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Informational gene phylogenies do not support a fourth domain of life for nucleocytoplasmic large DNA viruses.
PLoS One. 2011; 6(6):e21080.Plos

Abstract

Mimivirus is a nucleocytoplasmic large DNA virus (NCLDV) with a genome size (1.2 Mb) and coding capacity (1000 genes) comparable to that of some cellular organisms. Unlike other viruses, Mimivirus and its NCLDV relatives encode homologs of broadly conserved informational genes found in Bacteria, Archaea, and Eukaryotes, raising the possibility that they could be placed on the tree of life. A recent phylogenetic analysis of these genes showed the NCLDVs emerging as a monophyletic group branching between Eukaryotes and Archaea. These trees were interpreted as evidence for an independent "fourth domain" of life that may have contributed DNA processing genes to the ancestral eukaryote. However, the analysis of ancient evolutionary events is challenging, and tree reconstruction is susceptible to bias resulting from non-phylogenetic signals in the data. These include compositional heterogeneity and homoplasy, which can lead to the spurious grouping of compositionally-similar or fast-evolving sequences. Here, we show that these informational gene alignments contain both significant compositional heterogeneity and homoplasy, which were not adequately modelled in the original analysis. When we use more realistic evolutionary models that better fit the data, the resulting trees are unable to reject a simple null hypothesis in which these informational genes, like many other NCLDV genes, were acquired by horizontal transfer from eukaryotic hosts. Our results suggest that a fourth domain is not required to explain the available sequence data.

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Authors+Show Affiliations

Williams TA
Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, United Kingdom.
Embley TM
No affiliation info available
Heinz E
No affiliation info available

MeSH

Cell NucleusCytoplasmDNA VirusesGene Transfer, HorizontalPhylogeny

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

21698163

Citation

Williams, Tom A., et al. "Informational Gene Phylogenies Do Not Support a Fourth Domain of Life for Nucleocytoplasmic Large DNA Viruses." PloS One, vol. 6, no. 6, 2011, pp. e21080.
Williams TA, Embley TM, Heinz E. Informational gene phylogenies do not support a fourth domain of life for nucleocytoplasmic large DNA viruses. PLoS One. 2011;6(6):e21080.
Williams, T. A., Embley, T. M., & Heinz, E. (2011). Informational gene phylogenies do not support a fourth domain of life for nucleocytoplasmic large DNA viruses. PloS One, 6(6), e21080. https://doi.org/10.1371/journal.pone.0021080
Williams TA, Embley TM, Heinz E. Informational Gene Phylogenies Do Not Support a Fourth Domain of Life for Nucleocytoplasmic Large DNA Viruses. PLoS One. 2011;6(6):e21080. PubMed PMID: 21698163.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Informational gene phylogenies do not support a fourth domain of life for nucleocytoplasmic large DNA viruses. AU - Williams,Tom A, AU - Embley,T Martin, AU - Heinz,Eva, Y1 - 2011/06/16/ PY - 2011/04/12/received PY - 2011/05/18/accepted PY - 2011/6/24/entrez PY - 2011/6/24/pubmed PY - 2011/11/8/medline SP - e21080 EP - e21080 JF - PloS one JO - PLoS One VL - 6 IS - 6 N2 - Mimivirus is a nucleocytoplasmic large DNA virus (NCLDV) with a genome size (1.2 Mb) and coding capacity (1000 genes) comparable to that of some cellular organisms. Unlike other viruses, Mimivirus and its NCLDV relatives encode homologs of broadly conserved informational genes found in Bacteria, Archaea, and Eukaryotes, raising the possibility that they could be placed on the tree of life. A recent phylogenetic analysis of these genes showed the NCLDVs emerging as a monophyletic group branching between Eukaryotes and Archaea. These trees were interpreted as evidence for an independent "fourth domain" of life that may have contributed DNA processing genes to the ancestral eukaryote. However, the analysis of ancient evolutionary events is challenging, and tree reconstruction is susceptible to bias resulting from non-phylogenetic signals in the data. These include compositional heterogeneity and homoplasy, which can lead to the spurious grouping of compositionally-similar or fast-evolving sequences. Here, we show that these informational gene alignments contain both significant compositional heterogeneity and homoplasy, which were not adequately modelled in the original analysis. When we use more realistic evolutionary models that better fit the data, the resulting trees are unable to reject a simple null hypothesis in which these informational genes, like many other NCLDV genes, were acquired by horizontal transfer from eukaryotic hosts. Our results suggest that a fourth domain is not required to explain the available sequence data. SN - 1932-6203 UR - https://www.unboundmedicine.com/medline/citation/21698163/Informational_gene_phylogenies_do_not_support_a_fourth_domain_of_life_for_nucleocytoplasmic_large_DNA_viruses_ L2 - https://dx.plos.org/10.1371/journal.pone.0021080 DB - PRIME DP - Unbound Medicine ER -