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Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous

Ghezelayagh, Ava, Harrington, Richard C., Burress, Edward D., Campbell, Matthew A., Buckner, Janet C., Chakrabarty, Prosanta, Glass, Jessica R., McCraney, W. Tyler, Unmack, Peter J., Thacker, Christine E., Alfaro, Michael E., Friedman, Sarah T., Ludt, William B., Cowman, Peter F., Friedman, Matt, Price, Samantha A., Dornburg, Alex, Faircloth, Brant C., Wainwright, Peter C., Near, Thomas J.·2022·Nature Ecology & Evolution
DOI 10.1038/s41559-022-01801-3

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Research works printed but not linked: 56

  1. Wainwright, P. C. & Longo, S. J. Functional innovations and the conquest of the oceans by acanthomorph fishes. Curr. Biol. 27, R550–R557 (2017). · DOI
  2. Near, T. J. et al. Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes. Proc. Natl Acad. Sci. USA 110, 12738–12743 (2013). · DOI
  3. Dornburg, A. & Near, T. J. The emerging phylogenetic perspective on the evolution of actinopterygian fishes. Annu. Rev. Ecol., Evolution, Syst. 52, 427–452 (2021). · DOI · Paper page
  4. Chen, W.-J. et al. New insights on early evolution of spiny-rayed fishes (Teleostei: Acanthomorpha). Front. Mar. Sci. 1, 53 (2014). · DOI
  5. Friedman, M. Explosive morphological diversification of spiny-finned teleost fishes in the aftermath of the end-Cretaceous extinction. Proc. R. Soc. B 277, 1675–1683 (2010). · DOI · Paper page
  6. Alfaro, M. E. et al. Explosive diversification of marine fishes at the Cretaceous–Palaeogene boundary. Nat. Ecol. Evolution 2, 688–696 (2018). · DOI · Paper page
  7. Stadler, T. Mammalian phylogeny reveals recent diversification rate shifts. Proc. Natl Acad. Sci. USA 108, 6187–6192 (2011). · DOI
  8. Venditti, C., Meade, A. & Pagel, M. Multiple routes to mammalian diversity. Nature 479, 393–396 (2011). · DOI
  9. Liu, L. et al. Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary. Proc. Natl Acad. Sci. USA 114, E7282–E7290 (2017).
  10. Slater, G. J. Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the Cretaceous–Palaeogene boundary. Methods Ecol. Evol. 4, 734–744 (2013). · DOI
  11. Jetz, W. & Pyron, R. A. The interplay of past diversification and evolutionary isolation with present imperilment across the amphibian tree of life. Nat. Ecol. Evolution 2, 850–858 (2018). · DOI · Paper page
  12. Longrich, N. R., Bhullar, B.-A. S. & Gauthier, J. Mass extinction of lizards and snakes at the Cretaceous–Paleogene boundary. Proc. Natl Acad. Sci. USA 109, 21396–21401 (2012). · DOI
  13. Jarvis, E. D. et al. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346, 1320 (2014). · DOI · Paper page
  14. Patterson, C. An overview of the early fossil record of acanthomorphs. Bull. Mar. Sci. 52, 29–59 (1993).
  15. Betancur-R, R. et al. The tree of life and a new classification of bony fishes. PLOS Curr. https://doi.org/10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288 (2013). · DOI
  16. Hughes, L. C. et al. Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data. Proc. Natl Acad. Sci. USA 115, 6249–6254 (2018). · DOI · Paper page
  17. Johnson, G. D. & Patterson, C. Percomorph phylogeny: a survey of acanthomorphs and a new proposal. Bull. Mar. Sci. 52, 554–626 (1993).
  18. Near, T. J. et al. Resolution of ray-finned fish phylogeny and timing of diversification. Proc. Natl Acad. Sci. USA 109, 13698–13703 (2012). · DOI · Paper page
  19. Miya, M. et al. Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol. Phylogenet. Evol. 26, 121–138 (2003). · DOI
  20. Wainwright, P. C. et al. The evolution of pharyngognathy: a phylogenetic and functional appraisal of the pharyngeal jaw key innovation in labroid fishes and beyond. Syst. Biol. 61, 1001–1027 (2012). · DOI
  21. Ribeiro, E., Davis, A. M., Rivero-Vega, R. A., Ortí, G. & Betancur-R, R. Post-Cretaceous bursts of evolution along the benthic-pelagic axis in marine fishes. Proc. R. Soc. B 285, 20182010 (2018). · DOI
  22. Price, S. A. et al. Building a body shape morphospace of teleostean fishes. Integ. Comp. Biol. 59, 716–730 (2019). · DOI
  23. Smith, W. L., Stern, J. H., Girard, M. G. & Davis, M. P. Evolution of venomous cartilaginous and ray-finned fishes. Integ. Comp. Biol. 56, 950–961 (2016). · DOI
  24. Liem, K. Evolutionary strategies and morphological innovations: cichlid pharyngeal jaws. Syst. Zool. 22, 425–441 (1973). · DOI
  25. Chan, K. O., Hutter, C. R., Wood, P. L., Grismer, L. L. & Brown, R. M. Larger, unfiltered datasets are more effective at resolving phylogenetic conflict: Introns, exons, and UCEs resolve ambiguities in Golden-backed frogs (Anura: Ranidae; genus Hylarana). Mol. Phylogenet. Evol. 151, 106899 (2020). · DOI
  26. Minh, B. Q., Hahn, M. W. & Lanfear, R. New methods to calculate concordance factors for phylogenomic datasets. Mol. Biol. Evol. 37, 2727–2733 (2020). · DOI
  27. Gilbert, P. S. et al. Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes. Mol. Phylogenet. Evol. 92, 140–146 (2015). · DOI
  28. Alda, F., Ludt, W. B., Elías, D. J., McMahan, C. D. & Chakrabarty, P. Comparing ultraconserved elements and exons for phylogenomic analyses of Middle American cichlids: when data agree to disagree. Genome Biol. Evol. https://doi.org/10.1093/gbe/evab161 (2021). · DOI
  29. Harmon, L. J., Schulte, J. A., Larson, A. II & Losos, J. B. Tempo and mode of evolutionary radiation in iguanian lizards. Science 301, 961–964 (2003). · DOI
  30. Claverie, T. & Wainwright, P. C. A morphospace for reef fishes: elongation Is the dominant axis of body shape evolution. PLoS ONE 9, e112732 (2014). · DOI
  31. Friedman, S. T. et al. Body shape diversification along the benthic–pelagic axis in marine fishes. Proc. R. Soc. B 287, 20201053 (2020). · DOI
  32. Schwarzhans, W. & Stringer, G. Fish otoliths from the Late Maastrichtian Kemp Clay (Texas, USA) and the Early Dannian Clayton Formation (Arkansas, USA) and an assessment of extinction and survival of teleost lineages across the K–Pg boundary based on otoliths. Riv. Ital. Paleontol. Strat. 126, 395–446 (2020).
  33. Friedman, M. et al. A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean. Proc. R. Soc. B 286, 20191502 (2019). · DOI
  34. Price, S. A., Holzman, R., Near, T. J. & Wainwright, P. C. Coral reefs promote the evolution of morphological diversity and ecological novelty in labrid fishes. Ecol. Lett. 14, 462–469 (2011). · DOI
  35. Daane, J. M. et al. Historical contingency shapes adaptive radiation in Antarctic fishes. Nat. Ecol. Evolution https://doi.org/10.1038/s41559-019-0914-2 (2019). · DOI
  36. Faircloth, B. C. et al. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Syst. Biol. 61, 717–726 (2012). · DOI
  37. Glenn, T. C. et al. Adapterama I: universal stubs and primers for 384 unique dual-indexed of 147,456 combinatorially-indexed Illumina libraries (iTru & iNext). PeerJ 7, e7755 (2019). · DOI
  38. Faircloth, B. C. PHYLUCE is a software package for the analysis of conserved genomic loci. Bioinformatics 32, 786–788 (2016). · DOI
  39. Nguyen, L. T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015). · DOI · Paper page
  40. Kozlov, A. M., Darriba, D., Flouri, T., Morel, B. & Stamatakis, A. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35, 4453–4455 (2019). · DOI
  41. Puigbò, P., Garcia-Vallvé, S. & McInerney, J. O. TOPD/FMTS: a new software to compare phylogenetic trees. Bioinformatics 23, 1556–1558 (2007). · DOI
  42. Mai, U. & Mirarab, S. TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees. BMC Genomics 19, 23–40 (2018). · DOI
  43. Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software Version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013). · DOI · Paper page
  44. Zhang, C., Rabiee, M., Sayyari, E. & Mirarab, S. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics 19, 15–30 (2018). · DOI
  45. Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020). · DOI · Paper page
  46. Ronquist, F. et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539–542 (2012). · DOI
  47. Ane, C., Larget, B., Baum, D. A., Smith, S. D. & Rokas, A. Bayesian estimation of concordance among gene trees. Mol. Biol. Evol. 24, 412–426 (2007). · DOI
  48. Gernhard, T. The conditioned reconstructed process. J. Theor. Biol. 253, 769–778 (2008). · DOI
  49. Harrington, R. C. et al. Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye. BMC Evol. Biol. 16, 224 (2016). · DOI
  50. Lanfear, R., Frandsen, P. B., Wright, A. M., Senfeld, T. & Calcott, B. PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol. Biol. Evol. 34, 772–773 (2017).
  51. Drummond, A. J., Suchard, M. A., Xie, D. & Rambaut, A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969–1973 (2012). · DOI
  52. Höhna, S., May, M. R. & Moore, B. R. TESS: an R package for efficiently simulating phylogenetic trees and performing Bayesian inference of lineage diversification rates. Bioinformatics 32, 789–791 (2016). · DOI
  53. Rabosky, D. L. Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees. PLoS ONE 9, e89543 (2014). · DOI
  54. Rabosky, D. L. et al. BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees. Methods Ecol. Evol. 5, 701–707 (2014). · DOI
  55. Revell, L. J. phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3, 217–223 (2012). · DOI
  56. Harmon, L. J., Weir, J. T., Brock, C. D., Glor, R. E. & Challenger, W. GEIGER: investigating evolutionary radiations. Bioinformatics 24, 129–131 (2008). · DOI

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Metadata

Authors
Ghezelayagh, A., Harrington, R. C., Burress, E. D., Campbell, M. A., Buckner, J. C., Chakrabarty, P., Glass, J. R., McCraney, W. T., Unmack, P. J., Thacker, C. E., Alfaro, M. E., Friedman, S. T., Ludt, W. B., Cowman, P. F., Friedman, M., Price, S. A., Dornburg, A., Faircloth, B. C., Wainwright, P. C., & Near, T. J.
ORCID
Venue
Nature Ecology & Evolution
Publisher
Springer Science and Business Media LLC
Published
2022-07-14
Volume
6
Issue
8
Pages
1211-1220
ISSN
2397-334X
DOI
10.1038/s41559-022-01801-3
Cited by
127
References
9
Language
en
Licence
Funders
  • U.S. Department of Health & Human Services | National Institutes of Health (T32 GM 007499)
  • National Science Foundation (NSF DEB-1701323, NSF DEB-1839915, NSF DEB-1556953, NSF DEB-1830127, NSF IOS-1755242, NSF DEB-1655624)
  • Department of Education and Training | Australian Research Council (DE170100516)
  • Louisiana State University
  • Yale University
  • Bingham Oceanographic Fund maintained by the Peabody Museum of Natural History, Yale University

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