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Peer-reviewedCC BY-NC 4.0Molecular Biology and Evolution

Phylogenomics of Cypriniformes, the most diverse order of freshwater fishes: consensus, challenges and limitations

  • Hiranya Sudasinghe1,2
  • Ralf Britz3
  • Michael Matschiner4
  • Kevin Conway5
  • Heok Hui Tan6
  • Maurice Kottelat6,7
  • Rajeev Raghavan8
  • Neelesh Dahanukar9
  • Vasudevan Komalavally Anoop8,10
  • Joerg Bohlen11
  • Kerstin Howe12
  • Richard Michael Durbin13,12
3 more authors
  • Walter Salzburger14
  • Catherine L. Peichel1
  • Lukas Rüber15,2
15 affiliations
  1. 1Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern , Bern ,
  2. 2Natural History Museum of Bern , Bern ,
  3. 3Senckenberg Natural History Collections , Dresden ,
  4. 4Faculty of Biology, Ludwig Maximilian University of Munich , Planegg ,
  5. 5Department of Ecology and Conservation Biology and Biodiversity Research and Teaching Collections, Texas A&M University ,
  6. 6Lee Kong Chian Natural History Museum, National University of Singapore ,
  7. 7Rue des Rauraques 6 , 2800 Delémont ,
  8. 8Department of Fisheries Resource Management, Kerala University of Fisheries and Ocean Studies (KUFOS) , Kochi, Kerala ,
  9. 9Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence , Delhi NCR ,
  10. 10Faculty of Ocean Science and Technology, Kerala University of Fisheries and Ocean Studies (KUFOS) , Kochi, Kerala ,
  11. 11Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic , Liběchov ,
  12. 12Tree of Life, Wellcome Sanger Institute , Hinxton ,
  13. 13Department of Genetics, University of Cambridge , Cambridge ,
  14. 14Zoological Institute, Department of Environmental Sciences, University of Basel , Basel ,
  15. 15Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern , Bern ,
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Abstract

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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Cite

BibTeXRIS
BibTeX
@article{sudasinghe2026phylogenomics,
  title = {{Phylogenomics of Cypriniformes, the most diverse order of freshwater fishes: consensus, challenges and limitations}},
  author = {Hiranya Sudasinghe and Ralf Britz and Michael Matschiner and Kevin Conway and Heok Hui Tan and Maurice Kottelat and Rajeev Raghavan and Neelesh Dahanukar and Vasudevan Komalavally Anoop and Joerg Bohlen and Kerstin Howe and Richard Michael Durbin and Walter Salzburger and Catherine L. Peichel and Lukas Rüber},
  journal = {Molecular Biology and Evolution},
  year = {2026},
  month = oct,
  doi = {10.1093/molbev/msag261},
  url = {https://doi.org/10.1093/molbev/msag261},
  note = {CC BY-NC 4.0},
}
RIS
TY  - JOUR
TI  - Phylogenomics of Cypriniformes, the most diverse order of freshwater fishes: consensus, challenges and limitations
AU  - Hiranya Sudasinghe
AU  - Ralf Britz
AU  - Michael Matschiner
AU  - Kevin Conway
AU  - Heok Hui Tan
AU  - Maurice Kottelat
AU  - Rajeev Raghavan
AU  - Neelesh Dahanukar
AU  - Vasudevan Komalavally Anoop
AU  - Joerg Bohlen
AU  - Kerstin Howe
AU  - Richard Michael Durbin
AU  - Walter Salzburger
AU  - Catherine L. Peichel
AU  - Lukas Rüber
PY  - 2026
DA  - 2026/10/26
JO  - Molecular Biology and Evolution
DO  - 10.1093/molbev/msag261
UR  - https://doi.org/10.1093/molbev/msag261
AB  - 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.
SN  - 0737-4038
SN  - 1537-1719
ER  -