The Apicomplexan whole-genome phylogeny: an analysis of incongruence among gene trees.
The Apicomplexan whole-genome phylogeny: an analysis of incongruence among gene trees.
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DOI：
10.1093/molbev/msn213
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发表时间：
2008-12
影响因子：
10.7
通讯作者：
Kissinger, Jessica C.
中科院分区：
文献类型：
--
作者：
Kuo, Chih-Horng;Wares, John P.;Kissinger, Jessica C.
原生动物门Apicomplexa含有许多重要的病原体，是密集的基因组测序工作的对象。基于7个顶端复合体物种和一个纤毛虫外群的基因组序列，我们确定了268个适合于系统发育推断的单拷贝基因。串联和共识方法都推断出相同的树种拓扑结构。这种拓扑结构与大多数基于超微结构和发育特征的顶端复合体进化的先前概念是一致的，即锥虫属和巴贝斯虫属是疟原虫物种的姐妹群，球虫属和弓形虫属是单系进化，是疟原虫属和蝶形体属的姐妹群，隐孢子虫与上述物种形成姐妹群，纤毛虫四膜虫为外群。基因树之间的不一致程度乍一看似乎很高；只有19%的基因支持物种树，总共观察到48种不同的基因树拓扑结构。详细的研究表明，许多基因的低信噪比可能是不一致的主要来源。对于给定的基因树，与物种树一致的概率作为在树节点处观察到的最小引导支持度的函数而增加。此外，产生高引导支持度的基因序列对比对参数或所使用的系统发育方法的变化是稳健的。然而，需要注意的是，由于类比、违反模型或其他原因，某些基因可能会推断出具有强大支持的“错误”树。检查具有强烈系统发育信号的多个无关联基因的重要性怎么强调都不为过。
The protistan phylum Apicomplexa contains many important pathogens and is the subject of intense genome sequencing efforts. Based upon the genome sequences from seven apicomplexan species and a ciliate outgroup, we identified 268 single-copy genes suitable for phylogenetic inference. Both concatenation and consensus approaches inferred the same species tree topology. This topology is consistent with most prior conceptions of apicomplexan evolution based upon ultrastructural and developmental characters, that is, the piroplasm genera Theileria and Babesia form the sister group to the Plasmodium species, the coccidian genera Eimeria and Toxoplasma are monophyletic and are the sister group to the Plasmodium species and piroplasm genera, and Cryptosporidium forms the sister group to the above mentioned with the ciliate Tetrahymena as the outgroup. The level of incongruence among gene trees appears to be high at first glance; only 19% of the genes support the species tree, and a total of 48 different gene-tree topologies are observed. Detailed investigations suggest that the low signal-to-noise ratio in many genes may be the main source of incongruence. The probability of being consistent with the species tree increases as a function of the minimum bootstrap support observed at tree nodes for a given gene tree. Moreover, gene sequences that generate high bootstrap support are robust to the changes in alignment parameters or phylogenetic method used. However, caution should be taken in that some genes can infer a “wrong” tree with strong support because of paralogy, model violations, or other causes. The importance of examining multiple, unlinked genes that possess a strong phylogenetic signal cannot be overstated.
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影响因子：
10.7
作者：
Castresana, J
通讯作者：
Castresana, J
影响因子：
12.3
作者：
通讯作者：
--
影响因子：
2
作者：
Carreno, RA;Martin, DS;Barta, JR
通讯作者：
Barta, JR
影响因子：
56.9
作者：
Abrahamsen, MS;Templeton, TJ;Kapur, V
通讯作者：
Kapur, V
影响因子：
14.9
作者：
Bahl, A;Brunk, B;Whetzel, P
通讯作者：
Whetzel, P