title: Early-branching or fast-evolving eukaryotes? An answer based on slowly evolving positions.
abstract: The current paradigm of eukaryotic evolution is based primarily on comparative analysis of ribosomal RNA sequences. It shows several early-emerging lineages, mostly amitochondriate, which might be living relics of a progressive assembly of the eukaryotic cell. However, the analysis of slow-evolving positions, carried out with the newly developed slow-fast method, reveals that these lineages are, in terms of nucleotide substitution, fast-evolving ones, misplaced at the base of the tree by a long branch attraction artefact. Since the fast-evolving groups are not always the same, depending on which macromolecule is used as a marker, this explains most of the observed incongruent phylogenies. The current paradigm of eukaryotic evolution thus has to be seriously re-examined as the eukaryotic phylogeny is presently best summarized by a multifurcation. This is consistent with the Big Bang hypothesis that all extant eukaryotic lineages are the result of multiple cladogeneses within a relatively brief period, although insufficiency of data is also a possible explanation for the lack of resolution. For further resolution, rare evolutionary events such as shared insertions and/or deletions or gene fusions might be helpful.
authors.affiliation: Phylogénie et Evolution Moléculaires (UPRES-A 8080), Université Paris-Sud, Orsay, France. herve.philippe@bc4.u-psud.fr
authors.forename: H
authors.initials: H
authors.lastname: Philippe
authors.forename: P
authors.initials: P
authors.lastname: Lopez
authors.forename: H
authors.initials: H
authors.lastname: Brinkmann
authors.forename: K
authors.initials: K
authors.lastname: Budin
authors.forename: A
authors.initials: A
authors.lastname: Germot
authors.forename: J
authors.initials: J
authors.lastname: Laurent
authors.forename: D
authors.initials: D
authors.lastname: Moreira
authors.forename: M
authors.initials: M
authors.lastname: Müller
authors.forename: H
authors.initials: H
authors.lastname: Le Guyader
mesh_terms: D000199:Actins / Q000235:genetics; D005057:Eukaryotic Cells / Q000145:classification*; D019143:Evolution, Molecular; D020648:Peptide Elongation Factor 1; D010802:Phylogeny; D012319:RNA Polymerase II / Q000235:genetics; D012335:RNA, Ribosomal / Q000032:analysis; D017423:Sequence Analysis, RNA; D014404:Tubulin / Q000235:genetics
chemical_list: D000199:Actins; D020648:Peptide Elongation Factor 1; D012335:RNA, Ribosomal; D014404:Tubulin; D012319:RNA Polymerase II