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.

奠基者事件成种（Founder-event speciation）指通过罕见的长距离扩散事件建立一个新的遗传隔离支系，长期以来被众多历史生物地理学家视为关键演化过程，但在隔离分化（vicariance）学派中其重要性仍存在争议。地理分布区演化的概率建模为利用标准统计模型选择程序检验不同生物地理模型提供了可能，前提是需具备多个可供比较的模型。本文在R语言包BioGeoBEARS中重新实现了LAGRANGE的扩散-灭绝-成支（Dispersal-Extinction-Cladogenesis，DEC）模型，并对其进行修改以构建新模型DEC+J，该模型加入了奠基者事件成种模块，其重要性由新增自由参数j调控。本文在一系列地理分布与支系起源/灭绝事件协同演化的宏进化模型下生成的模拟数据集上，检验了DEC与DEC+J的可识别性。结果证实，尽管这两类模型未考虑分子系统发育中遗漏了大量成支与灭绝事件的事实，DEC与DEC+J仍具备可识别性。模拟结果还表明，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上的误差会显著增大。本文将DEC与DEC+J应用于13组取自岛屿支系研究的经验数据集进行对比。似然比检验显示，所有支系均拒绝DEC模型，而AICc模型权重则为DEC+J提供了从显著到压倒性的支持，这首次通过统计模型选择方法验证了奠基者事件成种在岛屿支系演化中的重要性。在DEC+J模型下，祖先节点的分布区通常被推断为仅占据单个岛屿，而非DEC模型常支持的广布祖先分布区。上述结果表明，历史生物地理模型的假设会对演化推断产生显著影响，因此需要通过统计方法进行检验与对比。