CRP-Tree: a phylogenetic association test for binary traits
CRP-Tree: a phylogenetic association test for binary traits
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DOI：
10.1093/jrsssc/qlad098
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发表时间：
2024-03-11
影响因子：
1.6
通讯作者：
Palacios，Julia A.
中科院分区：
文献类型：
--
作者：
Zhang，Julie;Preising，Gabriel A.;Palacios，Julia A.
进化基因组学的一个重要问题是研究每个样本上测量的某个性状是否与样本系统发育树相关。系统发育树代表了样本的共同进化历史，通常是根据某个位点的分子序列数据或其他类型的遗传数据来估计的。我们提出了一个受中餐馆流程启发的特征进化模型，其中包括一个控制优先依恋程度的参数，即树中节点与相同类型节点相对的倾向。该没有优先附着的模型相当于具有同时迁移和聚结事件的结构化聚结模型，并用作空模型。我们推导了一种具有线性计算复杂性的系统发育二元性状关联测试，并凭经验证明它比其他一些方法更强大。我们应用我们的测试来研究剑尾鱼、乳腺癌、黄热病病毒和甲型 H1N1 流感病毒的一些性状的系统发育关联。我们的方法的 R 包实现可在 https://github.com/jyzhang27/CRPTree 获取。
An important problem in evolutionary genomics is to investigate whether a certain trait measured on each sample is associated with the sample phylogenetic tree. The phylogenetic tree represents the shared evolutionary history of the samples and it is usually estimated from molecular sequence data at a locus or from other type of genetic data. We propose a model for trait evolution inspired by the Chinese Restaurant Process that includes a parameter that controls the degree of preferential attachment, that is, the tendency of nodes in the tree to subtend from nodes of the same type. This model with no preferential attachment is equivalent to a structured coalescent model with simultaneous migration and coalescence events and serves as a null model. We derive a test for phylogenetic binary trait association with linear computational complexity and empirically demonstrate that it is more powerful than some other methods. We apply our test to study the phylogenetic association of some traits in swordtail fish, breast cancer, yellow fever virus, and influenza A H1N1 virus. R-package implementation of our methods is available at https://github.com/jyzhang27/CRPTree.