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. 2009 Feb 22;276(1657):597-604.
doi: 10.1098/rspb.2008.1358.

Evolutionary position of breviate amoebae and the primary eukaryote divergence

Marianne A Minge  1 , Jeffrey D Silberman, Russell J S Orr, Thomas Cavalier-Smith, Kamran Shalchian-Tabrizi, Fabien Burki, Asmund Skjaeveland, Kjetill S Jakobsen
Affiliations

Evolutionary position of breviate amoebae and the primary eukaryote divergence

Marianne A Minge et al. Proc Biol Sci. .

Abstract

Integration of ultrastructural and molecular sequence data has revealed six supergroups of eukaryote organisms (excavates, Rhizaria, chromalveolates, Plantae, Amoebozoa and opisthokonts), and the root of the eukaryote evolutionary tree is suggested to lie between unikonts (Amoebozoa, opisthokonts) and bikonts (the other supergroups). However, some smaller lineages remain of uncertain affinity. One of these unassigned taxa is the anaerobic, free-living, amoeboid flagellate Breviata anathema, which is of key significance as it is unclear whether it is a unikont (i.e. possibly the deepest branching amoebozoan) or a bikont. To establish its evolutionary position, we sequenced thousands of Breviata genes and calculated trees using 78 protein sequences. Our trees and specific substitutions in the 18S RNA sequence indicate that Breviata is related to other Amoebozoa, thereby significantly increasing the cellular diversity of this phylum and establishing Breviata as a deep-branching unikont. We discuss the implications of these results for the ancestral state of Amoebozoa and eukaryotes generally, demonstrating that phylogenomics of phylogenetically 'nomadic' species can elucidate key questions in eukaryote evolution. Furthermore, mitochondrial genes among the Breviata ESTs demonstrate that Breviata probably contains a modified anaerobic mitochondrion. With these findings, remnants of mitochondria have been detected in all putatively deep-branching amitochondriate organisms.

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Figures

Figure 1
Figure 1
In vivo morphology of B. anathema. Light micrographs of unstained living B. anathema cells. (a) 400× DIC image highlighting the numerous branching pseudopodia and widened cell sheath at the base of the single flagellum. (b) Inset 630× DIC image showing the position of the nucleus containing a centrally located nucleolus. (c) 400× phase-contrast image highlighting the flattened pseudopodial attachments to the substrate. Scale bars, 5 μm.
Figure 2
Figure 2
A global phylogeny of eukaryotes. Maximum-likelihood tree with bootstrap support values (BV) from an amino acid alignment of 78 concatenated genes (17 283 characters) inferred using Raxml and Treefinder (both giving identical topology; the raxml tree is shown). Bayesian PP support values for bipartitions are also shown if more than 0.50. Filled circles denote support values of 100% BV and 1.0 PP, and dash (−) denotes support value below 50% BV or 0.50 PP. Nodes without denotation received less than 50% BV and less than 0.50 PP.
Figure 3
Figure 3
The placement of Breviata within Amoebozoa in three maximum-likelihood phylogenies with BV inferred with Raxml after removing categories of fast-evolving sites. Only the Amoebozoa branch is shown and global trees are shown in figure S2 in the electronic supplementary material. Categories 6, 7 and 8 refer to the sites removed; category 8 comprises the fastest evolving sites. Filled circles denote support values of 100% BV.
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