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Genome Biol Evol. 2018 Feb 1;10(2):427-433. doi: 10.1093/gbe/evy014.

Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-Group.

Author information

1
Department of Biological Sciences, Mississippi State University, USA.
2
Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, USA.
3
Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada.
4
Department of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA.
5
Graduate School of Human and Environmental Studies, Graduate School of Global Environmental Studies, Kyoto University, Japan.
6
Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan.
7
Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan.
8
Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan.
9
Department of Biochemistry and Molecular Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada.

Abstract

Recent phylogenetic analyses position certain "orphan" protist lineages deep in the tree of eukaryotic life, but their exact placements are poorly resolved. We conducted phylogenomic analyses that incorporate deeply sequenced transcriptomes from representatives of collodictyonids (diphylleids), rigifilids, Mantamonas, and ancyromonads (planomonads). Analyses of 351 genes, using site-heterogeneous mixture models, strongly support a novel super-group-level clade that includes collodictyonids, rigifilids, and Mantamonas, which we name "CRuMs". Further, they robustly place CRuMs as the closest branch to Amorphea (including animals and fungi). Ancyromonads are strongly inferred to be more distantly related to Amorphea than are CRuMs. They emerge either as sister to malawimonads, or as a separate deeper branch. CRuMs and ancyromonads represent two distinct major groups that branch deeply on the lineage that includes animals, near the most commonly inferred root of the eukaryote tree. This makes both groups crucial in examinations of the deepest-level history of extant eukaryotes.

KEYWORDS:

concatenated phylogenetic analysis; eukaryote tree of life; protist; site-heterogeneous models

PMID:
29360967
PMCID:
PMC5793813
DOI:
10.1093/gbe/evy014
[Indexed for MEDLINE]
Free PMC Article

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