Early–branching or fast–evolving eukaryotes? An answer based on slowly evolving positions

• Published in: Philosophical transactions of the Royal Society of London. Series B. Biological sciences Vol. 267; no. 1449; pp. 1213 - 1221
• Main Authors: Philippe, Hervé, Lopez, Philippe, Brinkmann, Henner, Budin, Karine, Germot, Agnés, Laurent, Jacqueline, Moreira, David, Müller, Miklós, Guyader, Hervé Le
• Format: Journal Article
• Language: English
• Published: England The Royal Society 22.06.2000; Royal Society, The
• Subjects: Actins; Actins - genetics; Brackish; Datasets; Early-Branching Organisms; Eukaryotes; Eukaryotic cells; Eukaryotic Cells - classification; Evolution; Evolution, Molecular; Freshwater; Fungi; Life Sciences; Long Branch Attraction Artefact; Loss Of Function; Marine; Microsporidia; Molecular Phylogeny; Peptide Elongation Factor 1; Phylogenetics; Phylogeny; RNA Polymerase II - genetics; RNA, Ribosomal - analysis; rRNA; Sequence Analysis, RNA; Taxa; Tubulin - genetics; We they distinction; PHYLOGENY; EUKARYOTES
• ISSN: 0962-8452; 0962-8436; 1471-2954; 1471-2970
• DOI: 10.1098/rspb.2000.1130

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.