Commonly used Bayesian diversification methods lead to biologically meaningful differences in branch-specific rates on empirical phylogenies
Commonly used Bayesian diversification methods lead to biologically meaningful differences in branch-specific rates on empirical phylogenies
复制标题
常用的贝叶斯多样化方法导致经验系统发育的分支特定率具有生物学意义的差异
DOI：
10.1093/evlett/qrad044
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发表时间：
2023
影响因子：
5
通讯作者：
Rothfels, Carl J.
中科院分区：
文献类型：
--
作者：
Martínez-Gómez, Jesús;Song, Michael J.;Tribble, Carrie M.;Kopperud, Bjørn T.;Freyman, William A.;Höhna, Sebastian;Specht, Chelsea D.;Rothfels, Carl J.
确定沿着哪些谱系发生多样化率的变化是比较遗传学的一个中心目标;这些变化可能与关键的进化事件相一致，如新的形态特征的发展，适应性性状的获得，多倍化或其他结构基因组变化，或分散到一个新的栖息地和随后的环境生态位空间的增加。然而，虽然现在存在多种方法来估计多样化率，并确定使用系统发育拓扑结构的变化，这些方法的适当使用和准确性是激烈的争论。在这里，我们测试是否五个贝叶斯方法贝叶斯分析的宏观进化混合（BAMM），两个实现的血统特定的死亡转移模型（LSBDS和PESTO），近似的多类型的死亡转移模型（MTBD;在BEAST 2中实现），和分支遗传多样性率转移模型（ClaDS 2）-产生可比的结果。我们将这些方法应用到一组65个经验时间校准的物种形成率，灭绝率和净多样化率的推论进行比较。我们发现，这五种方法往往推断出不同的物种形成，灭绝和净多样化率。因此，这些不同的估计可能会导致不同的解释的宏观进化动力学。不同的估计可以归因于比较模型之间的根本差异。因此，多样化率的变化的推断是强烈的方法依赖。我们建议生物学家应用多种方法来测试结论的稳健性，或者根据潜在模型假设对特定经验系统的有效性仔细选择方法。
Identifying along which lineages shifts in diversification rates occur is a central goal of comparative phylogenetics; these shifts may coincide with key evolutionary events such as the development of novel morphological characters, the acquisition of adaptive traits, polyploidization or other structural genomic changes, or dispersal to a new habitat and subsequent increase in environmental niche space. However, while multiple methods now exist to estimate diversification rates and identify shifts using phylogenetic topologies, the appropriate use and accuracy of these methods are hotly debated. Here we test whether five Bayesian methods—Bayesian Analysis of Macroevolutionary Mixtures (BAMM), two implementations of the Lineage-Specific Birth–Death–Shift model (LSBDS and PESTO), the approximate Multi-Type Birth–Death model (MTBD; implemented in BEAST2), and the Cladogenetic Diversification Rate Shift model (ClaDS2)—produce comparable results. We apply each of these methods to a set of 65 empirical time-calibrated phylogenies and compare inferences of speciation rate, extinction rate, and net diversification rate. We find that the five methods often infer different speciation, extinction, and net-diversification rates. Consequently, these different estimates may lead to different interpretations of the macroevolutionary dynamics. The different estimates can be attributed to fundamental differences among the compared models. Therefore, the inference of shifts in diversification rates is strongly method dependent. We advise biologists to apply multiple methods to test the robustness of the conclusions or to carefully select the method based on the validity of the underlying model assumptions to their particular empirical system.