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Rooted phylogeny of the three superkingdoms.

Harish, Ajith LU ; Tunlid, Anders LU and Kurland, Charles LU (2013) In Biochimie 95(8). p.1593-1604
Abstract
The traditional bacterial rooting of the three superkingdoms in sequence-based gene trees is inconsistent with new phylogenetic reconstructions based on genome content of compact protein domains. We find that protein domains at the level of the SCOP superfamily (SF) from sequenced genomes implement with maximum parsimony fully resolved rooted trees. Such genome content trees identify archaea and bacteria (akaryotes) as sister clades that diverge from an akaryote common ancestor, LACA. Several eukaryote sister clades diverge from a eukaryote common ancestor, LECA. LACA and LECA descend in parallel from the most recent universal common ancestor (MRUCA), which is not a bacterium. Rather, MRUCA presents 75% of the unique SFs encoded by extant... (More)
The traditional bacterial rooting of the three superkingdoms in sequence-based gene trees is inconsistent with new phylogenetic reconstructions based on genome content of compact protein domains. We find that protein domains at the level of the SCOP superfamily (SF) from sequenced genomes implement with maximum parsimony fully resolved rooted trees. Such genome content trees identify archaea and bacteria (akaryotes) as sister clades that diverge from an akaryote common ancestor, LACA. Several eukaryote sister clades diverge from a eukaryote common ancestor, LECA. LACA and LECA descend in parallel from the most recent universal common ancestor (MRUCA), which is not a bacterium. Rather, MRUCA presents 75% of the unique SFs encoded by extant genomes of the three superkingdoms, each encoding a proteome that partially overlaps all others. This alone implies that the common ancestor to the superkingdoms was very complex. Such ancestral complexity is confirmed by phylogenetic reconstructions. In addition, the divergence of proteomes from the complex ancestor in each superkingdom is both reductive in numbers of unique SFs as well as cumulative in the abundance of surviving SFs. These data suggest that the common ancestor was not the first cell lineage and that modern global phylogeny is the crown of a "recently" re-rooted tree. We suggest that a bottlenecked survivor of an environmental collapse, which preceded the flourishing of the modern crown, seeded the current phylogenetic tree. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Rooted phylogeny, Genome content/protein domain, Reductive evolution, Gene duplication, Innocuous HGT
in
Biochimie
volume
95
issue
8
pages
1593 - 1604
publisher
Elsevier
external identifiers
  • wos:000321801500010
  • pmid:23669449
  • scopus:84879691295
ISSN
1638-6183
DOI
10.1016/j.biochi.2013.04.016
language
English
LU publication?
yes
id
b23a1b3a-1e07-40ee-8dba-3863651bf7fe (old id 3804504)
date added to LUP
2013-08-19 11:17:30
date last changed
2019-08-07 01:23:32
@article{b23a1b3a-1e07-40ee-8dba-3863651bf7fe,
  abstract     = {The traditional bacterial rooting of the three superkingdoms in sequence-based gene trees is inconsistent with new phylogenetic reconstructions based on genome content of compact protein domains. We find that protein domains at the level of the SCOP superfamily (SF) from sequenced genomes implement with maximum parsimony fully resolved rooted trees. Such genome content trees identify archaea and bacteria (akaryotes) as sister clades that diverge from an akaryote common ancestor, LACA. Several eukaryote sister clades diverge from a eukaryote common ancestor, LECA. LACA and LECA descend in parallel from the most recent universal common ancestor (MRUCA), which is not a bacterium. Rather, MRUCA presents 75% of the unique SFs encoded by extant genomes of the three superkingdoms, each encoding a proteome that partially overlaps all others. This alone implies that the common ancestor to the superkingdoms was very complex. Such ancestral complexity is confirmed by phylogenetic reconstructions. In addition, the divergence of proteomes from the complex ancestor in each superkingdom is both reductive in numbers of unique SFs as well as cumulative in the abundance of surviving SFs. These data suggest that the common ancestor was not the first cell lineage and that modern global phylogeny is the crown of a "recently" re-rooted tree. We suggest that a bottlenecked survivor of an environmental collapse, which preceded the flourishing of the modern crown, seeded the current phylogenetic tree.},
  author       = {Harish, Ajith and Tunlid, Anders and Kurland, Charles},
  issn         = {1638-6183},
  keyword      = {Rooted phylogeny,Genome content/protein domain,Reductive evolution,Gene duplication,Innocuous HGT},
  language     = {eng},
  number       = {8},
  pages        = {1593--1604},
  publisher    = {Elsevier},
  series       = {Biochimie},
  title        = {Rooted phylogeny of the three superkingdoms.},
  url          = {http://dx.doi.org/10.1016/j.biochi.2013.04.016},
  volume       = {95},
  year         = {2013},
}