Capturing the Phylogeny of Holometabola with Mitochondrial Genome Data and Bayesian Site-Heterogeneous Mixture Models.
Capturing the Phylogeny of Holometabola with Mitochondrial Genome Data and Bayesian Site-Heterogeneous Mixture Models.
复制标题
利用线粒体基因组数据和贝叶斯位点异质混合模型捕获全代谢的系统发育
DOI：
10.1093/gbe/evw086
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发表时间：
2016-05-22
影响因子：
3.3
通讯作者：
Cai W
中科院分区：
文献类型：
--
作者：
Song F;Li H;Jiang P;Zhou X;Liu J;Sun C;Vogler AP;Cai W
经过几十年的争论，基于核基因的11个已知的全代谢昆虫目之间的关系已经达成了令人满意的解决方案，解决了生命树最重要的分支之一，但利用线粒体基因组数据仍然没有很好地建立这些关系。其主要原因是缺乏几个目的足够数据，以及缺乏适当的系统发育方法来避免昆虫线粒体基因组组成和突变偏向造成的系统错误。在这项研究中，我们收集了迄今为止最丰富的类群样本(11目199种)，并使用几种方法分析了核苷酸和氨基酸数据集。我们发现标准的贝叶斯推理和最大似然分析受到系统偏差的强烈影响，但在PhyloBayes中实现的位置-异质混合模型避免了表现出相似碱基组成和加速进化速度的不相关类群的虚假分组。RRNA基因的加入和快速进化位点的去除以及用于识别偏离平均速率的位置的观察到的变异性排序方法改进了位置异质性模型下的系统发育推断，正确地恢复了Holometoxa系统发育的大部分深层分支。我们认为，使用线粒体基因组数据来解决深层的系统发育关系，需要通过数据删除策略和使用位点-异质混合模型来评估替代饱和和组成偏差的潜在影响。我们的研究为如何在系统发育分析中使用密集采样的线粒体基因组数据提供了一种实用的方法。
After decades of debate, a mostly satisfactory resolution of relationships among the 11 recognized holometabolan orders of insects has been reached based on nuclear genes, resolving one of the most substantial branches of the tree-of-life, but the relationships are still not well established with mitochondrial genome data. The main reasons have been the absence of sufficient data in several orders and lack of appropriate phylogenetic methods that avoid the systematic errors from compositional and mutational biases in insect mitochondrial genomes. In this study, we assembled the richest taxon sampling of Holometabola to date (199 species in 11 orders), and analyzed both nucleotide and amino acid data sets using several methods. We find the standard Bayesian inference and maximum-likelihood analyses were strongly affected by systematic biases, but the site-heterogeneous mixture model implemented in PhyloBayes avoided the false grouping of unrelated taxa exhibiting similar base composition and accelerated evolutionary rate. The inclusion of rRNA genes and removal of fast-evolving sites with the observed variability sorting method for identifying sites deviating from the mean rates improved the phylogenetic inferences under a site-heterogeneous model, correctly recovering most deep branches of the Holometabola phylogeny. We suggest that the use of mitochondrial genome data for resolving deep phylogenetic relationships requires an assessment of the potential impact of substitutional saturation and compositional biases through data deletion strategies and by using site-heterogeneous mixture models. Our study suggests a practical approach for how to use densely sampled mitochondrial genome data in phylogenetic analyses.