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与灭绝之间的动态平衡。化石记录了生物的起源与消亡，而分子系统发育（molecular phylogeny）的分支模式可用于估算物种形成速率与灭绝速率，但这两类数据源所呈现的多样化模式往往并不一致。本研究基于约600个化石物种以及覆盖度达90%的现生物种系统发育数据，检验了两个关于灵长类多样化的假说：1）多样化速率随时间推移逐渐升高；2）渐新世时期曾发生一次显著的灭绝事件。与第一个假说相符的是，系统发育分析始终支持物种形成速率上升、灭绝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，但物种形成与灭绝速率近乎相等，最终净多样化速率为零。关于第二个假说，化石数据部分验证了该假设：尽管多样化速率接近零，但清晰记录了渐新世时期的生物多样性下降模式。系统发育分析则显示，约34 Ma以及约10 Ma两个时间点的灭绝速率均出现上升，其中10 Ma的灭绝速率升高时段与部分化石支系（clade）的多样性下降时期相吻合。本研究结果表明，仅依靠忽略化石记录的物种形成与灭绝速率估算，无法充分推断生物多样化过程，因此灭绝支系的相关信息应当被纳入系统发育分析当中。