Tekle Yonas I, Grant Jessica, Anderson O Roger, Nerad Thomas A, Cole Jeffrey C, Patterson David J, Katz Laura A
Department of Biological Sciences, Smith College, Northampton, MA 01063, USA.
Mol Phylogenet Evol. 2008 Apr;47(1):339-52. doi: 10.1016/j.ympev.2007.11.015. Epub 2007 Dec 3.
Placing amoeboid lineages on the eukaryotic tree of life is difficult due to the paucity of comparable morphological characters and the limited molecular data available for many groups. This situation has led to the lumping of distantly related lineages into large inclusive groups, such as Sarcodina, that do not reflect evolutionary relationships. Previous analyses of molecular markers with limited taxon sampling reveal members of Sarcodina are scattered in five of the six proposed supergroups. We have used multigene analyses to place seven diverse amoeboid lineages-two Nolandella spp., Rhizamoeba sp., Pessonella sp., Arcella hemisphaerica, Arachnula sp. and Trichosphaerium sp.-on the eukaryotic tree of life. Bayesian analysis of the concatenated data of the four genes sequenced (SSU-rDNA, actin, alpha-tubulin and beta-tubulin), including diverse representatives of eukaryotes, indicates that all seven taxa group within the 'Amoebozoa' supergroup. We further performed separate analyses of the well-sampled SSU-rDNA and actin genes using Bayesian and Maximum Likelihood analyses to assess the positions of our newly characterized taxa. In the case of SSU-rDNA, we performed extensive analyses with removal of the fastest rates classes to evaluate the stability and resolution of various taxonomic hypotheses within 'Amoebozoa'. Five of our seven amoeboid lineages fall within well-supported clades that are corroborated by morphology. In contrast, the positions of Arachnula sp. and Trichosphaerium sp. in the SSU-rDNA gene trees are unstable and vary by analyses. Placement of these taxa will require additional data from slowly evolving genes combined with taxon-rich phylogenetic analyses. Finally, the analyses without the fastest rate classes demonstrate that SSU-rDNA has a limited signal for deep relationships within the 'Amoebozoa'.
由于可比较的形态特征匮乏，且许多类群可用的分子数据有限，因此将变形虫谱系置于真核生物生命之树上颇具难度。这种情况导致将远缘谱系归为大型包容性类群，如肉足虫纲，而这些类群并未反映进化关系。先前对分子标记进行的分析，由于分类群采样有限，结果显示肉足虫纲的成员分散在六个拟议的超群中的五个之中。我们利用多基因分析，将七个不同的变形虫谱系——两个诺兰氏变形虫属物种、根变形虫属物种、佩索尼氏变形虫属物种、半球房变形虫、蛛形变形虫属物种和球辐变形虫属物种——置于真核生物生命之树上。对包括各种真核生物代表在内的四个测序基因（小亚基核糖体DNA、肌动蛋白、α - 微管蛋白和β - 微管蛋白）的串联数据进行贝叶斯分析，结果表明所有七个分类单元都聚集在“变形虫超群”内。我们还使用贝叶斯分析和最大似然分析，分别对采样充分的小亚基核糖体DNA和肌动蛋白基因进行分析，以评估我们新鉴定的分类单元的位置。就小亚基核糖体DNA而言，我们进行了广泛分析，去除了最快进化速率类别，以评估“变形虫超群”内各种分类假设的稳定性和分辨率。我们的七个变形虫谱系中有五个属于形态学证实的、得到有力支持的进化枝。相比之下，蛛形变形虫属物种和球辐变形虫属物种在小亚基核糖体DNA基因树中的位置不稳定，且因分析方法而异。确定这些分类单元的位置需要来自进化缓慢的基因的额外数据，并结合丰富分类群的系统发育分析。最后，去除最快进化速率类别的分析表明，小亚基核糖体DNA对于“变形虫超群”内的深层关系信号有限。
