@ARTICLE{TreeBASE2Ref20199, author = {Romain Derelle and Bernard Franz Lang}, title = {Rooting the eukaryotic tree with mitochondrial and bacterial proteins }, year = {2011}, keywords = {Phylogenomic, eukaryotic origin, Proteobacteria, unikonts, bikonts}, doi = {}, url = {http://}, pmid = {}, journal = {Molecular Biology and Evolution}, volume = {}, number = {}, pages = {}, abstract = {By exploiting the large body of genome data and the considerable progress in phylogenetic methodology, recent phylogenomic studies have provided new insights into the relationships among major eukaryotic groups. However, confident placement of the eukaryotic root remains a major challenge. This is due to the large evolutionary distance separating eukaryotes from their closest relatives, the Archaea, implying a weak phylogenetic signal and strong long-branch attraction artefacts. Here, we apply a new approach to the rooting of the eukaryotic tree by using a subset of genomic information with more recent evolutionary origin - mitochondrial sequences, whose closest relatives are α-Proteobacteria. For this, we identified and assembled a dataset of 42 mitochondrial proteins (mainly encoded by the nuclear genome) and performed Bayesian and ML analyses. Taxon sampling includes the recently sequenced Thecamonas trahens, a member of the phylogenetically elusive Apusozoa. This dataset confirms the relationships of several eukaryotic supergroups seen before, and places the eukaryotic root between the monophyletic ?unikonts? and ?bikonts?. We further show that T. trahens branches sister to Opisthokonta with significant statistical support, and question the bikont/excavate affiliation of Malawimonas species. The mitochondrial dataset developed here (to be expanded in the future) constitutes a unique alternative means in resolving deep eukaryotic relationships.} }

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