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The phylogenomics of protein structures: The backstory.

Kurland, Charles LU and Harish, Ajith (2015) In Biochimie 119(Online 31 July 2015). p.284-302
Abstract
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... (More)
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. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Biochimie
volume
119
issue
Online 31 July 2015
pages
284 - 302
publisher
Elsevier
external identifiers
  • pmid:26234735
  • wos:000367022800031
  • scopus:84951567012
ISSN
1638-6183
DOI
10.1016/j.biochi.2015.07.027
language
English
LU publication?
yes
id
dc9bfe8a-fb8b-47ee-8ae1-a8a11b8d47bb (old id 7845000)
date added to LUP
2015-09-11 13:22:52
date last changed
2017-10-22 03:21:09
@article{dc9bfe8a-fb8b-47ee-8ae1-a8a11b8d47bb,
  abstract     = {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.},
  author       = {Kurland, Charles and Harish, Ajith},
  issn         = {1638-6183},
  language     = {eng},
  number       = {Online 31 July 2015},
  pages        = {284--302},
  publisher    = {Elsevier},
  series       = {Biochimie},
  title        = {The phylogenomics of protein structures: The backstory.},
  url          = {http://dx.doi.org/10.1016/j.biochi.2015.07.027},
  volume       = {119},
  year         = {2015},
}