncertainty and accuracy in both types of datasets affect the
inference of divergence times used as a proxy for generating or testing
geological models. We used data simulation to generate a paleogeographic
scenario and a nuclear sequence dataset for lineages whose evolution is
correlated with geological patterns. Then, gene flow was simulated across
landscape units, such that biological patterns inferred from sequence data
would deviate from simulated times of paleogeographic change. Under those
two scenarios, we specified broad, incorrect, and accurate geological
priors. These various scenarios were analyzed through Biogeographic dating
analyses run in RevBayes and compared with our simulations. In
doing so, we test the potential for well-calibrated phylogenies and the
impact of accuracy and uncertainty in geological priors for estimating
paleogeographic events.

生物模式与地理模式、生物过程与地理过程之间存在紧密关联，因此生物数据蕴含着古地理模式与古地理过程的相关信息。本研究旨在验证生物地理年代学（Biogeographic dating）作为整合生物、古生物与地质数据的方法框架，用于检验古地理假说的可行性。在生物地理年代学分析中，两类数据会被同时指定并开展分析。本研究评估了两类数据集的不确定性与准确性，会如何影响以分化时间作为替代指标的推断过程——该过程用于生成或检验地质模型。我们通过数据模拟，为演化与地质模式相关的类群构建了古地理场景与核序列数据集。随后，我们在不同景观单元间模拟了基因流，使得基于序列数据推断得到的生物模式，与模拟得到的古地理变化时间出现偏差。针对上述两种模拟场景，我们分别设定了宽泛、错误以及准确的地质先验分布。我们借助在RevBayes中运行的生物地理年代学分析，对各类场景展开分析，并将分析结果与模拟结果进行对比。通过上述步骤，本研究检验了校准良好的系统发育树的应用潜力，同时评估了地质先验的准确性与不确定性对古地理事件估算的影响。