ArticleFrontiers in microbiology2017
Phylogenetic Tracings of Proteome Size Support the Gradual Accretion of Protein Structural Domains and the Early Origin of Viruses from Primordial Cells.
Article in Frontiers in microbiology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
21 citing papers in PubMed, 38 citations in OpenAlex.
- Why did some viruses evolve to be giants while others did not?Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Tracing the birth and intrinsic disorder of loops and domains in protein evolution.Biophysical reviews · 2024Review
- On Protein Loops, Prior Molecular States and Common Ancestors of Life.Journal of molecular evolution · 2024Review
- Article
- Are Viruses Taxonomic Units? A Protein Domain and Loop-Centric Phylogenomic Assessment.Viruses · 2024Review
- Linguistic laws in biology.Trends in ecology & evolution · 2022Review
- The Compressed Vocabulary of Microbial Life.Frontiers in microbiology · 2021Article
- The origin and evolution of viruses inferred from fold family structure.Archives of virology · 2020Review
- Comparisons between small ribosomal RNA and theoretical minimal RNA ring secondary structures confirm phylogenetic and structural accretion histories.Scientific reports · 2020Article
- First arrived, first served: competition between codons for codon-amino acid stereochemical interactions determined early genetic code assignments.Die Naturwissenschaften · 2020Article
- Bacterial Origin and Reductive Evolution of the CPR Group.Genome biology and evolution · 2020Article
- More Pieces of Ancient than Recent Theoretical Minimal Proto-tRNA-Like RNA Rings in Genes Coding for tRNA Synthetases.Journal of molecular evolution · 2019Article
- Testing Empirical Support for Evolutionary Models that Root the Tree of Life.Journal of molecular evolution · 2019Article
- Article
- Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis.Evolutionary bioinformatics online · 2019Review
- Evolution of macromolecular structure: a 'double tale' of biological accretion and diversification.Science progress · 2018Review
- Multiple evolutionary origins of giant viruses.F1000Research · 2018Review
- Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes.Frontiers in microbiology · 2018Article
- Protein Sequences Recapitulate Genetic Code Evolution.Computational and structural biotechnology journal · 2018Article
- Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions.Evolutionary bioinformatics online · 2018Review
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Untangling the origin and evolution of viruses remains a challenging proposition. We recently studied the global distribution of protein domain structures in thousands of completely sequenced viral and cellular proteomes with comparative genomics, phylogenomics, and multidimensional scaling methods. A tree of life describing the evolution of proteomes revealed viruses emerging from the base of the tree as a fourth supergroup of life. A tree of domains indicated an early origin of modern viral lineages from ancient cells that co-existed with the cellular ancestors. However, it was recently argued that the rooting of our trees and the basal placement of viruses was artifactually induced by small genome (proteome) size. Here we show that these claims arise from misunderstanding and misinterpretations of cladistic methodology. Trees are reconstructed unrooted, and thus, their topologies cannot be distorted
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.