Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.
Mol Phylogenet Evol. 2013 Apr;67(1):53-9. doi: 10.1016/j.ympev.2012.12.011. Epub 2012 Dec 29.
Rhizaria is one of the six supergroups of eukaryotes, which comprise the majority of amoeboid and skeleton-building protists living in freshwater and marine ecosystems. There is an overall lack of molecular data for the group and therefore the deep phylogeny of rhizarians is unresolved. Molecular data are particularly scarce for the clade of Retaria, which include two prominent groups of microfossils: foraminiferans and radiolarians. To fill this gap, we have produced and sequenced EST libraries for 14 rhizarian species including seven foraminiferans, Gromia and six taxa belonging to traditional Haeckel's Radiolaria: Acantharea, Polycystinea, and Phaeodarea. A matrix was constructed for phylogenetic analysis based on 109 genes and a total of 56 species, of which 22 are rhizarians. Our analyses provide the first multigene evidence for branching of Phaeodarea within Cercozoa, confirming the polyphyly of Haeckel's Radiolaria. It confirms the monophyly of Retaria, a clade grouping Foraminifera with other lineages of Radiolaria. However, contrary to what could be expected from morphological observations, Foraminifera do not form a sister group to radiolarians, but branch within them as sister to either Acantharea or Polycystinea depending on the multigene data set. While the monophyly of Foraminifera and Acantharea is well supported, that of Polycystinea, represented in our data by Spumellaria and Collodaria is questionable. In view of our study, Haeckel's Radiolaria appears as both, a polyphyletic and paraphyletic assemblage of independent groups that should be considered as separate lineages in protist classification.
根足虫是真核生物的六个超类群之一，包含了大多数在淡水和海洋生态系统中生活的变形虫和骨骼构建原生生物。该类群的分子数据总体缺乏，因此根足虫的系统发育关系尚未解决。分子数据对于 Retaria 类群特别稀缺，该类群包括两个重要的微体化石群：有孔虫和放射虫。为了填补这一空白，我们针对包括 7 种有孔虫、Gromia 和 6 种属于传统 Haeckel 放射虫的分类单元在内的 14 种根足虫物种，生成并测序了 EST 文库：Acantharea、Polycystinea 和 Phaeodarea。我们构建了一个基于 109 个基因和总共 56 个物种的矩阵进行系统发育分析，其中 22 个是根足虫。我们的分析为 Phaeodarea 在 Cercozoa 内分支提供了第一个多基因证据，证实了 Haeckel 放射虫的多系性。它证实了 Retaria 的单系性，该类群将有孔虫与放射虫的其他谱系组合在一起。然而，与形态学观察结果相反，有孔虫不是放射虫的姐妹群，而是在多基因数据集内与 Acantharea 或 Polycystinea 形成姐妹群。尽管有孔虫和 Acantharea 的单系性得到很好的支持，但在我们的数据中代表 Spumellaria 和 Collodaria 的 Polycystinea 的单系性是有问题的。鉴于我们的研究，Haeckel 放射虫似乎是一个多系和并系的独立群体集合，在原生生物分类中应被视为单独的谱系。
