Gene Family Evolution by Duplication, Speciation, and Loss
Gene Family Evolution by Duplication, Speciation, and Loss
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DOI：
10.1089/cmb.2008.0054
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发表时间：
2008-10-01
影响因子：
1.7
通讯作者：
El-Mabrouk, Nadia
中科院分区：
文献类型：
--
作者：
Chauve, Cedric;Doyon, Jean-Philippe;El-Mabrouk, Nadia
我们考虑与基因家族进化有关的两个算法问题。首先，给定一个基因家族的基因树，这个家族的进化史能否只用物种形成和复制事件来解释？这样的基因树被称为ds树。我们证明了这个问题可以在线性时间内得到答案，并且ds树可以推导出单物种树。然后我们研究这个问题的自然延伸：在进化历史中导致观察到的基因树或一组基因树的最小基因损失数是多少？基于ds树的特征，我们提出了一种启发式方法，并在植物基因家族数据集和模拟数据上对其进行了评估。
We consider two algorithmic questions related to the evolution of gene families. First, given a gene tree for a gene family, can the evolutionary history of this family be explained with only speciation and duplication events? Such gene trees are called DS-trees. We show that this question can be answered in linear time, and that a DS-tree induces a single species tree. We then study a natural extension of this problem: what is the minimum number of gene losses involved in an evolutionary history leading to an observed gene tree or set of gene trees? Based on our characterization of DS-trees, we propose a heuristic for this problem, and evaluate it on a dataset of plants gene families and on simulated data.