ArticleProtoplasma2005
Ancient gene duplications and the root(s) of the tree of life.
Article in Protoplasma, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 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
40 citing papers in PubMed, 75 citations in OpenAlex.
- Replicating lipid micelles: a feasible precursor to the origin of life and the earliest appearance of genomes.Human genomics · 2026Review
- Universal paralogs provide a window into evolution before the last universal common ancestor.Cell genomics · 2026Review
- Permeability selection of biologically relevant membranes matches the stereochemistry of life on Earth.PLoS biology · 2025Article
- The Last Universal Common Ancestor of Ribosome-Encoding Organisms: Portrait of LUCA.Journal of molecular evolution · 2024Review
- A New View of the Last Universal Common Ancestor.Journal of molecular evolution · 2024Article
- Evolution of Cellular Organization Along the First Branches of the Tree of Life.Journal of molecular evolution · 2024Article
- The nature of the last universal common ancestor and its impact on the early Earth system.Nature ecology & evolution · 2024Article
- Electron transport chains as a window into the earliest stages of evolution.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere.Genome biology and evolution · 2022Review
- Rooting Species Trees Using Gene Tree-Species Tree Reconciliation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- A distinct lineage of Caudovirales that encodes a deeply branching multi-subunit RNA polymerase.Nature communications · 2020Article
- Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria).Protoplasma · 2020Review
- Phylogenomics provides robust support for a two-domains tree of life.Nature ecology & evolution · 2020Article
- Investigating the Origins of Membrane Phospholipid Biosynthesis Genes Using Outgroup-Free Rooting.Genome biology and evolution · 2019Article
- Genome size evolution in the Archaea.Emerging topics in life sciences · 2018Article
- Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions.Evolutionary bioinformatics online · 2018Review
- Integrative modeling of gene and genome evolution roots the archaeal tree of life.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Quest for Ancestors of Eukaryal Cells Based on Phylogenetic Analyses of Aminoacyl-tRNA Synthetases.Journal of molecular evolution · 2017Article
- Rooting the tree of life: the phylogenetic jury is still out.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2015Review
- The neomuran revolution and phagotrophic origin of eukaryotes and cilia in the light of intracellular coevolution and a revised tree of life.Cold Spring Harbor perspectives in biology · 2014Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Tracing organismal histories on the timescale of the tree of life remains one of the challenging tasks in evolutionary biology. The hotly debated questions include the evolutionary relationship between the three domains of life (e.g., which of the three domains are sister domains, are the domains para-, poly-, or monophyletic) and the location of the root within the universal tree of life. For the latter, many different points of view have been considered but so far no consensus has been reached. The only widely accepted rationale to root the universal tree of life is to use anciently duplicated paralogous genes that are present in all three domains of life. To date only few anciently duplicated gene families useful for phylogenetic reconstruction have been identified. Here we present results from a systematic search for ancient gene duplications using twelve representative, completely sequenced, archaeal and bacterial genomes. Phylogenetic analyses of identified cases show that the majority of datasets support a root between Archaea and Bacteria; however, some datasets support alternative hypotheses, and all of them suffer from a lack of strong phylogenetic signal. The results are discussed with respect to the impact of horizontal gene transfer on the ability to reconstruct organismal evolution. The exchange of genetic information between divergent organisms gives rise to mosaic genomes, where different genes in a genome have different histories. Simulations show that even low rates of horizontal gene transfer dramatically complicate the reconstruction of organismal evolution, and that the different most recent common molecular ancestors likely existed at different times and in different lineages.
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Registered trials
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.