Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, École Normale Supérieure, Paris Sciences et Lettres (PSL) Research University, F-75005 Paris, France.
Department of Integrative Biology, Oklahoma State University, 517 Life Sciences West, Stillwater, OK 74078, USA.
Syst Biol. 2020 Mar 1;69(2):363-383. doi: 10.1093/sysbio/syz057.
Estimating how the number of species in a given group varied in the deep past is of key interest to evolutionary biologists. However, current phylogenetic approaches for obtaining such estimates have limitations, such as providing unrealistic diversity estimates at the origin of the group. Here, we develop a robust probabilistic approach for estimating diversity through time curves and uncertainty around these estimates from phylogenetic data. We show with simulations that under various realistic scenarios of diversification, this approach performs better than previously proposed approaches. We also characterize the effect of tree size and undersampling on the performance of the approach. We apply our method to understand patterns of species diversity in anurans (frogs and toads). We find that Archaeobatrachia-a species-poor group of old frog clades often found in temperate regions-formerly had much higher diversity and net diversification rate, but the group declined in diversity as younger, nested clades diversified. This diversity decline seems to be linked to a decline in speciation rate rather than an increase in extinction rate. Our approach, implemented in the R package RPANDA, should be useful for evolutionary biologists interested in understanding how past diversity dynamics have shaped present-day diversity. It could also be useful in other contexts, such as for analyzing clade-clade competitive effects or the effect of species richness on phenotypic divergence.
估计给定类群中物种数量在过去的变化情况是进化生物学家关注的关键。然而，目前用于获取此类估计的系统发育方法存在局限性，例如在群组起源时提供不切实际的多样性估计。在这里，我们开发了一种稳健的概率方法，用于从系统发育数据中估计多样性随时间的变化曲线及其估计值的不确定性。我们通过模拟表明，在各种多样化的现实情况下，这种方法的性能优于以前提出的方法。我们还描述了树大小和抽样不足对方法性能的影响。我们应用我们的方法来了解两栖动物（青蛙和蟾蜍）的物种多样性模式。我们发现，古两栖动物——一种在温带地区常见的古老青蛙进化枝种类较少的群体——以前的多样性和净多样化率要高得多，但随着年轻的、嵌套进化枝的多样化，该群体的多样性下降。这种多样性的下降似乎与物种形成率的下降而不是灭绝率的上升有关。我们的方法，在 R 包 RPANDA 中实现，对于有兴趣了解过去的多样性动态如何塑造当今的多样性的进化生物学家来说应该是有用的。它在其他情况下也可能有用，例如分析进化枝-进化枝竞争效应或物种丰富度对表型分歧的影响。
