{
  "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.",
  "abstract_shown": true,
  "affiliations": [
    "Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern , Bern ,",
    "Natural History Museum of Bern , Bern ,",
    "Senckenberg Natural History Collections , Dresden ,",
    "Faculty of Biology, Ludwig Maximilian University of Munich , Planegg ,",
    "Department of Ecology and Conservation Biology and Biodiversity Research and Teaching Collections, Texas A&M University ,",
    "Lee Kong Chian Natural History Museum, National University of Singapore ,",
    "Rue des Rauraques 6 , 2800 Delémont ,",
    "Department of Fisheries Resource Management, Kerala University of Fisheries and Ocean Studies (KUFOS) , Kochi, Kerala ,",
    "Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence , Delhi NCR ,",
    "Faculty of Ocean Science and Technology, Kerala University of Fisheries and Ocean Studies (KUFOS) , Kochi, Kerala ,",
    "Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic , Liběchov ,",
    "Tree of Life, Wellcome Sanger Institute , Hinxton ,",
    "Department of Genetics, University of Cambridge , Cambridge ,",
    "Zoological Institute, Department of Environmental Sciences, University of Basel , Basel ,",
    "Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern , Bern ,"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 15,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Hiranya Sudasinghe",
      "orcid": "0000-0003-0994-3462"
    },
    {
      "affs": [
        2
      ],
      "name": "Ralf Britz",
      "orcid": "0000-0002-0126-4660"
    },
    {
      "affs": [
        3
      ],
      "name": "Michael Matschiner",
      "orcid": "0000-0003-4741-3884"
    },
    {
      "affs": [
        4
      ],
      "name": "Kevin Conway",
      "orcid": "0000-0002-0161-8385"
    },
    {
      "affs": [
        5
      ],
      "name": "Heok Hui Tan",
      "orcid": "0000-0003-2227-8866"
    },
    {
      "affs": [
        5,
        6
      ],
      "name": "Maurice Kottelat",
      "orcid": "0000-0003-3638-2824"
    },
    {
      "affs": [
        7
      ],
      "name": "Rajeev Raghavan",
      "orcid": "0000-0002-0610-261X"
    },
    {
      "affs": [
        8
      ],
      "name": "Neelesh Dahanukar",
      "orcid": "0000-0001-7162-9023"
    },
    {
      "affs": [
        7,
        9
      ],
      "name": "Vasudevan Komalavally Anoop",
      "orcid": "0000-0003-4500-4972"
    },
    {
      "affs": [
        10
      ],
      "name": "Joerg Bohlen",
      "orcid": "0000-0002-7068-2321"
    },
    {
      "affs": [
        11
      ],
      "name": "Kerstin Howe",
      "orcid": "0000-0003-2237-513X"
    },
    {
      "affs": [
        12,
        11
      ],
      "name": "Richard Michael Durbin",
      "orcid": "0000-0002-9130-1006"
    },
    {
      "affs": [
        13
      ],
      "name": "Walter Salzburger",
      "orcid": "0000-0002-9988-1674"
    },
    {
      "affs": [
        0
      ],
      "name": "Catherine L. Peichel",
      "orcid": "0000-0002-7731-8944"
    },
    {
      "affs": [
        14,
        1
      ],
      "name": "Lukas Rüber",
      "orcid": "0000-0003-0125-008X"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/6ahd4x4rrj2jb.bib",
  "cited_by": 8,
  "doi": "10.1093/molbev/msag261",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13729133/",
  "id": "6ahd4x4rrj2jb",
  "issns": [
    "0737-4038",
    "1537-1719"
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  "landing_url": "https://doi.org/10.1093/molbev/msag261",
  "language": "en",
  "licence": "CC-BY-NC-4.0",
  "licence_label": "CC BY-NC 4.0",
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  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
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  "native_subjects": [
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      "heading",
      "AcademicSubjects/SCI01130"
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    [
      "heading",
      "AcademicSubjects/SCI01180"
    ],
    [
      "heading",
      "Discoveries"
    ],
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      "openalex",
      "1104|Fish Biology and Ecology Studies"
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  "pdf_url": "https://academic.oup.com/mbe/advance-article-pdf/doi/10.1093/molbev/msag261/72519525/msag261.pdf",
  "pmcid": "PMC13729133",
  "pmid": "42929157",
  "published": "2026-10-26",
  "publisher": "Oxford University Press",
  "ris": "https://research.draconitic.com/paper/6ahd4x4rrj2jb.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T13:26:50Z",
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      "url": "https://doi.org/10.1093/molbev/msag261"
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  "subjects": [
    {
      "field": "biology",
      "origin": "openalex:1104|Fish Biology and Ecology Studies",
      "subfield": "ecology"
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  ],
  "title": "Phylogenomics of Cypriniformes, the most diverse order of freshwater fishes: consensus, challenges and limitations",
  "title_text": "Phylogenomics of Cypriniformes, the most diverse order of freshwater fishes: consensus, challenges and limitations",
  "type": "peer-reviewed",
  "updated_at": "2026-11-08T13:20:44Z",
  "url": "https://research.draconitic.com/paper/6ahd4x4rrj2jb",
  "venue": "Molecular Biology and Evolution",
  "versions": []
}