Genome structures resolve the early diversification of teleost fishes
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Abstract
Accurate species phylogenies are a prerequisite for all evolutionary research. Teleosts are the largest and most diversified group of extant vertebrates, but relationships among their three oldest extant lineages remain unresolved. On the basis of seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited the topology of the deepest branches of the teleost phylogeny using independent gene sequence and chromosomal rearrangement phylogenomic approaches. These analyses converged to a single scenario that unambiguously places the Elopomorpha and Osteoglossomorpha (arapaima, elephantnose fish) in a monophyletic sister group to all other teleosts, i.e., the Clupeocephala lineage (zebrafish, medaka). This finding resolves more than 50 years of controversy on the evolutionary relationships of these lineages and highlights the power of combining different levels of genome-wide information to solve complex phylogenies.
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Locus entanglement, and more broadly genomic topology, can be viewed as a multi-scale unification of existing techniques that infer phylogenies from single genomic scales.
“In this sense, locus entanglement, and more broadly genomic topology, can be viewed as a multi-scale unification of existing techniques that infer phylogenies from single genomic scales, like locus adjacencies (202), microsyntenic clusters (203), macrosyntenic similarity (202), or irreversible FWM events (97).”
From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [202]
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Zebrafish relatives as models for functional comparative genetics and genomics
Podobnik, M., Lu, Y., Irion, U., & Currie, P. D. (2026) · Nature Reviews Genetics · doi:10.1038/s41576-026-01007-4 · Cited by 1 · see citing works
Topological Approaches in Animal Comparative Genomics
Schultz, D. T., & Simakov, O. (2026) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-030424-084541 · Cited by 1 · see citing works
- Authors
- Parey, E., Louis, A., Montfort, J., Bouchez, O., Roques, C., Iampietro, C., Lluch, J., Castinel, A., Donnadieu, C., Desvignes, T., Floi Bucao, C., Jouanno, E., Wen, M., Mejri, S., Dirks, R., Jansen, H., Henkel, C., Chen, W.-J., Zahm, M., Cabau, C., Klopp, C., Thompson, A. W., Robinson-Rechavi, M., Braasch, I., Lecointre, G., Bobe, J., Postlethwait, J. H., Berthelot, C., Roest Crollius, H., & Guiguen, Y.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- INRAE, LPGP, Rennes, France.
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- GeT-PlaGe, INRAE, Genotoul, Castanet-Tolosan, France.
- University of Oregon (US)
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
- Hunan Normal University (CN)
- Florida Atlantic University (US)
- Future Genomics Technologies, Leiden, Netherlands.
- Leiden University (NL)
- National Taiwan University (TW)
- École Nationale Vétérinaire de Toulouse (FR)
- Michigan State University (US)
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.
- Corresponding author
- Berthelot, Camille
- Guiguen, Yann
- ORCID
- Parey, Elise
- Louis, Alexandra
- Montfort, Jerome
- Bouchez, Olivier
- Roques, Céline
- Iampietro, Carole
- Castinel, Adrien
- Donnadieu, Cécile
- Desvignes, Thomas
- Floi Bucao, Christabel
- Jouanno, Elodie
- Wen, Ming
- Mejri, Sahar
- Dirks, Ron
- Jansen, Hans
- Henkel, Christiaan
- Chen, Wei-Jen
- Zahm, Margot
- Cabau, Cédric
- Klopp, Christophe
- Thompson, Andrew W.
- Robinson-Rechavi, Marc
- Braasch, Ingo
- Lecointre, Guillaume
- Bobe, Julien
- Postlethwait, John H.
- Berthelot, Camille
- Roest Crollius, Hugues
- Guiguen, Yann
- Venue
- Science
- Published
- 2023-02-10
- Volume
- 379
- Issue
- 6632
- Pages
- 572-575
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W4319825862
- Cited by
- 87
- References
- 3
- Citations by year
- 2026: 24 · 2025: 20 · 2024: 30 · 2023: 10 · 2022: 3
- FWCI
- 7.42
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nc
- Locations
- Science (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- PubMed (publishedVersion)
- HAL (submittedVersion, cc-by-nc)
- IRIS (submittedVersion, cc-by-nc)
- SERVAL (Université de Lausanne) (submittedVersion, cc-by-nc)
- Funders
- National Science Foundation
- European Commission (817923, 2016-2021, HORIZON2020)
- Agence Nationale de la Recherche (ANR-16-CE12-0035, ANR-16-CE12-003, 2016-2021, ANR-10-INBS-0009, ANR- 10-INBS-09, ANR-16-CE12-0003, ANR-16, ANR-10, ANR-16-CE12, 10-INBS-09)
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (173048)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Aquatic Science › Fish Biology and Ecology Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- teleost phylogeny, Elopomorpha, Osteoglossomorpha, genome structure, chromosomal rearrangements, deep divergence, tarpon, eel, arapaima, fish evolution
- MeSH terms
- Animals, Eels, Biological Evolution, Fishes, Phylogeny, Zebrafish, Genome
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