Estimating diversity through time using molecular phylogenies: old and species-poor frog families are the remnants of a diverse past.

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 (DTT) 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 dive...估算某一物种类群在远古时期的物种数量变化情况，是进化生物学家们极为关注的核心课题。然而，当前用于获取此类估算的系统发育分析方法存在一定局限，例如在类群起源节点处会给出脱离实际的多样性估值。本文提出一种鲁棒的概率分析方法，可基于系统发育数据估算时间跨度内多样性（Diversity-Through-Time, DTT）曲线及其估算结果的不确定性区间。我们通过模拟实验证实，在多种符合实际的物种分化演化场景下，该方法的表现优于既往提出的各类方法。此外，我们还分析了系统发育树规模与欠采样情况对该方法性能的影响。我们将该方法应用于无尾目（Anura，即蛙类与蟾蜍类）的物种多样性格局研究，以解析其多样性变化模式。研究发现，古蛙亚目（Archaeobatrachia）——一类物种稀少、多分布于温带区域的古老蛙类支系——曾拥有远高于当前的物种多样性与净物种分化速率，但该类群的多样性（原文此处截断）...