title: Evolutionary position of breviate amoebae and the primary eukaryote divergence.
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.
authors.affiliation: Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, 0316 Oslo, Norway.
authors.forename: Marianne A
authors.initials: MA
authors.lastname: Minge
authors.forename: Jeffrey D
authors.initials: JD
authors.lastname: Silberman
authors.forename: Russell J S
authors.initials: RJ
authors.lastname: Orr
authors.forename: Thomas
authors.initials: T
authors.lastname: Cavalier-Smith
authors.forename: Kamran
authors.initials: K
authors.lastname: Shalchian-Tabrizi
authors.forename: Fabien
authors.initials: F
authors.lastname: Burki
authors.forename: Asmund
authors.initials: A
authors.lastname: Skjaeveland
authors.forename: Kjetill S
authors.initials: KS
authors.lastname: Jakobsen
mesh_terms: D000818:Animals; D005057:Eukaryotic Cells / Q000145:classification* / Q000648:ultrastructure; D020224:Expressed Sequence Tags; D015723:Gene Library; D050259:Genes, Mitochondrial; D023281:Genomics; D008928:Mitochondria / Q000235:genetics / Q000502:physiology; D010802:Phylogeny; D012337:RNA, Ribosomal, 18S / Q000737:chemistry; D017422:Sequence Analysis, DNA
chemical_list: D012337:RNA, Ribosomal, 18S