Simonet C, Scherrer R, Rego-Costa A, Etienne R S
Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands.
J Evol Biol. 2018 Mar;31(3):469-479. doi: 10.1111/jeb.13233. Epub 2018 Jan 19.
The protracted speciation model presents a realistic and parsimonious explanation for the observed slowdown in lineage accumulation through time, by accounting for the fact that speciation takes time. A method to compute the likelihood for this model given a phylogeny is available and allows estimation of its parameters (rate of initiation of speciation, rate of completion of speciation and extinction rate) and statistical comparison of this model to other proposed models of diversification. However, this likelihood computation method makes an approximation of the protracted speciation model to be mathematically tractable: it sometimes counts fewer species than one would do from a biological perspective. This approximation may have large consequences for likelihood-based inferences: it may render any conclusions based on this method completely irrelevant. Here, we study to what extent this approximation affects parameter estimations. We simulated phylogenies from which we reconstructed the tree of extant species according to the original, biologically meaningful protracted speciation model and according to the approximation. We then compared the resulting parameter estimates. We found that the differences were larger for high values of extinction rates and small values of speciation-completion rates. Indeed, a long speciation-completion time and a high extinction rate promote the appearance of cases to which the approximation applies. However, surprisingly, the deviation introduced is largely negligible over the parameter space explored, suggesting that this approximate likelihood can be applied reliably in practice to estimate biologically relevant parameters under the original protracted speciation model.
长期物种形成模型通过考虑物种形成需要时间这一事实，对观察到的谱系积累随时间放缓现象给出了一个现实且简约的解释。一种在给定系统发育树的情况下计算该模型似然性的方法是可用的，它允许估计其参数（物种形成起始速率、物种形成完成速率和灭绝速率），并将该模型与其他提出的多样化模型进行统计比较。然而，这种似然性计算方法对长期物种形成模型进行了近似处理，以便在数学上易于处理：从生物学角度看，它有时计算的物种数量比实际情况少。这种近似处理可能会对基于似然性的推断产生重大影响：它可能会使基于此方法得出的任何结论完全不相关。在这里，我们研究这种近似处理在多大程度上影响参数估计。我们模拟了系统发育树，并根据原始的、具有生物学意义的长期物种形成模型以及该近似模型从中重建现存物种的树。然后我们比较了所得的参数估计值。我们发现，对于高灭绝率值和低物种形成完成率值，差异更大。确实，长的物种形成完成时间和高灭绝率会促使出现适用该近似处理的情况。然而，令人惊讶的是，在所探索的参数空间中引入的偏差在很大程度上可以忽略不计，这表明这种近似似然性在实践中可以可靠地应用于在原始长期物种形成模型下估计生物学相关参数。
