Estimating Diversity Through Time Using Molecular Phylogenies: Old and Species-Poor Frog Families are the Remnants of a Diverse Past
Estimating Diversity Through Time Using Molecular Phylogenies: Old and Species-Poor Frog Families are the Remnants of a Diverse Past
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DOI：
10.1093/sysbio/syz057
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发表时间：
2020-03-01
影响因子：
6.5
通讯作者：
Morlon，H.
中科院分区：
文献类型：
--
作者：
Billaud，O.;Moen，D. S.;Morlon，H.
估计一个特定群体中的物种数量在远古时期是如何变化的，是进化生物学家的主要兴趣。然而，目前的系统发育方法获得这样的估计有局限性，如提供不切实际的多样性估计组的起源。在这里，我们开发了一个强大的概率方法估计多样性，通过时间曲线和不确定性，这些估计从系统发育数据。我们的模拟表明，在各种现实的情况下多样化，这种方法比以前提出的方法表现更好。我们还描述了树的大小和欠采样的方法的性能的影响。我们应用我们的方法来了解无尾类（青蛙和蟾蜍）的物种多样性模式。我们发现，Archaeobatrachia-一个物种的穷人组的老青蛙分支经常发现在温带地区，以前有更高的多样性和净多样化率，但该组的多样性下降，年轻，嵌套的分支多样化。这种多样性的下降似乎与物种形成率的下降有关，而不是与灭绝率的增加有关。我们的方法，在R包RPANDA中实现，应该是有用的进化生物学家有兴趣了解过去的多样性动态如何塑造当今的多样性。它也可能是有用的，在其他情况下，如分析分支分支的竞争效应或物种丰富度对表型分化的影响。
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.