Phylogenomics of Cypriniformes, the most diverse order of freshwater fishes: consensus, challenges and limitations
Open accessAbstract
Cypriniformes, the most species-rich order of freshwater fishes (∼5,000 species), represents a key lineage for understanding vertebrate diversification in freshwater ecosystems. This clade includes several highly miniaturized and understudied lineages whose phylogenetic placements have long remained contentious. Here, we present the first phylogenomic analysis of Cypriniformes with complete family-level representation and broad genus-level coverage, encompassing 316 species comprising approximately 30% of all described genera. Our dataset integrates 257 newly assembled genomes with publicly available resources and analyzes multiple sets of genome-wide markers using both concatenation-based and coalescent-aware approaches. The general concordance among analytical frameworks indicates that the backbone topology of Cypriniformes is now established, allowing clear identification of well-supported clades and regions of persistent conflict. Our results strengthen the evolutionary relationships of several miniaturized lineages, while identifying recalcitrant relationships shaped by both biological processes and model artefacts that can yield superficially similar patterns of phylogenetic conflict. Our study substantially expands genomic representation and establishes a phylogenomic foundation for future comparative, developmental, and evolutionary research in this freshwater radiation.
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The ASTRAL-IV topology was chosen because it showed high overall congruence across alternative phylogenomic inference methods in the original study.
“We chose this topology because it showed high overall congruence across alternative phylogenomic inference methods in the original study.”
From Convergent genome streamlining accompanies independent miniaturization in the world’s smallest fishes (2026) · cites this paper as [19]
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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
Sudasinghe, H., Matschiner, M., Britz, R., Conway, K. W., Tan, H. H., Salzburger, W., Peichel, C. L., & Rüber, L. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2614605123
Self-citation
- Authors
- Sudasinghe, H., Britz, R., Matschiner, M., Conway, K. W., Tan, H. H., Kottelat, M., Raghavan, R., Dahanukar, N., Anoop, V. K., Bohlen, J., Howe, K., Durbin, R., Salzburger, W., Peichel, C. L., & Rüber, L.
- Affiliations
- University of Bern (CH)
- Senckenberg Natural History Collections Dresden (DE)
- Ludwig-Maximilians-Universität München (DE)
- Texas A&M University (US)
- National University of Singapore (SG)
- Kerala University of Fisheries and Ocean Studies (IN)
- Shiv Nadar University (IN)
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic , Liběchov ,
- Wellcome Sanger Institute (GB)
- University of Cambridge (GB)
- University of Basel (CH)
- Corresponding author
- Rüber, Lukas
- ORCID
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2026-10-26
- Volume
- 43
- Issue
- 11
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W7124261294
- Cited by
- 8
- References
- 0
- Citations by year
- 2026: 8
- FWCI
- 48.16
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Molecular Biology and Evolution (publishedVersion, cc-by-nc)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Open Access CRIS of the University of Bern
- Funders
- Swiss National Science Foundation (310030_185120)
- University of Bern
- Basler Stiftung für Biologische Forschung
- TAMU Agrilife Research
- TAMU Aquarium Research Laboratory
- Topics
- Life Sciences › Agricultural and Biological Sciences › Aquatic Science › Fish Biology and Ecology Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Keywords
- Cypriniformes, freshwater fish, phylogenomics, genome-wide markers, phylogenetic conflict, vertebrate diversification, genome assembly
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