Evolutionary History of “Early-Diverging” Eukaryotes: The Excavate Taxon Carpediemonas is a Close Relative of Giardia1

作者：Alastair G. B. Simpson, Andrew J. Roger, Jeffrey D. Silberman, Detlef D. Leipe, Virginia P. Edgcomb, Lars S. Jermiin, David J. Patterson, Mitchell L. Sogin · 发表于：Molecular Biology and Evolution · 年份：2002 · DOI：10.1093/oxfordjournals.molbev.a004000 · 被引用次数：95 · 研究领域：Parasitic Infections and Diagnostics、Protist diversity and phylogeny、Environmental DNA in Biodiversity Studies

Diplomonads, such as Giardia, and their close relatives retortamonads have been proposed as early-branching eukaryotes that diverged before the acquisition-retention of mitochondria, and they have become key organisms in attempts to understand the evolution of eukaryotic cells. In this phylogenetic study we focus on a series of eukaryotes suggested to be relatives of diplomonads on morphological grounds, the "excavate taxa". Phylogenies of small subunit ribosomal RNA (SSU rRNA) genes, alpha-tubulin, beta-tubulin, and combined alpha- + beta-tubulin all scatter the various excavate taxa across the diversity of eukaryotes. But all phylogenies place the excavate taxon Carpediemonas as the closest relative of diplomonads (and, where data are available, retortamonads). This novel relationship is recovered across phylogenetic methods and across various taxon-deletion experiments. Statistical support is strongest under maximum-likelihood (ML) (when among-site rate variation is modeled) and when the most divergent diplomonad sequences are excluded, suggesting a true relationship rather than an artifact of long-branch attraction. When all diplomonads are excluded, our ML SSU rRNA tree actually places retortamonads and Carpediemonas away from the base of the eukaryotes. The branches separating excavate taxa are mostly not well supported (especially in analyses of SSU rRNA data). Statistical tests of the SSU rRNA data, including an "expected likelihood weights" approach, do not reject tr...