Article

Phylotranscriptomic consolidation of the jawed vertebrate timetree

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Abstract

Phylogenomics is extremely powerful but introduces new challenges as no agreement exists on ‘standards’ for data selection, curation and tree inference. We use jawed vertebrates (Gnathostomata) as a model to address these issues. Despite considerable efforts in resolving their evolutionary history and macroevolution, few studies have included a full phylogenetic diversity of gnathostomes, and some relationships remain controversial. We tested a new bioinformatic pipeline to assemble large and accurate phylogenomic datasets from RNA sequencing and found this phylotranscriptomic approach to be successful and highly cost-effective. Increased sequencing effort up to about 10 Gbp allows more genes to be recovered, but shallower sequencing (1.5 Gbp) is sufficient to obtain thousands of full-length orthologous transcripts. We reconstruct a robust and strongly supported timetree of jawed vertebrates using 7,189 nuclear genes from 100 taxa, including 23 new transcriptomes from previously unsampled key species. Gene jackknifing of genomic data corroborates the robustness of our tree and allows calculating genome-wide divergence times by overcoming gene sampling bias. Mitochondrial genomes prove insufficient to resolve the deepest relationships because of limited signal and among-lineage rate heterogeneity. Our analyses emphasize the importance of large, curated, nuclear datasets to increase the accuracy of phylogenomics and provide a reference framework for the evolutionary history of jawed vertebrates.

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References

  1. 1.

    Brown, J. M. & Thomson, R. C. Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses. Syst. Biol. 66, 517–530 (2017).

  2. 2.

    Jeffroy, O., Brinkmann, H., Delsuc, F. & Hervé, P. Phylogenomics: the beginning of incongruence? Trends Genet. 22, 225–231 (2006).

  3. 3.

    Zardoya, R. & Meyer, A. The evolutionary position of turtles revised. Naturwissenschaften 88, 193–200 (2001).

  4. 4.

    Janke, A., Erpenbeck, D., Nilsson, M. & Arnason, U. The mitochondrial genomes of the iguana (Iguana iguana) and the caiman (Caiman crocodylus): implications for amniote phylogeny. Proc. R. Soc. B Biol. Sci. 268, 623–631 (2001).

  5. 5.

    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).

  6. 6.

    Irisarri, I. et al. The origin of modern frogs (Neobatrachia) was accompanied by acceleration in mitochondrial and nuclear substitution rates. BMC Genom. 13, 626 (2012).

  7. 7.

    Pyron, R. A., Burbrink, F. T. & Wiens, J. J. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evol. Biol. 13, 93 (2013).

  8. 8.

    Meredith, R. W. et al. Impacts of the Cretaceous terrestrial revolution and KPg extinction on mammal diversification. Science 334, 521–524 (2011).

  9. 9.

    Jetz, W., Thomas, G. H., Joy, J. B., Hartmann, K. & Mooers, A. O. The global diversity of birds in space and time. Nature 491, 444–448 (2012).

  10. 10.

    Chiari, Y., Cahais, V., Galtier, N. & Delsuc, F. Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria). BMC Biol. 10, 65 (2012).

  11. 11.

    Crawford, N. G. et al. More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs. Biol. Lett. 8, 783–786 (2012).

  12. 12.

    Chen, M. Y., Liang, D. & Zhang, P. Selecting question-specific genes to reduce incongruence in phylogenomics: a case study of jawed vertebrate backbone phylogeny. Syst. Biol. 64, 1104–1120 (2015).

  13. 13.

    Tarver, J. E. et al. The interrelationships of placental mammals and the limits of phylogenetic inference. Genome Biol. Evol. 8, 330–344 (2016).

  14. 14.

    Romiguier, J., Ranwez, V., Delsuc, F., Galtier, N. & Douzery, E. J. P. Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals. Mol. Biol. Evol. 30, 2134–2144 (2013).

  15. 15.

    Jarvis, E. D. et al. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346, 1320–1331 (2014).

  16. 16.

    Song, S., Liu, L., Edwards, S. V. & Wu, S. Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model. Proc. Natl Acad. Sci. USA 109, 14942–14947 (2012).

  17. 17.

    Morgan, C. C. et al. Heterogeneous models place the root of the placental mammal phylogeny. Mol. Biol. Evol. 30, 2145–2156 (2013).

  18. 18.

    Fong, J. J., Brown, J. M., Fujita, M. K. & Boussau, B. A phylogenomic approach to vertebrate phylogeny supports a turtle–archosaur affinity and a possible paraphyletic Lissamphibia. PLoS ONE 7, e48990 (2012).

  19. 19.

    Lyson, T. R. et al. MicroRNAs support a turtle + lizard clade. Biol. Lett. 8, 104–107 (2012).

  20. 20.

    Gauthier, J. A., Kearney, M., Maisano, J. A., Rieppel, O. & Behlke, A. D. B. Assembling the squamate tree of life: perspectives from the phenotype and the fossil record. Bull. Peabody Mus. Nat. Hist. 53, 3–308 (2012).

  21. 21.

    Townsend, T. M., Larson, A., Louis, E., Macey, J. R. & Sites, J. Molecular phylogenetics of Squamata: the position of snakes, amphisbaenians, and dibamids, and the root of the squamate tree. Syst. Biol. 53, 735–757 (2004).

  22. 22.

    Zheng, Y. & Wiens, J. J. Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species. Mol. Phylogenet. Evol. Part B 94, 537–547 (2016).

  23. 23.

    Irisarri, I., Vences, M., San Mauro, D., Glaw, F. & Zardoya, R. Reversal to air-driven sound production revealed by a molecular phylogeny of tongueless frogs, family Pipidae. BMC Evol. Biol. 11, 114 (2011).

  24. 24.

    Bewick, A. J., Chain, F. J. J., Heled, J. & Evans, B. J. The pipid root. Syst. Biol. 61, 913–926 (2012).

  25. 25.

    Philippe, H. et al. Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol. 9, e1000602 (2011).

  26. 26.

    Bininda-Emonds, O. R. P. et al. The delayed rise of present-day mammals. Nature 446, 507–512 (2007).

  27. 27.

    Springer, M. S. et al. Waking the undead: implications of a soft explosive model for the timing of placental mammal diversification. Mol. Phylogenet. Evol. 106, 86–102 (2017).

  28. 28.

    Phillips, M. J. Geomolecular dating and the origin of placental mammals. Syst. Biol. 65, 546–557 (2016).

  29. 29.

    Hara, Y. et al. Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation. BMC Genom. 16, 977 (2015).

  30. 30.

    Roure, B., Rodriguez-Ezpeleta, N. & Philippe, H. SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics. BMC Evol. Biol. 7, S2 (2007).

  31. 31.

    Delsuc, F., Tsagkogeorga, G., Lartillot, N. & Philippe, H. Additional molecular support for the new chordate phylogeny. Genesis 46, 592–604 (2008).

  32. 32.

    Irisarri, I. & Meyer, A. The identification of the closest living relative(s) of tetrapods: phylogenomic lessons for resolving short ancient internodes. Syst. Biol. 65, 1057–1075 (2016).

  33. 33.

    Zhu, M. & Schultze, H.-P. in Major Events in Early Vertebrate Evolution: Paleontology, Phylogeny and Development (ed. Ahlberg, P. E.) 289–314 (Taylor & Francis, 2001).

  34. 34.

    Pyron, R. A. & Wiens, J. J. A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians. Mol. Phylogenet. Evol. 61, 543–583 (2011).

  35. 35.

    San Mauro, D., Vences, M., Alcobendas, M., Zardoya, R. & Meyer, A. Initial diversification of living amphibians predated the breakup of Pangaea. Am. Nat. 165, 590–599 (2005).

  36. 36.

    Schoch, R. R. & Sues, H.-D. A Middle Triassic stem-turtle and the evolution of the turtle body plan. Nature 523, 584–587 (2015).

  37. 37.

    Zhang, P. & Wake, D. B. Higher-level salamander relationships and divergence dates inferred from complete mitochondrial genomes. Mol. Phylogenet. Evol. 53, 492–508 (2009).

  38. 38.

    Gregory, T. R. Insertion–deletion biases and the evolution of genome size. Gene 324, 15–34 (2004).

  39. 39.

    Dos Reis, M. et al. Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc. R. Soc. B Biol. Sci. 279, 3491–3500 (2012).

  40. 40.

    Lepage, T., Bryant, D., Philippe, H. & Lartillot, N. A general comparison of relaxed molecular clock models. Mol. Biol. Evol. 24, 2669–2680 (2007).

  41. 41.

    Near, T. J., Meylan, PeterA. & Shaffer, H. B. Assessing concordance of fossil calibration points in molecular clock studies: an example using turtles. Am. Nat. 165, 137–146 (2005).

  42. 42.

    Sanders, K. L. & Lee, M. S. Y. Evaluating molecular clock calibrations using Bayesian analyses with soft and hard bounds. Biol. Lett. 3, 275–279 (2007).

  43. 43.

    Warnock, R. C. M., Parham, J. F., Joyce, W. G., Lyson, T. R. & Donoghue, P. C. J. Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors. Proc. R. Soc. B Biol. Sci. 282, 20141013 (2014).

  44. 44.

    King, B. L. Bayesian morphological clock methods resurrect placoderm monophyly and reveal rapid early evolution in jawed vertebrates. Syst. Biol. 66, 499–516 (2017).

  45. 45.

    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).

  46. 46.

    Jones, M. et al. Integration of molecules and new fossils supports a Triassic origin for Lepidosauria (lizards, snakes, and tuatara). BMC Evol. Biol. 13, 208 (2013).

  47. 47.

    Hsiang, A. Y. et al. The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record. BMC Evol. Biol. 15, 87 (2015).

  48. 48.

    Inoue, J. G. et al. Evolutionary origin and phylogeny of the modern holocephalans (Chondrichthyes: Chimaeriformes): a mitogenomic perspective. Mol. Biol. Evol. 27, 2576–2586 (2010).

  49. 49.

    Dornburg, A., Townsend, J., Friedman, M. & Near, T. J. Phylogenetic informativeness reconciles ray-finned fish molecular divergence times. BMC Evol. Biol. 14, 169 (2014).

  50. 50.

    Coates, M. I., Gess, R. W., Finarelli, J. A., Criswell, K. E. & Tietjen, K. A symmoriiform chondrichthyan braincase and the origin of chimaeroid fishes. Nature 541, 208–211 (2017).

  51. 51.

    Lourenço, J. M., Claude, J., Galtier, N. & Chiari, Y. Dating cryptodiran nodes: origin and diversification of the turtle superfamily Testudinoidea. Mol. Phylogenet. Evol. 62, 496–507 (2012).

  52. 52.

    Wang, M. et al. The oldest record of Ornithuromorpha from the early Cretaceous of China. Nat. Commun. 6, 6987 (2015).

  53. 53.

    Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).

  54. 54.

    Lartillot, N., Rodrigue, N., Stubbs, D. & Richer, J. PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Syst. Biol. 62, 611–615 (2013).

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Acknowledgements

We thank the following people for tissue samples: T. Ziegler (Andrias), M. Hasselmann (Neoceratodus) and O. Guillaume (Calotriton, Proteus). We thank V. Michael for technical assistance. N. Galtier kindly provided access to the Salamandra transcriptome. We acknowledge the use of computational resources from the University of Konstanz (HPC2), the Institute of Physics of Cantabria IFCA-CSIC (Altamira), the Fédération Wallonie-Bruxelles (Tier-1; funded by Walloon Region, grant no. 1117545), the Consortium des Équipements de Calcul Intensif (CÉCI; funded by FRS-FNRS, grant no. 2.5020.11) and the Réseau Québecois de Calcul de Haute Performance. I.I. was supported by the Alexander von Humboldt Foundation (1150725) and the European Molecular Biology Organization (EMBO ALTF 440-2013). Further support came from the University of Konstanz (I.I.), the Deutsche Forschungsgemeinschaft (DFG) (A.M.), the European Research Council (ERC Advanced Grant ‘Genadapt’ no. 273900 to A.M.) and the Agence Nationale de la Recherche (TULIP Laboratory of Excellence ANR-10-LABX-41 to H.P. and ANR-12-BSV7-020 project ‘Jaws’ to F.D. and J.-Y.S.). This is contribution ISEM 2017-106 of the Institut des Sciences de l’Evolution de Montpellier.

Author information

Affiliations

  1. Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78464, Germany

    • Iker Irisarri
    •  & Axel Meyer
  2. InBioS–Eukaryotic Phylogenomics, Department of Life Sciences and PhytoSYSTEMS, University of Liège, Liège, 4000, Belgium

    • Denis Baurain
  3. Leibniz-Institut DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124, Germany

    • Henner Brinkmann
    •  & Jörn Petersen
  4. Institut des Sciences de l’Evolution, UMR 5554, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, 34095, France

    • Frédéric Delsuc
  5. Institut de Biologie Paris-Seine, UMR7138, Sorbonne Universities, Paris, 75005, France

    • Jean-Yves Sire
  6. Department of Zoology, Stuttgart State Museum of Natural History, Stuttgart, 70191, Germany

    • Alexander Kupfer
  7. Department of Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, 38124, Germany

    • Michael Jarek
  8. Zoological Institute, Braunschweig University of Technology, Braunschweig, 38106, Germany

    • Miguel Vences
  9. Centre for Biodiversity Theory and Modelling, UMR CNRS 5321, Station of Theoretical and Experimental Ecology, Moulis, 09200, France

    • Hervé Philippe
  10. Departement de Biochimie, Université de Montréal, Montréal, QC, H3C3J7, Canada

    • Hervé Philippe
  11. Systematic Biology Program, Department of Organismal Biology, Univeristy of Uppsala, Norbyvägen 18D, Uppsala, 75236, Sweden

    • Iker Irisarri

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Contributions

M.V., H.P. and I.I. designed the research. I.I. F.D., J.-Y.S., A.K., M.J., A.M. and M.V. contributed new data. I.I., D.B., H.B., M.V. and H.P. performed analyses. I.I., M.V. and H.P. drafted the manuscript, and all authors read and approved the final manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Iker Irisarri or Hervé Philippe.

Supplementary information

  1. 1.

    Supplementary Information

    Supplementary Methods, Supplementary Figures 1–19, Supplementary Tables 1–13 and Supplementary References