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Cited by 3Chromosomal and Genetic VariationsGenomics and Phylogenetic StudiesFish Biology and Ecology Studies

The DOI matches its Crossref record; 55 of the 57 references it cites were found in a registry or an index, and 2 are not checked yet; 16 of the 57 sources its claims cite were checked for support.

A genomic compendium of hundreds of teleost fishes reveals their evolutionary landscape

Open access
Song, Yue, Yuan, Zengbao, Fang, Chengchi, Zhang, Suyu, Yang, Liandong, Hu, Mingliang, Seim, Inge, Liu, Shanshan, Tian, Xiaolin, Wang, Cheng, Zhang, Yaolei, Pan, Zhaohui, Qu, Qingming, Liu, Hongyue, Li, Yuanning, Pan, Luyuan, Zhu, Chenglong, Yang, Hengjia, Chen, Xiao, Zhang, Mengqi, Hou, Gang, Liu, Meiru, Wang, Jiahao, Liu, Qun, Gan, Xiaoni, Zeng, Honghui, Xu, Wenjie, Feng, Chenguang, Wang, Mengjun, Zhou, Zhuocheng, He, Song, Liu, Chenglong, Yu, Mengjun, Li, Hanbo, Liang, Jian, Zhang, He, Li, Yongxin, Ming-Yuen Lee, Simon, Sun, Yonghua, Qiu, Qiang, Liu, Xin, Kristiansen, Karsten, Wang, Wen, Wang, Jian, Zhu, Min, Yang, Huanming, Chen, Songlin, Gui, Jianfang, Chen, Yiyu, Zhang, Guojie, Xu, Xun, Wang, Kun, Fan, Guangyi, He, Shunping·2026·The Innovation
DOI 10.1016/j.xinn.2025.101177PMC PMC12957567
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Abstract

The remarkable morphological diversity and species abundance of teleost fishes offer a valuable resource for understanding vertebrate evolution. In phase I of the Fish10K project, genomes of 110 teleost species were sequenced and assembled, filling gaps in 3 previously unrepresented orders, and integrated with existing data to generate a 464 species whole-genome alignment spanning all teleost orders-the largest such resource beyond mammals and birds. Comparative analyses reveal distinctive genomic features, including progressive genome compaction with shortened intron lengths relative to non-teleost ray-finned fishes. Analysis of the transposable element (TE) landscape suggests a potential association between TE expansion in teleost genomes and different habitats, as well as the uniqueness of teleosts' DNA-dominated transposon composition among vertebrates. Genome-wide phylogenetic analyses refute the widely accepted monophyly of "Siluriphysi" hypothesis and support the hypothesis of a single origin of electroreception followed by secondary loss in Characiformes. A refined evolutionary timeline of teleosts by whole-genome alignment resource placed teleosts at ∼253 million years ago, predating the Permian-Triassic extinction, and delineates three diversification phases punctuated by mass extinctions, challenging continuous post-Cretaceous-Palaeogene acceleration models. This study establishes a large-scale genomic database and a foundational whole-genome alignment resource, advancing insights into the landscape of teleost genomic architecture and macroevolution.

Verified 2026-11-10 · 2 references not checked yet

Overview

AI snapshot

Written from the paper’s full text.

TL;DR

Phase I of Fish10K reports 110 newly sequenced teleost genomes integrated into a 464-species whole-genome alignment spanning all teleost orders, enabling comparative and phylogenomic analyses. The compendium reveals genome compaction, a DNA-transposon-dominated TE landscape, conserved/accelerated elements, a challenge to Siluriphysi monophyly, and a teleost origin at ∼253 Ma with three diversification phases.

Key findings

  • The resource includes 110 newly assembled genomes (average scaffold N50 4.22 Mb; contig N50 288 kb; median BUSCO 95.17% in results; methods report average BUSCO 86.38%) and a 464-species alignment spanning all teleost orders, filling gaps for 3 previously unsequenced orders.
  • Teleost genomes show progressive compaction with shortened introns relative to non-teleost ray-finned fishes, while exon length remains conserved; TE content is DNA-transposon-dominated, unlike the LINE-dominant pattern in other vertebrates, and freshwater fish have significantly higher overall transposon content than marine fish (Cypriniformes 21.84%; Notacanthiformes 11.64% within Eloposteoglossocephala).
  • Single-base constraint screening found >30 Mb of constrained sites (∼2% of the zebrafish genome), lower than mammals and birds; 24,462 CCEs and 787 CAEs; 28,878 THCEs and 1,689 TSHCEs, with 60% of TSHCEs exonic; an rfx4 upstream TSHCE increased reporter activity by approximately 4.2-fold (p < 0.05).
  • Whole-genome phylogenomics refutes Siluriphysi monophyly, placing Gymnotiformes as sister to a Characiformes-Siluriformes clade (BS = 100%, LPP = 1.0); teleosts originated ∼253 Ma, before the Permian-Triassic extinction (251.9 Ma), with three diversification phases and stable net diversification from 60–23 Ma.

Methods

  • Phase I Fish10K collected 464 teleost genomes across 44 taxa; 110 were newly sequenced using stLFR and long-read technologies, assembled with Supernova 2.14, and integrated with 354 publicly available genomes.
  • A reference-free whole-genome alignment of 467 species (including coelacanth, bichir, and spotted gar outgroups) was built with Cactus v.2.1.1; the guide tree used BUSCO gene trees with RAxML and ASTRAL-III, and HAL was converted to MAF.
  • Analyses included neutral-model/PhyloP constraint and acceleration scoring, IQ-TREE concatenation and ASTRAL-III coalescent phylogenies, MCMCtree divergence dating with 19 fossil calibrations, and fossil diversity curves from 13,194 Actinopterygii records (9,841 Teleostei) from DeepBone.

Limitations

  • The paper states that the TE–habitat/adaptation association is a potential link requiring further comparative and phylogenetic analyses to validate, and it notes the need for denser taxon sampling to resolve the deepest branches.
  • Evident from the text: newly assembled genome completeness is reported inconsistently (methods average BUSCO 86.38% vs results median 95.17%), and fossil-based diversity analyses depend on database records after removal of ambiguous names and pre-Silurian records.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1016/j.xinn.2025.101177

Cites

55 of 57 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Verification

Claims the paper makes

16 of 57 cited sources checked · 7 supported · 0 flagged · accuracy not yet measured

  • Premisecitation

    Novel morphological features such as refined fin structures and the gas bladder played a pivotal role in seizing new ecological niches and displaying phenotypic diversity.

    “These novel morphological features, such as the refined fin structures enhancing swimming abilities and the evolution of the gas bladder, have played a pivotal role in seizing new ecological niches and displaying phenotypic diversity.23,31,32,33,34,35”
    Quote in the paperNot a substantial claim2 of 3 sources checked
    • cites [23] Wang, 2021, African lungfish genome sheds light on the vertebrate water-to-land transition, Cell source
    • cites [31] Bi, 2021, Tracing the genetic footprints of vertebrate landing in non-teleost ray-finned fishes, Cell source

      The Introduction describes adaptive changes to locomotion and respiration during vertebrate evolution and notes developed pectoral fins; the Results support the evolution of the swim bladder from the lung. But the paper does not establish that refined fins enhanced swimming or that these features played a pivotal role in occupying new ecological niches and producing phenotypic diversity. (LLM, conf=0.84)

      Experimental — accuracy not yet measured
    • cites [32] Erwin, 2015, Novelty and Innovation in the History of Life, Curr. Biol. source

      The Introduction links ecological opportunities with diversification into different niches and says morphological diversity can accompany adaptive radiation. It does not identify refined fin structures or the gas bladder as drivers of niche expansion, improved swimming, or phenotypic diversity. It also cautions that morphological novelties do not necessarily lead to diversification. (LLM, conf=0.85)

      Experimental — accuracy not yet measured
  • Findingown data

    ChIP-seq data show overlap between different peaks and TSHCE in brain and muscle data from the DANIO-CODE project.

    “ChIP-seq data showing overlap between different peaks and TSHCE, with data from the DANIO-CODE42 project of brain and muscle data.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [42] Baranasic, 2022, Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements, Nat. Genet. source
  • Premisecitation

    Although molecular phylogenetic studies have demonstrated frequent discordance between molecular data and morphological expectations, the monophyly of Siluriphysi has generally been maintained in traditional interpretations from early single-locus analyses to recent multiple genomic-scale loci, primarily to conform to morphological predictions.

    “Although numerous molecular phylogenetic studies have demonstrated frequent discordance between molecular data and morphological expectations, the monophyly of Siluriphysi has generally been maintained in traditional interpretations, from early single-locus analyses48 to recent multiple genomic-scale loci,49,50,51,52,53,54,55,56 primarily to conform to morphological predictions.”
    Quote in the paperSubstantial claim1 of 9 sources checked
    • cites [48] Orti, 1996, Molecular evolution of ependymin and the phylogenetic resolution of early divergences among euteleost fishes, Mol. Biol. Evol. source

      Checked before — its earlier verdict is held back until a new check runs.

    • cites [49] Arcila, 2017, Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life, Nat. Ecol. Evol. source
    • cites [50] Betancur-R, 2017, Phylogenetic classification of bony fishes, BMC Evol. Biol. source

      Checked before — its earlier verdict is held back until a new check runs.

    • cites [51] Chakrabarty, 2017, Phylogenomic Systematics of Ostariophysan Fishes: Ultraconserved Elements Support the Surprising Non-Monophyly of Characiformes, Syst. Biol. source
    • cites [52] Dai, 2018, Phylogenomic Perspective on the Relationships and Evolutionary History of the Major Otocephalan Lineages, Sci. Rep. source

      Checked before — its earlier verdict is held back until a new check runs.

    • cites [53] Nakatani, 2011, Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation, BMC Evol. Biol. source

      Checked before — its earlier verdict is held back until a new check runs.

    • cites [54] Hughes, 2018, Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data, Proc. Natl. Acad. Sci. USA source

      Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

      Experimental — accuracy not yet measured
    • cites [55] Near, 2012, Resolution of ray-finned fish phylogeny and timing of diversification, Proc. Natl. Acad. Sci. USA source

      Checked before — its earlier verdict is held back until a new check runs.

    • cites [56] Melo, 2021, Accelerated diversification explains the exceptional species richness of tropical characoid fishes, Syst. Biol. source

      Checked before — its earlier verdict is held back until a new check runs.

  • Premisecitation

    Some molecular phylogenetic studies failed to support Siluriphysi monophyly.

    “Nonetheless, some molecular phylogenetic studies (e.g., Figures S2, S4, and S5 in Hughes et al.’s study, and in Near et al.’s and Melo et al.’s studies)54,55,56 failed to support Siluriphysi monophyly.”
    Quote in the paperSubstantial claim1 of 3 sources checked
    • cites [54] Hughes, 2018, Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data, Proc. Natl. Acad. Sci. USA source

      The Tests of Alternative Hypotheses section reports conflicting phylogenetic signal among otophysan orders and says earlier molecular studies had not resolved the canonical morphological hypothesis. The Fig. 2 caption also reports discordance between nucleotide results (SI Appendix, Figs. S2 and S5) and results supporting monophyletic Characiformes. Our copy does not state whether Figs. S2, S4, or S5 fail to support Siluriphysi monophyly specifically. (LLM, conf=0.74)

      Experimental — accuracy not yet measured
    • cites [55] Near, 2012, Resolution of ray-finned fish phylogeny and timing of diversification, Proc. Natl. Acad. Sci. USA source

      Checked before — its earlier verdict is held back until a new check runs.

    • cites [56] Melo, 2021, Accelerated diversification explains the exceptional species richness of tropical characoid fishes, Syst. Biol. source

      Checked before — its earlier verdict is held back until a new check runs.

  • Premisecitation

    The evolutionary history of teleosts, characterized by rapid radiation events and long-time divergences, requires phylogenomic approaches to overcome the resolution limitations inherent to traditional molecular markers.

    “The evolutionary history of teleosts, characterized by rapid radiation events and long-time divergences, requires phylogenomic approaches to overcome the resolution limitations inherent to traditional molecular markers.8”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [8] Feng, 2020, Dense sampling of bird diversity increases power of comparative genomics, Nature source

      The Main section and the supplied Abstract discuss dense genome sampling and phylogenetic inference in birds, not teleost evolutionary history. Searches for teleost radiation, long divergences, and the resolution limits of traditional molecular markers found no passage addressing those claims. (LLM, conf=0.76)

      Experimental — accuracy not yet measured
  • Probably not a substantial claim. 25
  • It may state two separate claims as one. 34

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisecitation

    Genome-wide alignments have proved effective for identifying conserved genomic regions in birds, mammals, and primates.

    “Genome-wide alignments have proved effective for identifying conserved genomic regions in birds,8 mammals,9 and primates,28”
    Quote in the paperNot a substantial claim1 of 3 sources checked
    • cites [8] Feng, 2020, Dense sampling of bird diversity increases power of comparative genomics, Nature source
    • cites [9] Christmas, 2023, Evolutionary constraint and innovation across hundreds of placental mammals, Science source

      Checked before — its earlier verdict is held back until a new check runs.

    • cites [28] Kuderna, 2024, Identification of constrained sequence elements across 239 primate genomes, Nature source

      Checked before — its earlier verdict is held back until a new check runs.

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Premisecitation

    Comparative studies of multiple genomes indicate that the transition from aquatic to terrestrial environments was accompanied by an expansion of the LINE-CR1 superfamily and a higher proportion of DNA transposons in freshwater fish compared with marine fish.

    “Comparative studies of multiple genomes further indicate that the transition from aquatic to terrestrial environments was accompanied by an expansion of the LINE-CR1 superfamily and a higher proportion of DNA transposons in freshwater fish compared with marine fish.23,24”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites [23] Wang, 2021, African lungfish genome sheds light on the vertebrate water-to-land transition, Cell source
    • cites [24] Keane, 2015, Insights into the evolution of longevity from the bowhead whale genome, Cell Rep. source

      The Results section, “Analysis of the Draft Bowhead Whale Genome” (page unavailable), compares transposable elements in cetaceans and a cow, reporting LINE-1 abundance rather than LINE-CR1 expansion. Searches for LINE-CR1 and for DNA transposons in freshwater versus marine fish found no passage addressing either claim. (LLM, conf=0.76)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim. It may state two separate claims as one.

    Premisecitation

    The monophyly hypothesis of Siluriphysi (comprising Gymnotiformes and Siluriformes) was originally proposed based on morphological characteristics including the electroreception system and has long been widely accepted.

    “Within the Otocephala clade, the monophyly hypothesis of Siluriphysi (comprising Gymnotiformes and Siluriformes), originally proposed based on morphological characteristics including the electroreception system,45,46,47 has long been widely accepted.”
    Quote in the paperSubstantial claim1 of 3 sources checked
    • cites [45] Albert, 2001

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

    • cites [46] Fink, 1981, Interrelationships of the ostariophysan fishes (Teleostei), Zool. J. Linn. Soc. source
    • cites [47] Liu, 2016, The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts, Nat. Commun. source

      The Abstract identifies Siluriformes as catfish, but does not discuss Siluriphysi or its proposed monophyly. Searches for Gymnotiformes, electroreception, and morphological evidence found no passage addressing the hypothesis’s origin or how widely it was accepted. (LLM, conf=0.76)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisecitation

    Studies in mammals and birds have shown that highly conserved elements are enriched for transcriptional regulation and organ development pathways.

    “studies in both mammals and birds have shown that highly conserved elements are enriched for transcriptional regulation and organ development pathways.9,29”
    Quote in the paperNot a substantial claim2 of 2 sources checked
    • cites [9] Christmas, 2023, Evolutionary constraint and innovation across hundreds of placental mammals, Science source
    • cites [29] Seki, 2017, Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features, Nat. Commun. source

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisecitation

    The emergence of lineage-specific elements has been proposed as a key driver of morphological diversification during vertebrate evolution.

    “The emergence of lineage-specific elements has been proposed as a key driver of morphological diversification during vertebrate evolution.29,36,37,38”
    Quote in the paperNot a substantial claim3 of 3 sources checked
    • cites [29] Seki, 2017, Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features, Nat. Commun. source
    • cites [36] Glasauer, 2014, Whole-genome duplication in teleost fishes and its evolutionary consequences, Mol. Genet. Genomics. source

      The section on coding and noncoding regions in duplicate-gene evolution describes how changes to duplicated regulatory elements can enable evolutionary innovation. It does not identify the emergence of lineage-specific elements as a key driver of morphological diversification across vertebrates; its discussion is narrower and framed around genome duplication. (LLM, conf=0.78)

      Experimental — accuracy not yet measured
    • cites [37] Dornburg, 2021, Holosteans contextualize the role of the teleost genome duplication in promoting the rise of evolutionary novelties in the ray-finned fish innate immune system, Immunogenetics source

      The Results and Discussion discuss lineage-specific expansions of innate immune receptor genes, while the Summary discusses their possible role in responding to pathogens. Neither passage connects the emergence of lineage-specific elements to morphological diversification in vertebrates. Searches for morphological diversification and lineage-specific novelty found no such connection in our copy. (LLM, conf=0.76)

      Experimental — accuracy not yet measured

  • It may state two separate claims as one.

    Findingown data

    Microsynteny analyses among Otophysi species, based on 14,294 orthologous genes, revealed that 37.12% of gene trees supported monophyly of "Siluriphysi" while approximately 60% contradicted this hypothesis.

    “microsynteny analyses among Otophysi species, based on 14,294 orthologous genes located in conserved microsynteny blocks (zebrafish as the reference; Table S14) revealed that, while 37.12% of gene trees supported monophyly of “Siluriphysi,” approximately 60% contradicted this hypothesis (Figure S6).”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    The whole-genome alignment spans approximately 300 million years and all 44 orders.

    “spanning ∼300 My and all 44 orders”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    The study collected mitochondrial genome data from 506 teleost species, covering all currently recognized orders, and reconstructed a robust mitochondrial phylogeny using 12 mitochondrial protein-coding genes.

    “We also collected mitochondrial genome data from 506 teleost species, covering all currently recognized orders. Using 12 mitochondrial protein-coding genes, we reconstructed a robust mitochondrial phylogeny.”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Findingown data

    LINE transposons dominate in cartilaginous fish, amphibians, reptiles, and mammals, with a LINE/DNA transposon ratio distinct from teleosts.

    “LINE transposons dominate in cartilaginous fish, amphibians, reptiles, and mammals, exhibiting a LINE/DNA transposon ratio distinct from that observed in teleosts”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    The study establishes a large-scale genomic database and a foundational whole-genome alignment resource.

    “This study establishes a large-scale genomic database and a foundational whole-genome alignment resource”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    89% of internodes exhibited concordance, but persistent conflicts remained within certain lineages (e.g., Otophysi).

    “While 89% of internodes exhibited concordance, persistent conflicts remained within certain lineages (e.g., Otophysi; Figures 6A, 6B, and S5A–S5D; Table S12).”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    Using whole-genome alignments from 464 species (3.18 Mb of orthologous sequences partitioned into 3,185 1-kb windows and 1,000 BUSCO genes), the study reconstructed a robust phylogeny covering all ordinal-level lineages.

    “Using whole-genome alignments from 464 species (comprising 3.18 Mb of orthologous sequences partitioned into 3,185 1-kb windows and 1,000 BUSCO genes, Figure S4), we reconstructed a robust phylogeny covering all ordinal-level lineages.”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    Based on the whole-genome alignment, 0.11 Gb of ancestral sequences were identified in teleost lineages, lower than in mammals and birds.

    “we first identified 0.11 Gb of ancestral sequences in the teleost lineages that was lower than in mammals and birds”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Findingown data

    These major inflection points coincide with two key mass extinction events, the end-Permian (∼250 Ma) and K-Pg (∼66 Ma).

    “These major inflection points coincide with two key mass extinction events, the end-Permian (∼250 Ma) and K-Pg (∼66 Ma) (Figures 7C and S8).”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    24,462 contiguous constrained elements (CCEs) and 787 contiguous accelerated elements (CAEs) were identified.

    “we identified 24,462 CCEs (Table S5) and 787 CAEs (Table S6)”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: Ancestral repetitive elements provide a valid source of neutrally evolving sequences for defining the baseline rate of evolution.

  • It may state two separate claims as one.

    Findingown data

    Both concatenation and coalescent-based methods yielded highly supported trees (average bootstrap value = 88.27%) and high topological consistency of Robinson-Foulds distances across all methods.

    “Both concatenation and coalescent-based methods yielded highly supported trees (average bootstrap value = 88.27%) (Figures S5A–S5D) and high topological consistency of Robinson-Foulds distances (Figures S5E and S5F; Table S11) across all methods.”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    Zebrafish chromosomes 4 and 18 exhibit the lowest and highest proportions of constraint sites, respectively, with a 2-fold difference between them.

    “Chromosomes 4 and 18 exhibit the lowest and highest proportions of constraint sites, respectively, with a 2-fold difference between them”
    Quote in the paperNot a substantial claim
    • The authors state this as an assumption: Ancestral repetitive elements provide a valid source of neutrally evolving sequences for defining the baseline rate of evolution.

  • It may state two separate claims as one.

    Findingown data

    The remaining non-coding TSHCEs showed substantial overlap with ATAC-seq peaks but limited overlap with TEs.

    “The remaining non-coding TSHCEs showed substantial overlap with ATAC-seq peaks but limited overlap with TEs”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    Integrating paleontological and molecular clock data, the analysis indicates that teleosts originated ∼253 Ma, preceding the Permian-Triassic extinction (251.9 Ma).

    “Integrating paleontological and molecular clock data, our analysis indicates that teleosts originated ∼253 Ma, preceding the Permian-Triassic extinction (251.9 Ma) (Figures 6A and S7).”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    The newly sequenced genomes show similar or better contig N50 continuity and BUSCO completeness compared with most previously published teleost fish genomes.

    “The newly sequenced genomes show similar (or better) contig N50 continuity (see Figure S1B) and BUSCO completeness (see Figure S1C) to most of the previously published teleost fish genomes”
    • Also stated in: § A comprehensive comparative genomics resource covering all extant teleost orders · plain
      “These newly sequenced genomes are comparable in continuity and completeness to most published fish genomes”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Findingown data

    A refined evolutionary timeline placed teleosts at approximately 253 million years ago, predating the Permian-Triassic extinction.

    “placed teleosts at ∼253 million years ago, predating the Permian-Triassic extinction”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    The precise molecular clock and lineage-through-time (LTT) analyses reveal three evolutionary phases in crown teleosts: (1) rapid diversification (origin to ∼170 Ma), (2) a period of declining diversification (∼170-66 Ma), and (3) post-K-Pg phase beginning with a brief stabilization, followed by a transient resurgence in diversification before decreasing to modern levels.

    “The precise molecular clock and lineage-through-time (LTT) analyses reveal three evolutionary phases in crown teleosts: (1) rapid diversification (origin to ∼170 Ma), (2) a period of declining diversification (∼170–66 Ma), and (3) post-K-Pg phase beginning with a brief stabilization, followed by a transient resurgence in diversification before decreasing to modern levels (Figures 7A, 7B, and S7).”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Findingown data

    Based on large-scale whole-genome alignment, the study identified genome-wide constraint sites in teleost fish at single-base resolution and systematically characterized genome sequences specifically generated in teleosts.

    “Furthermore, based on large-scale whole-genome alignment, we have for the first time identified genome-wide constraint sites in teleost fish at single-base resolution and systematically characterized genome sequences specifically generated in teleosts.”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Interpretationcitation

    rfx4 expression during posterior neural development and motor coordination potentially contributes to teleost-specific adaptations in axial patterning and swimming efficiency, including modular axial skeletons, reconfigured myomeres for enhanced propulsion, and homocercal caudal fins.

    “rfx4 expression during posterior neural development and motor coordination, potentially contributing to teleost-specific adaptations in axial patterning and swimming efficiency, including modular axial skeletons, reconfigured myomeres for enhanced propulsion, and homocercal caudal fins.44,45”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [44] Grillner, 2021, Evolution of the vertebrate motor system - from forebrain to spinal cord, Curr. Opin. Neurobiol. source
    • cites [45] Albert, 2001

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Premisecitation

    Conserved elements play pivotal roles in shaping specific traits, often being under strong evolutionary constraint and involved in crucial regulatory functions.

    “Previous studies have indicated that conserved elements play pivotal roles in shaping specific traits, often being under strong evolutionary constraint and involved in crucial regulatory functions.28,29”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [28] Kuderna, 2024, Identification of constrained sequence elements across 239 primate genomes, Nature source

      Checked before — its earlier verdict is held back until a new check runs.

    • cites [29] Seki, 2017, Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features, Nat. Commun. source

      Checked before — its earlier verdict is held back until a new check runs.

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisecitation

    Dornburg and Near recently identified the Siluriphysi issue as one of the unresolved questions in teleost evolution.

    “Dornburg and Near57 recently identified this issue as one of the unresolved questions in teleost evolution.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [57] Dornburg, 2021, The emerging phylogenetic perspective on the evolution of actinopterygian fishes, Annu. Rev. Ecol. Evol. Syst. source

      Checked before — its earlier verdict is held back until a new check runs.

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisecitation

    Evolutionary rates on microchromosomes and sex chromosomes differ from those on autosomes in vertebrates.

    “Previous studies have shown that the evolutionary rates on microchromosomes and sex chromosomes differ from those on autosomes in vertebrates.29,30”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [29] Seki, 2017, Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features, Nat. Commun. source

      Checked before — its earlier verdict is held back until a new check runs.

    • cites [30] Lindblad-Toh, 2011, A high-resolution map of human evolutionary constraint using 29 mammals, Nature source

  • Probably not a substantial claim. It may state two separate claims as one.

    Study design and conductown data

    The input phylogeny for divergence time estimation was pruned to 47 taxa, ensuring representation from all teleost fish orders or families included in the original dataset.

    “This pruning process reduced the tree to 47 taxa (Table S16), ensuring representation from all teleost fish orders (families) included in the original dataset”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Interpretationreasoning

    The limited molecular markers employed in these studies resulted in inconsistent topological structures, precluding definitive challenges to the Siluriphysi hypothesis.

    “The limited molecular markers employed in these studies resulted in inconsistent topological structures, precluding definitive challenges to the Siluriphysi hypothesis.”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Interpretationcitation

    This pattern aligns with established phylogenetic models and supports the study's three-phase evolutionary framework.

    “This pattern aligns with established phylogenetic models62 and supports our three-phase evolutionary framework.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [62] Ghezelayagh, 2022, Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous, Nat. Ecol. Evol. source

      Checked before — its earlier verdict is held back until a new check runs.

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Study design and conductnone given

    All phylogenetic analyses were independently performed using IQ-TREE v.2.3.6 with 1,000 ultrafast bootstrap replicates and the -bnni parameter.

    “All phylogenetic analyses were independently performed using IQ-TREE, v.2.3.611 with 1,000 ultrafast bootstrap replicates and “-bnni” parameter”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Interpretationown data

    TGD not only duplicated protein-coding genes but also potentially facilitated the emergence of novel regulatory elements.

    “indicating that TGD not only duplicated protein-coding genes but also potentially facilitated the emergence of novel regulatory elements”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim. It may state two separate claims as one.

    Study design and conductreasoning

    Fossil data cleaning removed species with ambiguous names and fossil records dating beyond the Silurian period due to uncertainty.

    “Data cleaning involved the removal of species with ambiguous names and fossil records dating beyond the Silurian period due to their uncertainty”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Premisecitation

    Long-term evolutionary conserved sequences are typically subject to purifying selection and tend to retain conserved functions.

    “Long-term evolutionary conserved sequences are typically subject to purifying selection and tend to retain conserved functions.27”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [27] McLean, 2011, Human-specific loss of regulatory DNA and the evolution of human-specific traits, Nature source

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Premisecitation

    Accelerated genes in mammals are linked to immunity, skin development, and certain sensory capabilities.

    “Previous studies indicate that these accelerated genes are linked to mammalian immunity, skin development, and certain sensory capabilities.9”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [9] Christmas, 2023, Evolutionary constraint and innovation across hundreds of placental mammals, Science source

      Checked before — its earlier verdict is held back until a new check runs.

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Premisenone given

    Teleost fishes exhibit extensive morphological and ecological diversification, driven by a long history of adaptive radiation.

    “Teleost fishes exhibit extensive morphological and ecological diversification, driven by a long history of adaptive radiation”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Study design and conductnone given

    Rigorous manual verification ensured the integrity of the fossil data.

    “Rigorous manual verification ensured data integrity”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisecitation

    Previous studies suggested that TE expansions correlate with adaptive evolution in fishes.

    “Previous studies suggested that TE expansions correlate with adaptive evolution in fishes”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Interpretationown data

    Some TSHCEs may be linked to genes regulating teleost organ development and contributed to the evolution of lineage-specific morphological traits in teleosts.

    “Our findings suggest that some TSHCEs may be linked to genes regulating teleost organ development and contributed to the evolution of lineage-specific morphological traits in teleosts”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Study design and conductown data

    For each locus or gene tree, topological robustness was evaluated by 1,000 ultrafast bootstrap replicates and the -bnni parameter.

    “For each locus or gene tree, the topological robustness of each tree was evaluated by 1,000 ultrafast bootstrap replicates and “-bnni” parameter”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Premisecitation

    rfx4 controls dorsal and ventral midline formation in the neural tube, and its loss-of-function mutants in zebrafish exhibit caudal neural defects, impaired swimming, and swim bladder inflation failure.

    “rfx4 controls dorsal and ventral midline formation in the neural tube, and its loss-of-function mutants in zebrafish exhibit caudal neural defects, impaired swimming, and swim bladder inflation failure.43”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [43] Sedykh, 2018, Zebrafish Rfx4 controls dorsal and ventral midline formation in the neural tube, Dev. Dyn. source

      Checked before — its earlier verdict is held back until a new check runs.

  • Probably not a substantial claim.

    Study design and conductown data

    Divergence time estimation was calibrated using 19 soft-bound fossil calibrations that were carefully reviewed and adjusted according to the fossil record and the International Chronostratigraphic Chart.

    “The MCMCtree analysis was calibrated using 19 soft-bound fossil calibrations (Table S17) that were carefully reviewed and adjusted according to our fossil record and the International Chronostratigraphic Chart”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim.

    Study design and conductreasoning

    Taxa flagged as brackish or euryhaline were excluded to avoid confounding effects in the freshwater and marine classification.

    “any taxa flagged as brackish or euryhaline were excluded to avoid confounding effects”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Study design and conductnone given

    Scripts used in this study, such as phylogenetic and gene annotation pipelines, are available on the GitHub page of Fish10K.

    “For code availability, scripts used in this study, such as phylogenetic and gene annotation pipelines, are available on the GitHub page of Fish10K (https://github.com/BGI-Qingdao/fish10k).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Study design and conductown data

    All data produced in this study are stored in publicly available databases.

    “For data availability, all the data produced in this study are stored in publicly available databases.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Study design and conductown data

    The whole-genome HAL format alignment files for 467 fish species (including 3 non-teleost fishes as the outgroup) have been submitted to the CNSA database of CNGBdb (CNP0004661).

    “The whole-genome HAL format alignment files for 467 fish species (including 3 non-teleost fishes as the outgroup) have also been submitted to the CNSA database of CNGBdb: ftp://ftp.cngb.org/pub/CNSA/data5/CNP0004661/Other/467-Bony-fish.hal and can be accessed using accession number CNP0004661”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Interpretationnone given

    The Fish10K project has produced a comprehensive genomic foundation to systematically reconstruct teleost evolutionary history and decipher the genomic basis of their phenotypic diversity.

    “The Fish10K project has produced a comprehensive genomic foundation to systematically reconstruct teleost evolutionary history and decipher the genomic basis of their phenotypic diversity.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Study design and conductnone given

    The Newick format tree file for all 467 fish species (including 3 non-teleost fishes as the outgroup) can be found in the "Data S1-S4."

    “The Newick format tree file for all 467 fish species (including 3 non-teleost fishes as the outgroup) can be found in the “Data S1–S4.””
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Study design and conductown data

    The newly assembled genomes of 110 fishes from this study have been submitted to the CNSA of CNGBdb (CNP0004403).

    “The newly assembled genomes of 110 fishes from this study have been submitted to the CNSA of CNGBdb (https://db.cngb.org/cnsa/): CNP0004403.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Study design and conductnone given

    All experimental animal treatments in this study have been verified and identified by taxonomic experts and museum taxonomists according to guidelines approved by the instituted Review Board of Bioethics and Biosafety (BGI-IRB, ethical permit ID: BGI-IRB A20007-T1).

    “All experimental animal treatments in this study have been verified and identified by taxonomic experts and museum taxonomists according to the guidelines approved by the instituted Review Board of Bioethics and Biosafety (BGI-IRB, ethical permit ID: BGI-IRB A20007-T1).”
    Quote in the paperNot a substantial claim
50 of 50

  • The paper relies on this without support.

    A robust whole-genome comparative context for teleosts was lacking and was a critical bottleneck preventing systematic investigation of the evolutionary landscape.

    “However, the lack of a robust, whole-genome comparative context has been a critical bottleneck, preventing a systematic investigation into the evolutionary landscape”

  • The authors state this as an assumption.

    Ancestral repetitive elements provide a valid source of neutrally evolving sequences for defining the baseline rate of evolution.

    “Following previous studies,8,9 we used ancestral repetitive elements as our source for these neutrally evolving sequences”

  • The paper relies on this without support.

    FishBase salinity flags accurately classify teleost species as exclusively freshwater or exclusively marine.

    “we classified these 464 species into “freshwater” and “marine” categories based on the salinity flags provided by FishBase”
3 of 3

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Fugu genome publication year disagrees with the cited reference

    Minor

    The introduction gives 2003 as the publication year, while its cited reference lists 2002.

  • The paper calls 44 taxa "44 orders"

    Minor

    The paper defines the 44 taxa as 37 orders and 7 unclassified families, but later describes the alignment as spanning "all 44 orders."

2 of 2

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 1

  1. Lauder, 2000, Function of the caudal fin during locomotion in fishes: kinematics, flow visualization, and evolutionary patterns, Am. Zool., 40, 101

Cited by

Sorted by citations

Related

Metadata

Authors
Song, Y., Yuan, Z., Fang, C., Zhang, S., Yang, L., Hu, M., Seim, I., Liu, S., Tian, X., Wang, C., Zhang, Y., Pan, Z., Qu, Q., Liu, H., Li, Y., Pan, L., Zhu, C., Yang, H., Chen, X., Zhang, M., Hou, G., Liu, M., Wang, J., Liu, Q., Gan, X., Zeng, H., Xu, W., Feng, C., Wang, M., Zhou, Z., He, S., Liu, C., Yu, M., Li, H., Liang, J., Zhang, H., Li, Y., Ming-Yuen Lee, S., Sun, Y., Qiu, Q., Liu, X., Kristiansen, K., Wang, W., Wang, J., Zhu, M., Yang, H., Chen, S., Gui, J., Chen, Y., Zhang, G., Xu, X., Wang, K., Fan, G., & He, S.
Affiliations
  • University of Copenhagen (DK)
  • Southwest University (CN)
  • Chinese Academy of Sciences (CN)
  • BGI Research (CN)
  • Northwestern Polytechnical University (CN)
  • Shandong University (CN)
  • Xiamen University (CN)
  • South China Agricultural University (CN)
  • Guangdong Ocean University (CN)
  • Kunming Institute of Zoology (CN)
  • Yellow Sea Fisheries Research Institute (CN)
  • Women's Hospital, School of Medicine, Zhejiang University (CN)
  • BGI Group (China) (CN)
Corresponding author
  • Zhang, Guojie
  • Xu, Xun
  • Wang, Kun
  • Fan, Guangyi
  • He, Shunping
ORCID
Venue
The Innovation
Publisher
Elsevier BV
Published
2026-03
Volume
7
Issue
3
Pages
101177
ISSN
2666-6758 (ISSN-L)
DOI
10.1016/j.xinn.2025.101177
PMC
PMC12957567
OpenAlex
W4415944018
Semantic Scholar
5435c4e71880224ebb1458a87db8ff83f16fb711
Cited by
3
References
55
Citations by year
2026: 3
FWCI
1.28
Type
journal article
Language
en
Open access
Licence
Locations
  • The Innovation (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by-nc-nd)
Funders
  • National Natural Science Foundation of China (32170438, 32170439, 32122021, 32293252)
  • Key Technology Research and Development Program of Shandong Province (2023CXPT057)
  • Jiangsu Provincial Department of Science and Technology (JSSCTD202142)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
  • 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
Keywords
teleosts, whole-genome alignment, comparative genomics, genome compaction, intron length, transposable elements, DNA transposons, habitat associations, Characiformes, divergence time estimation, mass extinction, macroevolution, vertebrate evolution

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

A language model drew the claims from the paper on 2026-11-10, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).

A second model labelled each claim on 2026-11-10 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).

Cited sources are checked with a language model’s help (gpt-6-sol).

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

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