Data from: Identifying biases at different spatial and temporal scales of diversification: a case study in the Neotropical parrotlet genus Forpus

The temporal origins of the extraordinary biodiversity of the Neotropical region are highly debated. Recent empirical work has found support for alternative models on the tempo of speciation in Neotropical species further fuelling the debate. However, relationships within many Neotropical lineages are poorly understood and it is unclear how this uncertainty impacts inferences on the evolution of taxa in the region. We examined the robustness of diversification patterns in the avian genus Forpus by testing whether the use of different units of biodiversity (i.e. biological species and statistically inferred species) impacted diversification rates and inferences regarding important biogeographic breaks in the genus. We found that the best-fit model of diversification for the biological species data set was a declining rate of diversification; whereas a model of constant diversification was the best-fit model for statistically inferred species or subspecies. Moreover, the relative importance of different landscape features in delimiting genetic structure across the landscape varied across data sets with differing units of biodiversity. Patterns based on divergence times among biological species indicated old speciation events across major geographic and river barriers, in contrast, data sets more inclusive of the diversity in Forpus illustrate the role of both old divergence across major landscape features as well as more recent divergences that are possibly attributed to Pleistocene climatic changes. Overall, these results indicate that conflicting models on the temporal origins of Neotropical birds may be attributable to sampling biases.

新热带区（Neotropical region）非凡生物多样性的时间起源问题长期存在激烈学术争论。近期的实证研究为新热带类群物种形成速率的多种对立模型提供了实证支持，进一步加剧了相关学术争议。然而，诸多新热带类群的内部系统发育关系仍未得到充分解析，目前尚不明确这种认知不确定性会如何影响该区域类群演化的相关推断。本研究以福普斯鹦鹉属（Forpus）鸟类为研究对象，通过检验不同生物多样性划分单元（即生物学物种与统计学推断物种）对分化速率推断以及该属关键生物地理分界相关结论的影响，探究了其多样化模式的稳健性。研究结果显示，针对生物学物种数据集的最优拟合多样化模型为分化速率随时间衰减的模型；而针对统计学推断物种或亚种的数据集，最优拟合模型则为恒定分化速率模型。此外，不同景观特征在界定种群遗传结构时的相对重要性，也因采用的生物多样性划分单元不同而存在差异。基于生物学物种间分化时间的分析结果显示，主要地理与河流屏障两侧均存在古老的物种形成事件；与之形成鲜明对比的是，纳入更多福普斯鹦鹉属多样性的数据集则表明，该类群的演化既存在跨越主要景观屏障的古老分化事件，也存在可能与更新世（Pleistocene）气候变化相关的较晚近分化事件。综上，本研究结果表明，有关新热带鸟类生物多样性时间起源的各类对立模型，或许均可归因于采样偏差。