Inferring incomplete lineage sorting, duplications, transfers and losses with reconciliations
Inferring incomplete lineage sorting, duplications, transfers and losses with reconciliations
复制标题
DOI：
10.1016/j.jtbi.2017.08.008
复制
发表时间：
2017-11-07
影响因子：
2
通讯作者：
Scornavaccac, Celine
中科院分区：
文献类型：
--
作者：
Chan, Yao-ban;Ranwez, Vincent;Scornavaccac, Celine
基因树和物种树可能由于几个过程而不一致。调和的标准模型考虑基因水平上的宏观进化事件：基因的复制、丢失和转移。然而，另一个常见的来源基因树物种树不一致是不完全谱系排序（ILS），即对应于物种形成的基因分歧发生“无序”。然而，ILS很少在协调模型中考虑。在本文中，我们设计了一个统一的正式MTL和解模型，其中包括所有上述过程。我们将展示如何在此模型下适当的成本ILS，然后给出一个固定参数易处理（FPT）算法，计算最简约的MTL和解，保证时间一致性的传输事件。如果允许ILS的物种树的相邻区域中的分支数由常数限定，则该算法在基因数上是线性的，在物种数上是二次的。这提供了一个正式的基础，在和解框架的ILS的推理。(C)2017爱思唯尔有限公司版权所有
Gene trees and species trees can be discordant due to several processes. Standard models of reconciliations consider macro-evolutionary events at the gene level: duplications, losses and transfers of genes. However, another common source of gene tree-species tree discordance is incomplete lineage sorting (ILS), whereby gene divergences corresponding to speciations occur "out of order". However, ILS is seldom considered in reconciliation models. In this paper, we devise a unified formal MTL reconciliation model which includes all the above mentioned processes. We show how to properly cost ILS under this model, and then give a fixed-parameter tractable (FPT) algorithm which calculates the most parsimonious MTL reconciliation, with guaranteed time-consistency of transfer events. Provided that the number of branches in contiguous regions of the species tree in which ILS is allowed is bounded by a constant, this algorithm is linear in the number of genes and quadratic in the number of species. This provides a formal foundation to the inference of ILS in a reconciliation framework. (C) 2017 Elsevier Ltd. All rights reserved.