Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic “supergroups”

Abstract

Nearly all of eukaryotic diversity has been classified into 6 suprakingdom-level groups (supergroups) based on molecular and morphological/cell-biological evidence; these are Opisthokonta, Amoebozoa, Archaeplastida, Rhizaria, Chromalveolata, and Excavata. However, molecular phylogeny has not provided clear evidence that either Chromalveolata or Excavata is monophyletic, nor has it resolved the relationships among the supergroups. To establish the affinities of Excavata, which contains parasites of global importance and organisms regarded previously as primitive eukaryotes, we conducted a phylogenomic analysis of a dataset of 143 proteins and 48 taxa, including 19 excavates. Previous phylogenomic studies have not included all major subgroups of Excavata, and thus have not definitively addressed their interrelationships. The enigmatic flagellate Andalucia is sister to typical jakobids. Jakobids (including Andalucia), Euglenozoa and Heterolobosea form a major clade that we name Discoba. Analyses of the complete dataset group Discoba with the mitochondrion-lacking excavates or ''metamonads'' (diplomonads, parabasalids, and Preaxostyla), but not with the final excavate group, Malawimonas. This separation likely results from a long-branch attraction artifact. Gradual removal of rapidly-evolving taxa from the dataset leads to moderate bootstrap support (69%) for the monophyly of all Excavata, and 90% support once all metamonads are removed. Most importantly, Excavata robustly emerges between unikonts (Amoebozoa ؉ Opisthokonta) and ''megagrouping'' of Archaeplastida, Rhizaria, and chromalveolates. Our analyses indicate that Excavata forms a monophyletic suprakingdom-level group that is one of the 3 primary divisions within eukaryotes, along with unikonts and a megagroup of Archaeplastida, Rhizaria, and the chromalveolate lineages.Chromalveolata ͉ Discoba ͉ long-branch attraction

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

“…This is the largest ''ciliate-based'' phylogenetic dataset assembled to date in terms of number of bases included. All previous studies were based either on single or a couple of genes or contained extremely limited sampling of ciliates (Bapteste et al, 2002;Brown et al, 2012;Budin and Philippe, 1998;Burki et al, 2009Burki et al, , 2013Greenwood et al, 1991;Hampl et al, 2009;Hammerschmidt et al, 1996;Katz et al, 2004;Lynn and Sogin, 1988;Sogin and Elwood, 1986).…”

“…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.…”

“…Over the past few years, phylogenomic approaches have been employed to untangle deep relationships among major microbial eukaryotic lineages and place divergent taxa of evolutionary significance (Brown et al, 2012, in press;Burki et al, 2007Burki et al, , 2009Burki et al, , 2012Hampl et al, 2009;Parfrey et al, 2010;Zhao et al, 2012). Largescale phylogenomic analyses are now being utilized to resolve questions associated with the shallower nodes of the eukaryotic tree of life (Bachvaroff et al, 2011;Burki et al, 2010).…”

Phylogenomic analyses reveal subclass Scuticociliatia as the sister group of subclass Hymenostomatia within class Oligohymenophorea

“…Therefore, in order to resolve these relationships more clearly, an analysis based on genomic data was carried out. Phylogenomic analyses that used omics data have generally improved the robustness of molecular phylogenetic reconstructions and untangled many previously debated phylogenies among major eukaryotic lineages (Chiari et al, 2012;Hampl et al, 2009;Liang et al, 2013;Philippe et al, 2009;Philippe et al, 2005;Philippe and Telford, 2006;Ryan et al, 2013;Struck and Fisse, 2008). With respect to the phylum Ciliophora, the first phylogenomic analysis was carried out to explore the phylogenetic position of the ambiguous taxon Protocruzia (Gentekaki et al, 2014).…”

From simple to supercomplex: mitochondrial genomes of euglenozoan protists

“…The well-known representatives of these groups are Euglena for euglenids and Trypanosoma for kinetoplastids, whereas diplonemids are very poorly known. Although the Euglenozoa is a stable and highly supported group, mutual phylogenetic relationships among these three groups are not yet fully resolved, and euglenids likely constitute the earliest offshoot ( Figure 1) 1– 3 .…”