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Cypriniformes, the most species-rich order of freshwater fishes (∼5,000 species), represents a key lineage for understanding vertebrate diversification in freshwater ecosystems. 🔓 academic.oup.com/mbe/advance… Here, researchers present the first phylogenomic analysis of Cypriniformes with complete family-level representation, encompassing 316 species (comprising ∼30% of all described genera). "Our results strengthen the evolutionary relationships of several miniaturized lineages, while identifying recalcitrant relationships shaped by both biological processes and model artifacts 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." Lead author Hiranya Sudasinghe has made available an A0 poster, print-size image file, 'The Cypriniformes Tree of Life' - facebook.com/HiranyaSud/post… 𝗥𝗲𝘀𝗲𝗮𝗿𝗰𝗵 𝗧𝗶𝘁𝗹𝗲 Phylogenomics of Cypriniformes, the most diverse order of freshwater fishes: consensus, challenges, and limitations 𝗖𝗶𝘁𝗮𝘁𝗶𝗼𝗻 Hiranya Sudasinghe, Ralf Britz, Michael Matschiner, Kevin W Conway, Heok Hui Tan, Maurice Kottelat, Rajeev Raghavan, Neelesh Dahanukar, Vasudevan Komalavally Anoop, Jörg Bohlen, Kerstin Howe, Richard Durbin, Walter Salzburger, Catherine L Peichel, Lukas Rüber, Phylogenomics of Cypriniformes, the most diverse order of freshwater fishes: consensus, challenges, and limitations, Molecular Biology and Evolution, Volume 43, Issue 11, November 2026, msag261, doi.org/10.1093/molbev/msag2… 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 ∼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 artifacts 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. 𝗣𝗵𝗼𝘁𝗼 𝗖𝗿𝗲𝗱𝗶𝘁 a) ASTRAL-IV species tree showing the hypothesis of phylogenomic relationships of Cypriniformes inferred from 335 species and 1,167 loci (total alignment length: 541,983 bp), based on combined first and second codon positions of BUSCO.NT.C12 and UCE nucleotide dataset. The numbers indicate the different Cypriniformes families. The major conflicting zones of phylogenetic relationships are highlighted in gray (see Fig. 2; Figures S11 and S12). Simplified family-level topologies are shown for (b) the ASTRAL-IV species tree and (c) the IQ-TREE2 concatenated phylogeny for the same dataset. Fish illustrations by Nadeela Hirimuthugoda. © 2026 the Author(s). Published in the journal Molecular Biology and Evolution. An open access article, distributed under the terms of the Creative Commons Attribution 4.0 International (CC-BY-4.0) licence. creativecommons.org/licenses… #Phylogenomics #Cypriniformes #Ichthyology #Taxonomy #Biodiversity #AquariumHobby #Fishkeeping #Aquarist #TropicalFish #FishTank