The Cretaceous–Palaeogene (K–Pg) mass extinction is linked to the rapid emergence of ecologically divergent higher taxa (for example, families and orders) across terrestrial vertebrates, but its impact on the diversification of marine vertebrates is less clear. Spiny-rayed fishes (Acanthomorpha) provide an ideal system for exploring the effects of the K–Pg on fish diversification, yet despite decades of morphological and molecular phylogenetic efforts, resolution of both early diverging lineages and enormously diverse subclades remains problematic. Recent multilocus studies have provided the first resolved phylogenetic backbone for acanthomorphs and suggested novel relationships among major lineages. However, these new relationships and associated timescales have not been interrogated using phylogenomic approaches. Here, we use targeted enrichment of >1,000 ultraconserved elements in conjunction with a divergence time analysis to resolve relationships among 120 major acanthomorph lineages and provide a new timescale for acanthomorph radiation. Our results include a well-supported topology that strongly resolves relationships along the acanthomorph backbone and the recovery of several new relationships within six major percomorph subclades. Divergence time analyses also reveal that crown ages for five of these subclades, and for the bulk of the species diversity in the sixth, coincide with the K–Pg boundary, with divergences between anatomically and ecologically distinctive suprafamilial clades concentrated in the first 10 million years of the Cenozoic.

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We thank J. Johnson for the illustrations used in the figures. This work was partially supported by National Science Foundation grants DEB-0842397 (to M.E.A.); DEB-1242260, DEB-1655624 (to B.C.F.); and startup funds from Louisiana State University (to B.C.F.). DNA alignment was supported in part by resources and technical expertise from the Georgia Advanced Computing Resource Center—a partnership between the University of Georgia’s Office of the Vice President for Research and Office of the Vice President for Information Technology. Phylogenetic analysis portions of this research were conducted using high-performance computing resources provided by Louisiana State University (http://www.hpc.lsu.edu).

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Author notes

  1. These authors contributed equally: Michael E. Alfaro and Brant C. Faircloth.


  1. Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA

    • Michael E. Alfaro
    • , Laurie Sorenson
    •  & David Černý
  2. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA

    • Brant C. Faircloth
    •  & Carl H. Oliveros
  3. Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA

    • Brant C. Faircloth
  4. Department of Earth Sciences, University of Oxford, Oxford, UK

    • Richard C. Harrington
    •  & Matt Friedman
  5. Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA

    • Richard C. Harrington
    •  & Thomas J. Near
  6. Museum of Paleontology, University of Michigan, Ann Arbor, MI, USA

    • Matt Friedman
  7. Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, USA

    • Matt Friedman
  8. Natural History Museum of Los Angeles County, Los Angeles, CA, USA

    • Christine E. Thacker
  9. Peabody Museum of Natural History, Yale University, New Haven, CT, USA

    • Thomas J. Near


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M.E.A. conceived the study. M.E.A., B.C.F., R.C.H., M.F. and T.J.N. designed the study. L.S., R.C.H. and B.C.F. collected the sequence data from enriched UCE loci. M.F. selected appropriate calibration points. B.C.F., M.E.A., D.Č. and C.H.O. performed the data analyses. M.E.A. and B.C.F. wrote the manuscript with help from R.C.H., L.S., M.F., D.Č. and T.J.N. All authors read and approved the final version of the manuscript.

Competing interests

The authors declare no competing interests.

Corresponding authors

Correspondence to Michael E. Alfaro or Brant C. Faircloth.

Supplementary information

  1. Supplementary Information

    Supplementary Information, Methods, Results, References and Figures

  2. Life Sciences Reporting Summary

  3. Supplementary Table 1

    Species, family, institutional or personal voucher code, preparation method (Prep.), enrichment method (Enrich.), sequencing platform (Plat.), and NCBI BioSample and SRA accession information for each individual used in this study

  4. Supplementary Table 2

    Statistics for trimmed sequence reads collected from each library enriched for ultraconserved element loci

  5. Supplementary Table 3

    Statistics for all contigs assembled from trimmed sequence data collected from each library enriched for ultraconserved element loci

  6. Supplementary Table 4

    Statistics for ultraconserved element (UCE) contigs assembled from trimmed sequence data collected from each library enriched for ultraconserved element loci

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