Genome-Scale Phylogenetics: Inferring the Plant Tree of Life from 18,896 Gene Trees
Genome-Scale Phylogenetics: Inferring the Plant Tree of Life from 18,896 Gene Trees
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DOI：
10.1093/sysbio/syq072
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发表时间：
2011-03-01
影响因子：
6.5
通讯作者：
Vision, Todd J.
中科院分区：
文献类型：
--
作者：
Burleigh, J. Gordon;Bansal, Mukul S.;Vision, Todd J.
使用基因组规模数据集的系统发育分析必须面对基因树之间的不一致，在植物中，频繁的基因复制和丢失加剧了这种不一致。基因树简约性（GTP）是一种系统发育优化准则，在该准则中，选择使一组基因树中诱导的基因重复数最小化的物种树。以前实现的运行时性能限制了它在大规模数据集上的使用。我们使用新的软件，结合最新的算法进展，以检查GTP在植物数据集上的性能，该数据集由18，896个基因树组成，包含来自136个植物分类群的510，922个蛋白质序列（组合比对长度> 290万个字符）。从GTP分析推断的关系在很大程度上是一致的，与以前的大规模研究的骨干植物发生，并解决了一些有争议的节点。存在于少数基因树中的分类群的位置通常在GTP自举重复中变化最大。排除这些类群之前或之后的GTP分析揭示了高水平的系统发育支持跨植物。这些分析支持木兰科植物姐妹真双子叶+单子叶植物分支，不支持eurosid I和II分支。这项研究提出了一个核基因组的观点，在植物之间的广泛的遗传关系，它表明，核基因的复制和损失的历史可以为解决植物的生命树的遗传信息。
Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony (GTP) is a phylogenetic optimization criterion in which a species tree that minimizes the number of gene duplications induced among a set of gene trees is selected. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic advances to examine the performance of GTP on a plant data set consisting of 18,896 gene trees containing 510,922 protein sequences from 136 plant taxa (giving a combined alignment length of >2.9 million characters). The relationships inferred from the GTP analysis were largely consistent with previous large-scale studies of backbone plant phylogeny and resolved some controversial nodes. The placement of taxa that were present in few gene trees generally varied the most among GTP bootstrap replicates. Excluding these taxa either before or after the GTP analysis revealed high levels of phylogenetic support across plants. The analyses supported magnoliids sister to a eudicot + monocot clade and did not support the eurosid I and II clades. This study presents a nuclear genomic perspective on the broad-scale phylogenic relationships among plants, and it demonstrates that nuclear genes with a history of duplication and loss can be phylogenetically informative for resolving the plant tree of life.