Removal of Noisy Characters from Chloroplast Genome-Scale Data Suggests Revision of Phylogenetic Placements of Amborella and Ceratophyllum
Removal of Noisy Characters from Chloroplast Genome-Scale Data Suggests Revision of Phylogenetic Placements of Amborella and Ceratophyllum
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DOI：
10.1007/s00239-009-9206-9
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发表时间：
2009-03-01
影响因子：
3.9
通讯作者：
Hellwig, Frank H.
中科院分区：
文献类型：
--
作者：
Goremykin, Vadim V.;Viola, Roberto;Hellwig, Frank H.
人们普遍认识到，有噪声的、高度可变的数据可能会阻碍重复重建。长期以来，研究人员在系统发育分析中忽略了有问题的数据，如第三密码子位置和可变区。然而，在被子植物系统发育关系的分析中，将完整的基因序列纳入基因组规模的比对已成为一种常见的做法。在这里，我们证明这种做法可能是误导。我们表明，支持的最基本的位置Amborella apropoda之间的被子植物中的叶绿体基因组数据是基于只有一个很小的子集（< 1%的总比对长度）的最可变的位置对齐，表现出平均最大似然（ML）之间的距离被子植物操作分类单位（OTU）约36个取代/网站。这些位置的排除导致基Amborella分支的消失。同样，最近报道的姐妹组金鱼藻的真双子叶植物的关系是基于基因组比对中存在的2%的最可变的位置，表现出平均20个取代/位点之间的比较被子植物OTU。这些观察结果强调了从测序基因组分析中排除一定比例的饱和位置的需要。
It is widely appreciated that noisy, highly variable data can impede phylogeney reconstruction. Researchers have for a long time omitted problematic data from phylogenetic analyses, such as the third-codon positions and variable regions. In the analyses of the phylogenetic relations of the angiosperms; however, inclusion of complete gene sequences into genomic-scale alignments has become a common practice. Here we demonstrate that this practice can be misleading. We show that support of the basal-most position of Amborella trichopoda among the angiosperms in the chloroplast genomic data is based only on a tiny subset (< 1% of the total alignment length) of the most variable positions in alignment, exhibiting mean maximum likelihood (ML) distance among the angiosperm operational taxonomic units (OTUs) approximately 36 substitutions/site. Exclusion of these positions leads to disappearance of the basal Amborella branch. Likewise, the recently reported sister-group relationship of Ceratophyllum to the eudicots is based on the presence of 2% of the most variable positions in the genomic alignment, exhibiting, on average, 20 substitutions/site in comparison among the angiosperm OTUs. These observations highlight a need for excluding a certain proportion of saturated positions in alignment from phylogenomic analyses.