Cited by 206

The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.

Explosive diversification of marine fishes at the Cretaceous–Palaeogene boundary

Alfaro, Michael E., Faircloth, Brant C., Harrington, Richard C., Sorenson, Laurie, Friedman, Matt, Thacker, Christine E., Oliveros, Carl H., Černý, David, Near, Thomas J.·2018·Nature Ecology & Evolution

Abstract

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 su…

Overview

Integrity signals

Registry

Crossref · 10.1038/s41559-018-0494-6

Cites

4 of 4 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Verification

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • The study's results challenge previous hypotheses suggesting a continuous increase in diversification rates following the K-Pg extinction.

    “Additionally, our results challenge previous hypotheses suggesting a continuous increase in diversification rates following the K-Pg extinction.58,59,60,61”

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 56

  1. Erwin, D. H. Lessons from the past: biotic recoveries from mass extinctions. Proc. Natl Acad. Sci. USA 98, 5399–5403 (2001). · DOI · Paper page
  2. Krug, A. Z., Jablonski, D. & Valentine, J. W. Signature of the end-Cretaceous mass extinction in the modern biota. Science 323, 767–771 (2009). · DOI
  3. Jarvis, E. D. et al. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346, 1320–1331 (2014). · DOI · Paper page
  4. O’Leary, M. A. et al. The placental mammal ancestor and the post-K–Pg radiation of placentals. Science 339, 662–667 (2013). · DOI
  5. Longrich, N. R., Bhullar, B.-A. S. & Gauthier, J. A. Mass extinction of lizards and snakes at the Cretaceous–Paleogene boundary. Proc. Natl Acad. Sci. USA 109, 21396–21401 (2012). · DOI
  6. 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
  7. Sanciangco, M. D., Carpenter, K. E. & Betancur-R, R. Phylogenetic placement of enigmatic percomorph families (Teleostei: Percomorphaceae). Mol. Phylogenet. Evol. 94, 565–576 (2016). · DOI
  8. Santini, F., Harmon, L. J., Carnevale, G. & Alfaro, M. E. Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes. BMC Evol. Biol. 9, 194 (2009). · DOI
  9. 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
  10. Patterson, C. & Smith, A. B. Periodicity in extinction: the role of systematics. Ecology 70, 802–811 (1989). · DOI
  11. MacLeod, N. et al. The Cretaceous–Tertiary biotic transition. J. Geol. Soc. Lond. 154, 265–292 (1997). · DOI
  12. Cavin, L. in Geological and Biological Effects of Impact Events (eds Buffetaut, E. & Koeberl, C.) 141–158 (Springer, Berlin & Heidelberg, 2002). · DOI
  13. 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
  14. Friedman, M. Ecomorphological selectivity among marine teleost fishes during the end-Cretaceous extinction. Proc. Natl Acad. Sci. USA 106, 5218–5223 (2009). · DOI · Paper page
  15. Sibert, E. C. & Norris, R. D. New age of fishes initiated by the Cretaceous–Paleogene mass extinction. Proc. Natl Acad. Sci. USA 112, 8537–8542 (2015). · DOI
  16. Patterson, C. An overview of the early fossil record of the acanthomorphs. Bull. Mar. Sci. 52, 29–59 (1993).
  17. Johnson, D. G. Percomorph phylogeny: progress and problems. Bull. Mar. Sci. 52, 3–28 (1993).
  18. Johnson, D. G. & Patterson, C. Percomorph phylogeny: a survey of acanthomorphs and a new proposal. Bull. Mar. Sci. 52, 554–626 (1993).
  19. Davesne, D. et al. The phylogenetic intrarelationships of spiny-rayed fishes (Acanthomorpha, Teleostei, Actinopterygii): fossil taxa increase the congruence of morphology with molecular data. Front. Ecol. Evol. 4, 129 (2016). · DOI
  20. Alfaro, M. E. et al. Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proc. Natl Acad. Sci. USA 106, 13410–13414 (2009). · DOI
  21. Nelson, J. S. Fishes of the World 4th edn (Wiley, Hoboken, 2006).
  22. Betancur, R. et al. The tree of life and a new classification of bony fishes. PLoS Curr. 5, https://doi.org/10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288 (2013). · DOI
  23. 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
  24. Faircloth, B. C., Sorenson, L., Santini, F. & Alfaro, M. E. A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs). PLoS ONE 8, e65923 (2013). · DOI
  25. Bejerano, G. et al. Ultraconserved elements in the human genome. Science 304, 1321–1325 (2004). · DOI · Paper page
  26. Faircloth, B. C. et al. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Syst. Biol. 61, 717–726 (2012). · DOI
  27. Setiamarga, D. H. E. et al. Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates. Biol. Lett. 5, 812–816 (2009). · DOI
  28. Yamanoue, Y., Miya, M., Inoue, J. G., Matsuura, K. & Nishida, M. The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetraodontiformes) and divergence time estimation among model organisms in fishes. Genes Genet. Syst. 81, 29–39 (2006). · DOI
  29. Yang, Z. & Rannala, B. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol. Biol. Evol. 23, 212–226 (2006). · DOI
  30. Zheng, Y., Peng, R., Kuro-o, M. & Zeng, X. Exploring patterns and extent of bias in estimating divergence time from mitochondrial DNA sequence data in a particular lineage: a case study of salamanders (order Caudata). Mol. Biol. Evol. 28, 2521–2535 (2011). · DOI
  31. Brown, J. W. & Van Tuinen, M. (eds) in Living Dinosaurs: The Evolutionary History of Modern Birds 306–324 (Wiley, Chichester, 2011). · DOI
  32. Smith, B. T. & Klicka, J. Examining the role of effective population size on mitochondrial and multilocus divergence time discordance in a songbird. PLoS ONE 8, e55161 (2013). · DOI
  33. Friedman, M. & Sallan, L. C. Five hundred million years of extinction and recovery: a Phanerozoic survey of large-scale diversity patterns in fishes. Palaeontology 55, 707–742 (2012). · DOI
  34. Miya, M. et al. Evolutionary origin of the scombridae (tunas and mackerels): members of a Paleogene adaptive radiation with 14 other pelagic fish families. PLoS ONE 8, e73535 (2013). · DOI
  35. 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
  36. Carnevale, G. & Johnson, G. D. A Cretaceous cusk-eel (Teleostei, Ophidiiformes) from Italy and the Mesozoic diversification of percomorph fishes. Copeia 103, 771–791 (2015). · DOI
  37. Faircloth, B. C. & Glenn, T. C. Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels. PLoS ONE 7, e42543 (2012). · DOI
  38. Glenn, T. C. et al. Adapterama I: universal stubs and primers for thousands of dual-indexed Illumina libraries (iTru & iNext). Preprint at https://doi.org/10.1101/049114 (2016). · DOI
  39. Blumenstiel, B. et al. Targeted exon sequencing by in-solution hybrid selection. Curr. Protoc. Hum. Genet. 66, 18.4.1–18.4.24 (2010).
  40. Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–652 (2011). · DOI
  41. Faircloth, B. C. PHYLUCE is a software package for the analysis of conserved genomic loci. Bioinformatics 32, 786–788 (2015). · DOI
  42. Lanfear, R., Calcott, B., Ho, S. Y. W. & Guindon, S. Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol. Biol. Evol. 29, 1695–1701 (2012). · DOI · Paper page
  43. Aberer, A. J., Kobert, K. & Stamatakis, A. ExaBayes: massively parallel Bayesian tree inference for the whole-genome era. Mol. Biol. Evol. 31, 2553–2556 (2014). · DOI
  44. Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014). · DOI · Paper page
  45. Phillips, M. J. & Penny, D. The root of the mammalian tree inferred from whole mitochondrial genomes. Mol. Phylogenet. Evol. 28, 171–185 (2003). · DOI
  46. Phillips, M. J., Delsuc, F. & Penny, D. Genome-scale phylogeny and the detection of systematic biases. Mol. Biol. Evol. 21, 1455–1458 (2004). · DOI · Paper page
  47. Seo, T.-K. Calculating bootstrap probabilities of phylogeny using multilocus sequence data. Mol. Biol. Evol. 25, 960–971 (2008). · DOI
  48. Mirarab, S. & Warnow, T. ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics 31, i44–i52 (2015). · DOI
  49. Sukumaran, J. & Holder, M. T. DendroPy: a Python library for phylogenetic computing. Bioinformatics 26, 1569–1571 (2010). · DOI
  50. Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007). · DOI · Paper page
  51. Dos Reis, M. & Yang, Z. Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times. Mol. Biol. Evol. 28, 2161–2172 (2011). · DOI
  52. Smith, S., Brown, J. W. & Walker, J. F. So many genes, so little time: comments on divergence-time estimation in the genomic era. Preprint at https://doi.org/10.1101/114975 (2017). · DOI
  53. Huerta-Cepas, J., Serra, F. & Bork, P. ETE 3: reconstruction, analysis, and visualization of phylogenomic data. Mol. Biol. Evol. 33, 1635–1638 (2016). · DOI
  54. Vaidya, G., Lohman, D. J. & Meier, R. SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information. Cladistics 27, 171–180 (2011). · DOI
  55. 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).
  56. Chen, W.-J. et al. New insights on early evolution of spiny-rayed fishes (Teleostei: Acanthomorpha). Front. Mar. Sci. 1, 1–17 (2014). · DOI

Cited by

Sorted by citations

Metadata

Authors
Alfaro, M. E., Faircloth, B. C., Harrington, R. C., Sorenson, L., Friedman, M., Thacker, C. E., Oliveros, C. H., Černý, D., & Near, T. J.
Venue
Nature Ecology & Evolution
Published
2018-03-12
Volume
2
Issue
4
Pages
688-696
ISSN
2397-334X
Cited by
206
References
4
Language
en

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.

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.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review