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Branching patterns in phylogenies cannot distinguish diversity‐dependent diversification from time‐dependent diversification
Evolution ( IF 3.1 ) Pub Date : 2020-12-02 , DOI: 10.1111/evo.14124
Théo Pannetier 1, 2 , César Martinez 1 , Lynsey Bunnefeld 2 , Rampal S Etienne 1
Affiliation  

One of the primary goals of macroevolutionary biology has been to explain general trends in long‐term diversity patterns, including whether such patterns correspond to an upscaling of processes occurring at lower scales. Reconstructed phylogenies often show decelerated lineage accumulation over time. This pattern has often been interpreted as the result of diversity‐dependent (DD) diversification, where the accumulation of species causes diversification to decrease through niche filling. However, other processes can also produce such a slowdown, including time dependence without diversity dependence. To test whether phylogenetic branching patterns can be used to distinguish these two mechanisms, we formulated a time‐dependent, but diversity‐independent model that matches the expected diversity through time of a DD model. We simulated phylogenies under each model and studied how well likelihood methods could recover the true diversification mode. Standard model selection criteria always recovered diversity dependence, even when it was not present. We correct for this bias by using a bootstrap method and find that neither model is decisively supported. This implies that the branching pattern of reconstructed trees contains insufficient information to detect the presence or absence of diversity dependence. We advocate that tests encompassing additional data, for example, traits or range distributions, are needed to evaluate how diversity drives macroevolutionary trends.

中文翻译:

系统发育中的分支模式无法区分依赖于多样性的多样化和依赖于时间的多样化

宏观进化生物学的主要目标之一是解释长期多样性模式的一般趋势,包括这些模式是否对应于发生在较低尺度的过程的升级。随着时间的推移,重建的系统发育通常显示出减速的谱系积累。这种模式通常被解释为多样性依赖(DD)多样化的结果,其中物种的积累通过生态位填充导致多样化减少。然而,其他过程也可以产生这样的减速,包括没有多样性依赖的时间依赖。为了测试系统发育分支模式是否可用于区分这两种机制,我们制定了一个时间依赖性但与多样性无关的模型,该模型与 DD 模型随时间变化的预期多样性相匹配。我们模拟了每个模型下的系统发育,并研究了似然方法如何恢复真正的多样化模式。标准模型选择标准总能恢复多样性依赖,即使它不存在。我们使用 bootstrap 方法纠正了这种偏差,发现这两种模型都没有得到决定性的支持。这意味着重建树的分支模式包含的信息不足以检测是否存在多样性依赖。我们主张需要包含额外数据(例如特征或范围分布)的测试来评估多样性如何驱动宏观进化趋势。即使它不存在。我们使用 bootstrap 方法纠正了这种偏差,发现这两种模型都没有得到决定性的支持。这意味着重建树的分支模式包含的信息不足以检测是否存在多样性依赖。我们主张需要包含额外数据(例如特征或范围分布)的测试来评估多样性如何驱动宏观进化趋势。即使它不存在。我们使用 bootstrap 方法纠正了这种偏差,发现这两种模型都没有得到决定性的支持。这意味着重建树的分支模式包含的信息不足以检测是否存在多样性依赖。我们主张需要包含额外数据(例如特征或范围分布)的测试来评估多样性如何驱动宏观进化趋势。
更新日期:2020-12-02
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