Diversification Models Conflate Likelihood and Prior, and Cannot be Compared Using Conventional Model-Comparison Tools
Diversification Models Conflate Likelihood and Prior, and Cannot be Compared Using Conventional Model-Comparison Tools
复制标题
多样化模型将可能性和先验混为一谈，无法使用传统的模型比较工具进行比较
DOI：
10.1093/sysbio/syad010
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发表时间：
2023
影响因子：
6.5
通讯作者：
Hoehna, ed., Sebastian
中科院分区：
文献类型：
--
作者：
May, Michael R.;Rothfels, Carl J.;Hoehna, ed., Sebastian
时间校准的系统发育树是研究进化、生态和流行病学现象的一个非常强大的工具。这类树主要是在贝叶斯框架下推断的，系统发育本身被视为具有先验分布的参数(“树先验”)。然而，我们发现树的“参数”部分由分类单元样本形式的数据组成。将树视为参数无法解释这些数据，并影响了我们使用标准技术(例如，使用路径采样和步进式采样算法估计的边际可能性)在模型之间进行比较的能力。由于所推断的系统发育的准确性在很大程度上取决于树的先验与导致树产生的真实多样化过程的近似程度，因此无法准确地比较竞争树的先验对于基于时间校准树的应用具有广泛的意义。我们概述了这个问题的潜在补救措施，并为对评估树木模型的适合性感兴趣的研究人员提供指导。[贝叶斯因素；贝叶斯模型比较；出生-死亡模型；分歧-时间估计；谱系多样化]
Time-calibrated phylogenetic trees are a tremendously powerful tool for studying evolutionary, ecological, and epidemiological phenomena. Such trees are predominantly inferred in a Bayesian framework, with the phylogeny itself treated as a parameter with a prior distribution (a “tree prior”). However, we show that the tree “parameter” consists, in part, of data, in the form of taxon samples. Treating the tree as a parameter fails to account for these data and compromises our ability to compare among models using standard techniques (e.g., marginal likelihoods estimated using path-sampling and stepping-stone sampling algorithms). Since accuracy of the inferred phylogeny strongly depends on how well the tree prior approximates the true diversification process that gave rise to the tree, the inability to accurately compare competing tree priors has broad implications for applications based on time-calibrated trees. We outline potential remedies to this problem, and provide guidance for researchers interested in assessing the fit of tree models. [Bayes factors; Bayesian model comparison; birth-death models; divergence-time estimation; lineage diversification]