The DOI matches its Crossref record; 15 of the 15 references it cites were found in a registry or an index.
The Eukaryotic Tree of Life from a Global Phylogenomic Perspective
Open accessAbstract
Molecular phylogenetics has revolutionized our knowledge of the eukaryotic tree of life. With the advent of genomics, a new discipline of phylogenetics has emerged: phylogenomics. This method uses large alignments of tens to hundreds of genes to reconstruct evolutionary histories. This approach has led to the resolution of ancient and contentious relationships, notably between the building blocks of the tree (the supergroups), and allowed to place in the tree enigmatic yet important protist lineages for understanding eukaryote evolution. Here, I discuss the pros and cons of phylogenomics and review the eukaryotic supergroups in light of earlier work that laid the foundation for the current view of the tree, including the position of the root. I conclude by presenting a picture of eukaryote evolution, summarizing the most recent progress in assembling the global tree.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
The origins of genome complexity
Lynch, M., & Conery, J. S. (2003) · Science · doi:10.1126/science.1089370 · Cited by 1,698
Toward Automatic Reconstruction of a Highly Resolved Tree of Life
Ciccarelli, F. D., Doerks, T., von Mering, C., Creevey, C. J., Snel, B., & Bork, P. (2006) · Science · doi:10.1126/science.1123061 · Cited by 1,663
Resolving difficult phylogenetic questions: Why more sequences are not enough
Philippe, H., Brinkmann, H., Lavrov, D. V., Littlewood, D. T. J., Manuel, M., Wörheide, G., & Baurain, D. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1000602 · Cited by 1,129
Eukaryotic evolution, changes and challenges
Embley, T. M., & Martin, W. (2006) · Nature · doi:10.1038/nature04546 · Cited by 867
Phylogenomics: The beginning of incongruence?
JEFFROY, O., BRINKMANN, H., DELSUC, F., & PHILIPPE, H. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.02.003 · Cited by 698
Keeling, P. J., Burger, G., Durnford, D. G., Lang, B. F., Lee, R. W., Pearlman, R. E., Roger, A. J., & Gray, M. W. (2005) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2005.09.005 · Cited by 579
A photosynthetic alveolate closely related to apicomplexan parasites
Moore, R. B., Oborník, M., Janouškovec, J., Chrudimský, T., Vancová, M., Green, D. H., Wright, S. W., Davies, N. W., Bolch, C. J. S., Heimann, K., et al. (2008) · Nature · doi:10.1038/nature06635 · Cited by 476
Modeling compositional heterogeneity
Foster, P. G. (2004) · Systematic Biology · doi:10.1080/10635150490445779 · Cited by 474
The highly reduced genome of an enslaved algal nucleus
Douglas, S., Zauner, S., Fraunholz, M., Beaton, M., Penny, S., Deng, L.-T., Wu, X., Reith, M., Cavalier-Smith, T., & Maier, U.-G. (2001) · Nature · doi:10.1038/35074092 · Cited by 454
Cited by
The Origin and Diversification of Mitochondria
Roger, A. J., Muñoz-Gómez, S. A., & Kamikawa, R. (2017) · Current Biology · doi:10.1016/j.cub.2017.09.015 · Cited by 1,142
Earth BioGenome Project: Sequencing life for the future of life
Lewin, H. A., Robinson, G. E., Kress, W. J., Baker, W. J., Coddington, J., Crandall, K. A., Durbin, R., Edwards, S. V., Forest, F., Gilbert, M. T. P., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1720115115 · Cited by 962
Levy Karin, E., Mirdita, M., & Söding, J. (2020) · Microbiome · doi:10.1186/s40168-020-00808-x · Cited by 299
“…(black) expand major eukaryotic lineages, including deeply rooted supergroups (denoted with star) Thus, we expect the resources produced in this study and further analyses of eukaryotic metagenomic data using MetaEuk to produce a more comprehensive description of the tree of life [16, 52 – 54].”
BackgroundThe origin of Metazoa: a unicellular perspective
Sebé-Pedrós, A., Degnan, B. M., & Ruiz-Trillo, I. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.21 · Cited by 332
STRIDE: Species Tree Root Inference from Gene Duplication Events
Emms, D. M., & Kelly, S. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx259 · Cited by 311
Metadata
- Authors
- Burki, F.
- Venue
- Cold Spring Harbor Perspectives in Biology
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2014-05-01
- Volume
- 6
- Issue
- 5
- Pages
- a016147-a016147
- ISSN
- 1943-0264 (ISSN-L)
- OpenAlex
- W2170074068
- Cited by
- 366
- References
- 15
- Type
- posted content
- Language
- en
- Open access
- bronze
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: The Eukaryotic Tree of Life from a Global Phylogenomic Perspective. https://app.cochat.ai/papers/10.1101/cshperspect.a016147
- The paper
- Burki, F. (2014). The Eukaryotic Tree of Life from a Global Phylogenomic Perspective. Cold Spring Harbor Perspectives in Biology. https://doi.org/10.1101/cshperspect.a016147
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
