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The phylogenomics of protein structures: The backstory
Lund Univ, Microbial Ecol, Dept Biol, SE-22362 Lund, Sweden..
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
2015 (English)In: Biochimie, ISSN 0300-9084, E-ISSN 1638-6183, Vol. 119, 284-302 p.Article, review/survey (Refereed) Published
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Abstract [en]

In this introductory retrospective, evolution as viewed through gene trees is inspected through a lens compounded from its founding operational assumptions. The four assumptions of the gene tree culture that are singularly important to evolutionary interpretations are: a. that protein-coding sequences are molecular fossils; b. that gene trees are equivalent to species trees; c. that the tree of life is assumed to be rooted in a simple akaryote cell implying that akaryotes are primitive, and d. that the notion that all or most incongruities between alignment-based gene trees are due to horizontal gene transfer (HGT), which includes the endosymbiotic models postulated for the origins of eukaryotes. What has been unusual about these particular assumptions is that though each was taken on board explicitly, they are defended in the face of factual challenge by a stolid disregard for the conflicting observations. The factual challenges to the mainstream gene tree-inspired evolutionary view are numerous and most convincingly summarized as: Genome trees tell a very different story. Phylogeny inferred from genomic assortments of homologous protein structural-domains does not support any one of the four principle evolutionary interpretations of gene trees: a. 3D protein domain structures are the molecular fossils of evolution, while coding sequences are transients; b. Species trees are very different from gene trees; c. The ToL is rooted in a surprisingly complex universal common ancestor (UCA) that is distinct from any specific modern descendant and d. HGT including endosymbiosis is a negligible player in genome evolution from UCA to the present.

Place, publisher, year, edition, pages
2015. Vol. 119, 284-302 p.
Keyword [en]
Phylogeny, Tree of life, Horizontal gene transfer, Protein superfamily, Autogenous evolution of eukaryotes
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:uu:diva-279530DOI: 10.1016/j.biochi.2015.07.027ISI: 000367022800031OAI: oai:DiVA.org:uu-279530DiVA: diva2:908325
Funder
The Royal Swedish Academy of Sciences
Available from: 2016-03-02 Created: 2016-03-02 Last updated: 2017-11-30Bibliographically approved

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