How reliably can we infer diversity-dependent diversification from phylogenies?
How reliably can we infer diversity-dependent diversification from phylogenies?
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DOI：
10.1111/2041-210x.12565
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发表时间：
2016-09-01
影响因子：
6.6
通讯作者：
Phillimore, Albert B.
中科院分区：
文献类型：
--
作者：
Etienne, Rampal S.;Pigot, Alex L.;Phillimore, Albert B.
系统发育中谱系积累的放缓表明，物种形成率随着多样性的增加而下降。已经开发了可能性方法来检测这种多样性依赖性。然而，缺乏对这些方法是否正确推断多样性依赖性的彻底测试。在这里，我们在线性负多样性依赖和多样性无关模型下模拟系统发育分支，并从模拟的系统发育中估计三种不同条件的最大似然参数——给定树冠年龄的生死过程的存活、树木大小（N）和给定树冠年龄的树木大小。我们基于（2）似然比检验报告了恢复模拟参数的准确性和模型选择的可靠性。参数估计准确性：给定树冠年龄的生存条件会产生承载能力 K 向 N 的严重偏差以及物种形成率的向上偏差，特别是在多样性依赖反馈仍然较弱的进化枝中（N
Slowdowns in lineage accumulation in phylogenies suggest that speciation rates decline as diversity increases. Likelihood methods have been developed to detect such diversity dependence. However, a thorough test of whether such approaches correctly infer diversity dependence is lacking. Here, we simulate phylogenetic branching under linear negative diversity-dependent and diversity-independent models and estimate from the simulated phylogenies the maximum-likelihood parameters for three different conditionings - on survival of the birth-death process given the crown age, on tree size (N) and on tree size given the crown age. We report the accuracy of recovering the simulation parameters and the reliability of the model selection based on the (2) likelihood ratio test. Parameter estimate accuracy: Conditioning on survival given the crown age yields a severe bias of the carrying capacity K towards N and an upward bias of the speciation rate, particularly in clades where diversity-dependent feedbacks are still weak (N