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

Matthew W Brown; Aaron A Heiss; Ryoma Kamikawa; Yuji Inagaki; Akinori Yabuki; Alexander K Tice; Takashi Shiratori; Ken-Ichiro Ishida; Tetsuo Hashimoto; Alastair G B Simpson; Andrew J Roger

doi:10.1093/gbe/evy014

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

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

Authors

Matthew W Brown^{1 2}, Aaron A Heiss^{3 4}, Ryoma Kamikawa⁵, Yuji Inagaki^{6 7}, Akinori Yabuki⁸, Alexander K Tice^{1 2}, Takashi Shiratori⁶, Ken-Ichiro Ishida⁶, Tetsuo Hashimoto^{6 7}, Alastair G B Simpson³, Andrew J Roger⁹

Affiliations

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.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Eukaryota / classification
Eukaryota / genetics*
Genomics / methods
High-Throughput Nucleotide Sequencing
Phylogeny*
Transcriptome