ArticleSystematic biology2012
Turning the crown upside down: gene tree parsimony roots the eukaryotic tree of life.
Article in Systematic biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
What it found
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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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
40 citing papers in PubMed, 96 citations in OpenAlex.
- Hypothesis that ancestral eukaryotes sexually proliferated without kinetochores or mitosis.Journal of cell science · 2025Article
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- Evolutionary trajectory of transcription factors and selection of targets for metabolic engineering.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- The persistent homology of mitochondrial ATP synthases.iScience · 2023Article
- The Ancestral Mitotic State: Closed Orthomitosis With Intranuclear Spindles in the Syncytial Last Eukaryotic Common Ancestor.Genome biology and evolution · 2023Article
- Phylogenomic Analyses of 2,786 Genes in 158 Lineages Support a Root of the Eukaryotic Tree of Life between Opisthokonts and All Other Lineages.Genome biology and evolution · 2022Article
- Realistic Gene Transfer to Gene Duplication Ratios Identify Different Roots in the Bacterial Phylogeny Using a Tree Reconciliation Method.Life (Basel, Switzerland) · 2022Article
- Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere.Genome biology and evolution · 2022Review
- Phylogenomics of the Epigenetic Toolkit Reveals Punctate Retention of Genes across Eukaryotes.Genome biology and evolution · 2020Article
- The origin of phagocytosis in Earth history.Interface focus · 2020Review
- From pairs of most similar sequences to phylogenetic best matches.Algorithms for molecular biology : AMB · 2020Article
- Article
- Measuring the impact of gene prediction on gene loss estimates in Eukaryotes by quantifying falsely inferred absences.PLoS computational biology · 2019Article
- Article
- Extensive molecular tinkering in the evolution of the membrane attachment mode of the Rheb GTPase.Scientific reports · 2018Article
- Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-Group.Genome biology and evolution · 2018Article
- The Isochores as a Fundamental Level of Genome Structure and Organization: A General Overview.Journal of molecular evolution · 2017Review
- Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction.PloS one · 2017Article
- The unconventional kinetoplastid kinetochore: from discovery toward functional understanding.Biochemical Society transactions · 2016Review
- A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction.Systematic biology · 2016Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
Abstract
The first analyses of gene sequence data indicated that the eukaryotic tree of life consisted of a long stem of microbial groups "topped" by a crown-containing plants, animals, and fungi and their microbial relatives. Although more recent multigene concatenated analyses have refined the relationships among the many branches of eukaryotes, the root of the eukaryotic tree of life has remained elusive. Inferring the root of extant eukaryotes is challenging because of the age of the group (∼1.7-2.1 billion years old), tremendous heterogeneity in rates of evolution among lineages, and lack of obvious outgroups for many genes. Here, we reconstruct a rooted phylogeny of extant eukaryotes based on minimizing the number of duplications and losses among a collection of gene trees. This approach does not require outgroup sequences or assumptions of orthology among sequences. We also explore the impact of taxon and gene sampling and assess support for alternative hypotheses for the root. Using 20 gene trees from 84 diverse eukaryotic lineages, this approach recovers robust eukaryotic clades and reveals evidence for a eukaryotic root that lies between the Opisthokonta (animals, fungi and their microbial relatives) and all remaining eukaryotes.
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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.