Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites
Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites
复制标题
DOI：
10.1016/j.jtbi.2015.03.006
复制
发表时间：
2015-06-07
影响因子：
2
通讯作者：
Kubatko, Laura
中科院分区：
文献类型：
--
作者：
Chifman, Julia;Kubatko, Laura
对一群生物的进化史进行推断是进化生物学中一个非常重要的问题。基因组测序项目产生的大量DNA序列数据导致了这些系统发育关系推断的重大挑战。这些挑战之一是基于基因组中几个不同基因的序列信息来推断物种集合的进化史。人们普遍认为，每个基因都有自己的系统发育，这可能与物种树不一致。这种基因树不一致的许多可能原因是已知的。研究得最好的是不完全谱系分选，它通常是由聚结过程建模的。在给定DNA序列数据的情况下，已经提出了许多基于聚结过程的方法来估计系统发育物种树。然而，使用这些方法假设系统发育物种树可以从树的叶子处的DNA序列数据中识别，尽管这还没有正式建立。我们证明了n叶系统发育物种树的无根拓扑结构是一般可识别的，给出了在树的叶子上观察到的数据，假设这些数据是在时间可逆的替代过程中产生的，该过程具有由离散伽马分布和不变位点比例建模的特定位点速率变化的可能性。Elsevier Ltd.出版。
The inference of the evolutionary history of a collection of organisms is a problem of fundamental importance in evolutionary biology. The abundance of DNA sequence data arising from genome sequencing projects has led to significant challenges in the inference of these phylogenetic relationships. Among these challenges is the inference of the evolutionary history of a collection of species based on sequence information from several distinct genes sampled throughout the genome. It is widely accepted that each individual gene has its own phylogeny, which may not agree with the species tree. Many possible causes of this gene tree incongruence are known. The best studied is the incomplete lineage sorting, which is commonly modeled by the coalescent process. Numerous methods based on the coalescent process have been proposed for the estimation of the phylogenetic species tree given DNA sequence data. However, use of these methods assumes that the phylogenetic species tree can be identified from DNA sequence data at the leaves of the tree, although this has not been formally established. We prove that the unrooted topology of the n-leaf phylogenetic species tree is generically identifiable given observed data at the leaves of the tree that are assumed to have arisen from the coalescent process under a time-reversible substitution process with the possibility of site-specific rate variation modeled by the discrete gamma distribution and a proportion of invariable sites. Published by Elsevier Ltd.