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What is an archaeon and are the Archaea really unique?
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology. Uppsala Univ, Dept Cell & Mol Biol, Program Mol Biol, Uppsala, Sweden.
2018 (English)In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 6, article id e5770Article in journal (Refereed) Published
Abstract [en]

The recognition of the group Archaea as a major branch of the tree of life (ToL) prompted a new view of the evolution of biodiversity. The genomic representation of archaeal biodiversity has since significantly increased. In addition, advances in phylogenetic modeling of multi-locus datasets have resolved many recalcitrant branches of the ToL. Despite the technical advances and an expanded taxonomic representation, two important aspects of the origins and evolution of the Archaea remain controversial, even as we celebrate the 40th anniversary of the monumental discovery. These issues concern (i) the uniqueness (monophyly) of the Archaea, and (ii) the evolutionary relationships of the Archaea to the Bacteria and the Eukarya; both of these are relevant to the deep structure of the ToL. To explore the causes for this persistent ambiguity, I examine multiple datasets and different phylogenetic approaches that support contradicting conclusions. I find that the uncertainty is primarily due to a scarcity of information in standard datasets-universal core-genes datasets-to reliably resolve the conflicts. These conflicts can be resolved efficiently by comparing patterns of variation in the distribution of functional genomic signatures, which are less diffused unlike patterns of primary sequence variation. Relatively lower heterogeneity in distribution patterns minimizes uncertainties and supports statistically robust phylogenetic inferences, especially of the earliest divergences of life. This case study further highlights the limitations of primary sequence data in resolving difficult phylogenetic problems, and raises questions about evolutionary inferences drawn from the analyses of sequence alignments of a small set of core genes. In particular, the findings of this study corroborate the growing consensus that reversible substitution mutations may not be optimal phylogenetic markers for resolving early divergences in the ToL, nor for determining the polarity of evolutionary transitions across the ToL.

Place, publisher, year, edition, pages
PEERJ INC , 2018. Vol. 6, article id e5770
Keywords [en]
Tree of life, Rooting, Clade, Archaea, Non-stationary, Directional evolution, Phylogenomics, Asgard, Chimeric genome, Genome fusion
National Category
Evolutionary Biology
Identifiers
URN: urn:nbn:se:uu:diva-369092DOI: 10.7717/peerj.5770ISI: 000447739500003PubMedID: 30357005OAI: oai:DiVA.org:uu-369092DiVA, id: diva2:1289529
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation, KAW 2017.0055Swedish Research Council, 2016-06264Available from: 2019-02-18 Created: 2019-02-18 Last updated: 2019-02-18Bibliographically approved

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