Data from: Model selection in historical biogeography reveals that founder-event speciation is a crucial process in island clades

Founder-event speciation, where a rare jump dispersal event founds a new genetically isolated lineage, has long been considered crucial by many historical biogeographers, but its importance is disputed within the vicariance school. Probabilistic modeling of geographic range evolution creates the potential to test different biogeographical models against data using standard statistical model choice procedures, as long as multiple models are available. I re-implement the Dispersal-Extinction-Cladogenesis (DEC) model of LAGRANGE in the R package BioGeoBEARS, and modify it to create a new model, DEC+J, which adds founder-event speciation, the importance of which is governed by a new free parameter, j. The identifiability of DEC and DEC+J is tested on datasets simulated under a wide range of macroevolutionary models where geography evolves jointly with lineage birth/death events. The results confirm that DEC and DEC+J are identifiable even though these models ignore the fact that molecular phylogenies are missing many cladogenesis and extinction events. The simulations also indicate that DEC will have substantially increased errors in ancestral range estimation and parameter inference when the true model includes +J. DEC and DEC+J are compared on 13 empirical datasets drawn from studies of island clades. Likelihood ratio tests indicate that all clades reject DEC, and AICc model weights show large to overwhelming support for DEC+J, for the first time verifying the importance of founder-event speciation in island clades via statistical model choice. Under DEC+J, ancestral nodes are usually estimated to have ranges occupying only one island, rather than the widespread ancestors often favored by DEC. These results indicate that the assumptions of historical biogeography models can have large impacts on inference and require testing and comparison with statistical methods.

长期以来，众多历史生物地理学家均认为，奠基者事件成种(Founder-event speciation)——通过罕见的长距离扩散事件建立全新遗传隔离支系的过程——至关重要，但该过程的重要性在隔离分化(vicariance)学派中尚存争议。
地理分布区演化的概率建模方法，为借助标准统计模型选择流程对多组生物地理模型开展数据检验提供了可能，前提是需拥有多组可用模型。
本研究在R语言扩展包BioGeoBEARS中重新实现了LAGRANGE的扩散-灭绝-分支成种(Dispersal-Extinction-Cladogenesis, DEC)模型，并对其进行改良，构建了新增奠基者事件成种过程的DEC+J新模型，该过程的重要性由新增的自由参数j进行调控。
我们在涵盖地理演化与支系发生、灭绝事件协同演化的各类宏观进化模型模拟数据集上，对DEC与DEC+J的可识别性开展了测试。结果证实，即便上述模型未考虑分子系统发育中存在大量分支成种与灭绝事件缺失的情况，DEC与DEC+J仍具备可识别性。
模拟实验还显示，当真实演化模型包含J项时，DEC在祖先分布区推断与参数推断环节的误差将显著升高。
研究针对13个取自岛屿支系相关研究的经验数据集，对DEC与DEC+J进行了对比分析。似然比检验结果表明，所有支系均拒绝DEC模型；修正赤池信息准则(Akaike Information Criterion corrected, AICc)模型权重则显示，DEC+J获得了从显著到压倒性的支持，这首次通过统计模型选择方法证实了奠基者事件成种在岛屿支系中的重要性。
在DEC+J模型框架下，祖先节点的分布区通常被推断为仅占据单个岛屿，而非DEC模型往往支持的广布祖先分布区。
上述研究结果表明，历史生物地理模型的假设会对推断结果产生显著影响，因此需通过统计方法对模型进行检验与比较。