Data from: Primate diversification inferred from phylogenies and fossils

Biodiversity arises from the balance between speciation and extinction. Fossils record the origins and disappearance of organisms, and the branching patterns of molecular phylogenies allow estimation of speciation and extinction rates, but the patterns of diversification are frequently incongruent between these two data sources. I tested two hypotheses about the diversification of primates based on ~600 fossil species and 90% complete phylogenies of living species: 1) diversification rates increased through time; 2) a significant extinction event occurred in the Oligocene. Consistent with the first hypothesis, analyses of phylogenies consistently supported increasing speciation rates and negligible extinction rates. In contrast, fossils showed that while speciation rates increased, speciation and extinction rates tended to be nearly equal, resulting in zero net diversification. Partially supporting the second hypothesis, the fossil data recorded a clear pattern of diversity decline in the Oligocene, although diversification rates were near zero. The phylogeny supported increased extinction ~34 Ma, but also elevated extinction ~10 Ma, coinciding with diversity declines in some fossil clades. The results demonstrated that estimates of speciation and extinction ignoring fossils are insufficient to infer diversification and information on extinct lineages should be incorporated into phylogenetic analyses.生物多样性源于物种形成（speciation）与绝灭（extinction）之间的动态平衡。化石记录了生物类群的起源与消亡，而分子系统发育树（molecular phylogenies）的分支模式可用于估算物种形成速率与绝灭速率，但这两类数据来源所揭示的多样化模式往往存在显著不一致。本研究基于约600个化石物种以及完整度达90%的现存物种系统发育树，检验了两项关于灵长类（primates）多样化的假说：1）多样化速率随时间推移不断提升；2）渐新世（Oligocene）时期曾发生过显著绝灭事件。与第一项假说相符的是，系统发育树的分析结果始终支持物种形成速率上升、绝灭速率可忽略不计的结论。与之形成鲜明对比的是，化石数据显示尽管物种形成速率有所提升，但物种形成与绝灭速率近乎相等，最终导致净多样化速率为零。第二项假说得到了部分支持：化石数据记录了渐新世时期明确的多样性下降模式，尽管当时的多样化速率接近零。系统发育分析则支持约34 Ma时绝灭速率上升，同时还发现约10 Ma时绝灭速率同样升高，这与部分化石类群的多样性下降时间相吻合。研究结果表明，仅依靠不包含化石信息的物种形成与绝灭速率估算，无法准确推断类群的多样化过程，因此应将灭绝谱系的相关信息纳入系统发育分析当中。