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（Biodiversity）源于成种作用（speciation）与灭绝作用（extinction）之间的动态平衡。化石记录了生物的起源与消亡，而分子系统发育树（molecular phylogenies）的分支模式可用于估算成种速率与灭绝速率，但这两类数据来源所揭示的多样化模式往往并不一致。
本研究基于约600个化石物种与覆盖率达90%的现生灵长类（primates）物种系统发育树，检验了两项关于灵长类多样化的假说：其一，多样化速率随时间推移不断提升；其二，渐新世（Oligocene）曾发生过一次显著的灭绝事件。
与第一项假说相符的是，系统发育树分析结果始终支持成种速率上升、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，尽管成种速率有所提升，但成种与灭绝速率近乎相等，最终导致净多样化速率为零。
关于第二项假说，本研究得到了部分支持：化石数据清晰记录了渐新世时期的多样性下降趋势，尽管当时的多样化速率接近零。系统发育树分析则显示，约34 Ma及约10 Ma均存在灭绝速率升高的现象，这与部分化石演化支（clades）的多样性下降时间相吻合。
研究结果表明，仅依靠忽略化石记录的成种与灭绝速率估算，无法有效推断生物多样化过程，因此灭绝谱系的相关信息应当被纳入系统发育分析（phylogenetic analyses）当中。