Comprehensive phylogenetic reconstruction of amoebozoa based on concatenated analyses of SSU-rDNA and actin genes.
Comprehensive phylogenetic reconstruction of amoebozoa based on concatenated analyses of SSU-rDNA and actin genes.
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DOI：
10.1371/journal.pone.0022780
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Katz LA
中科院分区：
文献类型：
--
作者：
Lahr DJ;Grant J;Nguyen T;Lin JH;Katz LA
阿米巴原虫的进化关系一直是争议的主题，原因有两个：1)传统调查中形态学特征的缺乏和2)现代分子重建中随意的分类抽样。这些因素以及其他因素阻碍了建立一个能够自信地解决高层和低层关系的确定系统。此外，最近认识到许多原柱状变形虫实际上分散在变形虫中，这表明系统发育重建已经排除了一个广泛而完整的生物群体。本文利用SSU-rDNA和actin基因的分子信息，对139个分类群进行了系统发育重建。我们提供了其中13个分类群的分子数据，其中12个以前没有被表征过。我们对数据集进行了广泛的探索，通过生成18个替代重建来评估缺失数据、长分支分类群、不稳定分类群、快速进化的位点和包含环境序列的影响。我们将重建结果相互比较，并与先前发表的系统发生进行比较。我们的分析表明，许多形态学上建立的低级关系（这里定义为大致相当于目级或以下的关系）与分子数据一致。然而，除了Tubulinea、Archamoebae和Myxogastrea外，这些数据不足以证实或拒绝大多数被提出的更高层次的关系（高于目级）。此外，与之前的预期相反，包含可用的环境序列并没有显著改善阿米巴原虫的重建。这可能是因为关键的阿米巴原虫类群由于分子进化的高速率和大索引子和内含子的规律出现，不容易通过环境测序方法扩增。最后，为了促进未来关键阿米巴原虫类群的采样，我们提供了一种新的方法，用于从单个或几个细胞中扩增基因组和提取cDNA，这种方法不依赖于培养，允许从自然样本中提取多个基因。
Evolutionary relationships within Amoebozoa have been the subject of controversy for two reasons: 1) paucity of morphological characters in traditional surveys and 2) haphazard taxonomic sampling in modern molecular reconstructions. These along with other factors have prevented the erection of a definitive system that resolves confidently both higher and lower-level relationships. Additionally, the recent recognition that many protosteloid amoebae are in fact scattered throughout the Amoebozoa suggests that phylogenetic reconstructions have been excluding an extensive and integral group of organisms. Here we provide a comprehensive phylogenetic reconstruction based on 139 taxa using molecular information from both SSU-rDNA and actin genes. We provide molecular data for 13 of those taxa, 12 of which had not been previously characterized. We explored the dataset extensively by generating 18 alternative reconstructions that assess the effect of missing data, long-branched taxa, unstable taxa, fast evolving sites and inclusion of environmental sequences. We compared reconstructions with each other as well as against previously published phylogenies. Our analyses show that many of the morphologically established lower-level relationships (defined here as relationships roughly equivalent to Order level or below) are congruent with molecular data. However, the data are insufficient to corroborate or reject the large majority of proposed higher-level relationships (above the Order-level), with the exception of Tubulinea, Archamoebae and Myxogastrea, which are consistently recovered. Moreover, contrary to previous expectations, the inclusion of available environmental sequences does not significantly improve the Amoebozoa reconstruction. This is probably because key amoebozoan taxa are not easily amplified by environmental sequencing methodology due to high rates of molecular evolution and regular occurrence of large indels and introns. Finally, in an effort to facilitate future sampling of key amoebozoan taxa, we provide a novel methodology for genome amplification and cDNA extraction from single or a few cells, a method that is culture-independent and allows both photodocumentation and extraction of multiple genes from natural samples.
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