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.

Informational Gene Phylogenies Do Not Support a Fourth Domain of Life for Nucleocytoplasmic Large DNA Viruses

“…Both of these problems can cause errors in tree inference [24], [26], raising the possibility that the support for the “4 domains” hypothesis obtained from these proteins might be influenced by model misspecification.…”

On the origin and functions of RNA-mediated silencing: from protists to man

“…home.html ); Spo Dcr1 S. pombe Dcr1 (Q09884); Tt Dcr2 T. thermophila Dcr2 (BAD34723) "rooted" with these mitochondrion-lacking unicellular eukaryotes (Sogin et al 1989;Sogin 1991). Recent studies have suggested that this rooting may have been patterned by methodological artefacts (Philippe et al 2000). Arisue et al (2004) have argued that two possibilities seem to exist for the root of the eukaryotic tree, namely the branch leading to Opisthokonta (animals and fungi) or that leading to the common ancestor of Diplomonadida/Parabasalia (within Excavata).…”

Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages

“…The discrepancy between the ML and BI analyses may suggest that they are affected by long-branch attraction (LBA) . To test whether the ML topology might be the result of LBA, we performed removal of fast evolving sites, one of the most common ways for suppressing such artifacts (Brown et al, in press;Hampl et al, 2009;Philippe et al, 2000). Nevertheless, even after doing so, the results of our analyses remained unchanged.…”