A flexible method for estimating tip diversification rates across a range of speciation and extinction scenarios
A flexible method for estimating tip diversification rates across a range of speciation and extinction scenarios
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DOI：
10.1111/evo.14517
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发表时间：
2021-11
期刊：
影响因子：
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通讯作者：
T. Vasconcelos;B. O’Meara;Jeremy M Beaulieu
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文献类型：
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作者：
T. Vasconcelos;B. O’Meara;Jeremy M Beaulieu
估计多样化率的尖端的遗传学提供了一个灵活的方法，多个性状的相关性分析，并在空间上映射多样化率，同时也避免了深时间率重建的不确定性。可用的小费率估计方法有不同的假设，因此它们的准确性通常取决于生成树的基础模型的特性。在这里，我们介绍了MiSSE，一种无特征，状态依赖的物种形成和灭绝方法，可用于估计不同的物种形成，灭绝，净多样化，周转率和灭绝分数在树的顶端。我们比较了MiSSE与类似方法推断的尖端率的准确性，并证明，由于模型的某些特性，在广泛的物种形成和灭绝场景中，误差通常较低。MiSSE可以与常规的系统发育比较方法一起用于性状相关的多样化假设，我们还描述了一个简单的校正，以避免在独立对比分析中从姐妹提示的伪复制。最后，我们展示了MiSSE的能力，重新关注经典的比较方法，研究株高和周转率之间的相关性，在euclets，一个物种丰富的血统显花植物。
Estimates of diversification rates at the tips of a phylogeny provide a flexible approach for correlation analyses with multiple traits and to map diversification rates in space, while also avoiding the uncertainty of deep time rate reconstructions. Available methods for tip rate estimation make different assumptions, and thus their accuracy usually depends on characteristics of the underlying model generating the tree. Here we introduce MiSSE, a trait-free, state-dependent speciation and extinction approach that can be used to estimate varying speciation, extinction, net-diversification, turnover rates, and extinction fraction at the tips of the tree. We compare the accuracy of tip rates inferred by MiSSE against similar methods and demonstrate that, due to certain characteristics of the model, the error is generally low across a broad range of speciation and extinction scenarios. MiSSE can be used alongside regular phylogenetic comparative methods in trait related diversification hypotheses, and we also describe a simple correction to avoid pseudoreplication from sister tips in analyses of independent contrasts. Finally, we demonstrate the capabilities of MiSSE, with a renewed focus on classic comparative methods, to examine correlation between plant height and turnover rates in eucalypts, a species-rich lineage of flowering plants.