A novel phylogenetic comparative method for evaluating the strength of branch-specific directional selection
A novel phylogenetic comparative method for evaluating the strength of branch-specific directional selection
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DOI：
10.1093/evolut/qpac015
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发表时间：
2023-01-06
期刊：
影响因子：
3.3
通讯作者：
Koizumi，Itsuro
中科院分区：
文献类型：
--
作者：
Ohkubo，Yusaku;Kutsukake，Nobuyuki;Koizumi，Itsuro
系统发育比较方法（PCMs）在研究表型性状的进化中发挥了重要作用。然而，当一个性状经历定向选择时，以前的PCM面临着数学上易处理但限制性模型（即，简单的高斯过程模型）和灵活但棘手的方法（即，基于群体遗传学框架的表型进化的基于模拟的过程模型）。本文提出了一种新的高斯过程宏进化模型，称为“分支特定的方向选择（BSDS）”，用于评估方向选择的强度，以调和这两种方法。该模型基于先前基于模拟的过程模型的二阶近似，但具有封闭形式的似然函数。这也可以扩展到纳入种内变异和线性混合模型，这是荟萃分析所必需的。我们进行了数值实验，以验证所提出的方法，并将其应用到人科物种的大脑体积。结果表明，所提出的方法产生统计上更可靠的推理和计算时间是以前的模拟为基础的方法的大约十万倍。BSDS模型的进一步扩展，预计将提供一个更清晰的画面连接的微观进化过程和宏观进化模式。
Phylogenetic comparative methods (PCMs) have played a central role in studying the evolution of phenotypic traits. However, when a trait experienced directional selection, previous PCMs have faced a dilemma between mathematically tractable but restrictive models (i.e., simple Gaussian process models) and flexible but intractable approaches (i.e., a simulation-based process model of phenotype evolution built on population genetics frameworks). This paper proposes a novel Gaussian process macroevolutionary model, called the “branch-specific directional selection (BSDS),” for evaluating the strength of directional selection to reconcile these two approaches. This model is based on a second-order approximation of a previous simulation-based process model but has a closed-form likelihood function. This can also be extended to incorporate intraspecies variations and to linear mixed models, which are necessary for meta-analysis. We conduct numerical experiments to validate the proposed method and apply it to the brain volume of Hominidae species. The results show that the proposed methods yield statistically more reliable inferences and computational time is about hundred thousand times faster than the previous simulation-based methods. Further extensions of the BSDS model are expected to provide a clearer picture of the connection of microevolutionary processes and macroevolutionary patterns.