Molecular signatures of fossil leaves provide unexpected new evidence for extinct plant relationships

Abstract

Gene sequences form the primary basis for understanding the relationships among extant plant groups, but genetic data are unavailable from fossils to evaluate the affinities of extinct taxa. Here we show that geothermally resistant fossil cuticles of seed-bearing plants, analysed with Fourier transform infrared (FTIR) spectroscopy and hierarchical cluster analysis (HCA), retain biomolecular suites that consistently distinguish major taxa even after experiencing different diagenetic histories. Our results reveal that similarities between the cuticular biochemical signatures of major plant groups (extant and fossil) are mostly consistent with recent phylogenetic hypotheses based on molecular and morphological data. Our novel chemotaxonomic data also support the hypothesis that the extinct Nilssoniales and Bennettitales are closely allied, but only distantly related to Cycadales. The chemical signature of the cuticle of Czekanowskia (Leptostrobales) is strongly similar to that of Ginkgo leaves and supports a close evolutionary relationship between these groups. Finally, our results also reveal that the extinct putative araucariacean, Allocladus, when analysed through HCA, is grouped closer to Ginkgoales than to conifers. Thus, in the absence of modern relatives yielding molecular information, FTIR spectroscopy provides valuable proxy biochemical data complementing morphological characters to distinguish fossil taxa and to help elucidate extinct plant relationships.

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References

  1. 1.

    Lindgren, J. et al. Molecular preservation of the pigment melanin in fossil melanosomes. Nat. Commun. 3, 824 (2012).

    Article  PubMed  Google Scholar 

  2. 2.

    Lindgren, J. et al. Skin pigmentation provides evidence of convergent melanism in extinct marine reptiles. Nature 506, 484–488 (2014).

    CAS  Article  PubMed  Google Scholar 

  3. 3.

    van Bergen, P. F. et al. Resistant biomacromolecules in the fossil record. Acta Bot. Neerl. 44, 319–342 (1995).

    Article  Google Scholar 

  4. 4.

    Mösle, B., Finch, P., Collinson, M. E. & Scott, A. C. Comparison of modern and fossil plant cuticles by selective chemical extraction monitored by flash pyrolysis–gas chromatography–mass spectrometry and electron microscopy. J. Anal. Appl. Pyrol. 40–41, 585–597 (1997).

    Article  Google Scholar 

  5. 5.

    Mösle, B. et al. Factors influencing the preservation of plant cuticles: a comparison of morphology and chemical composition of modern and fossil examples. Org. Geochem. 29, 1369–1380 (1998).

    Article  Google Scholar 

  6. 6.

    Gupta, N. S., Collinson, M. E., Briggs, D. E. G., Evershed, R. P. & Pancost, R. D. Reinvestigation of the occurrence of cutan in plants: implications for the leaf fossil record. Paleobiol. 32, 432–449 (2006).

    Article  Google Scholar 

  7. 7.

    de Leeuw, J. W., Versteegh, G. J. M. & van Bergen, P. F. Biomacromolecules of algae and plants and their fossil analogues. Plant Ecol. 182, 209–233 (2006).

    Article  Google Scholar 

  8. 8.

    Amijaya, H., Schwarzbauer, J. & Littke, R. Organic geochemistry of the Lower Suban coal seam, South Sumatra Basin, Indonesia: palaeoecological and thermal metamorphism implications. Org. Geochem. 37, 261–279 (2006).

    CAS  Article  Google Scholar 

  9. 9.

    Lara, I., Belge, B. & Goulao, L. F. A focus on the biosynthesis and composition of cuticle in fruits. J. Agric. Food Chem. 63, 4005–4019 (2015).

    CAS  Article  PubMed  Google Scholar 

  10. 10.

    Versteegh, G. J. M. & Riboulleau, A. An organic geochemical perspective on terrestrialization. Geol. Soc. Spec. Publ. 339, 11–36 (2010).

    Article  Google Scholar 

  11. 11.

    Crane, P. R. Phylogenetic analysis of seed plants and the origin of angiosperms. Ann. Mo. Bot. Gard. 72, 716–793 (1985).

    Article  Google Scholar 

  12. 12.

    Hilton, J. & Bateman, R. M. Pteridosperms are the backbone of seed-plant phylogeny. J. Torrey Bot. Soc. 133, 119–168 (2006).

    Article  Google Scholar 

  13. 13.

    Doyle, J. A. Seed ferns and the origin of angiosperms. J. Torrey Bot. Soc. 133, 169–209 (2006).

    Article  Google Scholar 

  14. 14.

    Briggs, D. E. G. Molecular taphonomy of animal and plant cuticles: selective preservation and diagenesis. Phil. Trans. R. Soc. Lond. B 354, 7–17 (1999).

    CAS  Article  Google Scholar 

  15. 15.

    Hatcher, P. G., Wilson, M. A., Vassallo, A. M. & Lerch, H. E. III. Studies of angiospermous wood in Australian brown coal by nuclear magnetic resonance and analytical pyrolysis: new insights into the early coalification process. Int. J. Coal Geol. 13, 99–126 (1989).

    CAS  Article  Google Scholar 

  16. 16.

    Qu, Y., Engdahl, A., Zhu, S., Vajda, V. & McLoughlin, N. Ultrastructural heterogeneity of carbonaceous material in ancient cherts: investigating biosignature origin and preservation. Astrobiology 15, 825–842 (2015).

    CAS  Article  PubMed  Google Scholar 

  17. 17.

    Heredia-Guerrero, J. A. et al. Infrared and Raman spectroscopic features of plant cuticles: a review. Front. Plant Sci. 5, 305 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  18. 18.

    Alencar, W. J. et al. Spectroscopic analysis and X-ray diffraction of trunk fossils from the Parnaíba Basin, northeast Brazil. Spectrochim. Acta A Mol. Biomol. Spectrosc 135, 1052–1058 (2014).

    Article  PubMed  Google Scholar 

  19. 19.

    Bomfleur, B., McLoughlin, S. & Vajda, V. Fossilized nuclei and chromosomes reveal 180 million years of genomic stasis in royal ferns. Science 343, 1376–1377 (2014).

    CAS  Article  PubMed  Google Scholar 

  20. 20.

    Boyce, C. K. et al. Organic chemical differentiation within fossil plant cell walls detected with X-ray spectromicroscopy. Geology 30, 1039–1042 (2002).

    CAS  Article  Google Scholar 

  21. 21.

    D’Angelo, J. A., Zodrow, E. L. & Camargo, A. Chemometric study of functional groups in Pennsylvanian gymnosperm plant organs (Sydney Coalfield, Canada): implications for chemotaxonomy and assessment of kerogen formation. Org. Geochem. 41, 1312–1325 (2010).

    Article  Google Scholar 

  22. 22.

    D’Angelo, J. A. & Zodrow, E. L. Chemometric study of functional groups in different layers of Trigonocarpus grandis ovules (Pennsylvanian seed fern, Canada). Org. Geochem. 42, 1039–1054 (2011).

    Article  Google Scholar 

  23. 23.

    D’Angelo, J. A. & Zodrow, E. L. Chemometric study of structural groups in medullosalean foliage (Carboniferous, fossil Lagerstätte, Canada): chemotaxonomic implications. Int. J. Coal Geol. 138, 42–54 (2015).

    Article  Google Scholar 

  24. 24.

    Lomax, B. H. et al. A novel palaeoaltimetry proxy based on spore and pollen wall chemistry. Earth Planet. Sci. Lett. 353–354, 22–28 (2012).

    Article  Google Scholar 

  25. 25.

    Steemans, P., Lepot, K., Marshall, C. P., Le Hérissé, A. & Javaux, E. J. FTIR characterisation of the chemical composition of Silurian miospores (cryptospores and trilete spores) from Gotland, Sweden. Rev. Palaeobot. Palynol. 162, 577–590 (2010).

    Article  Google Scholar 

  26. 26.

    Seyfullah, L. J., Sadowski, E.-M. & Schmidt, A. Species-level determination of closely related araucarian resins using FTIR spectroscopy and its implications for the provenance of New Zealand amber. Peer J. 3, e1067 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  27. 27.

    Lu, H.-F., Shen, J.-B., Lin, X.-Y. & Fu, J.-L. Relevance of fourier transform infrared spectroscopy and leaf anatomy for species classification in Camellia (Theaceae). Taxon 57, 1274–1288 (2008).

    Google Scholar 

  28. 28.

    Zimmermann, B. & Kohler, A. Infrared spectroscopy of pollen identifies plant species and genus as well as environmental conditions. PLoS ONE 9, e95417 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  29. 29.

    Niklas, K. J. & Gensel, P. G. Chemotaxonomy of some Paleozoic vascular plants. Part II: chemical characterization of major plant groups. Brittonia 29, 100–111 (1977).

    CAS  Article  Google Scholar 

  30. 30.

    Jones, W. G., Hill, K. D. & Allen, J. M. Wollemia nobilis, a new living Australian genus and species in the Araucariaceae. Telopea (Syd.) 6, 173–176 (1995).

    Article  Google Scholar 

  31. 31.

    Escapa, I. H. & Catalano, S. A. Phylogenetic analysis of Araucariaceae: integrating molecules, morphology, and fossils. Int. J. Plant Sci. 174, 1153–1170 (2013).

    Article  Google Scholar 

  32. 32.

    Hermsen, E. J., Taylor, T. N., Taylor, E. L. & Stevenson, D. W. Cataphylls of the Middle Triassic cycad Antarcticycas schopfii and new insights into cycad evolution. Am. J. Bot. 93, 724–738 (2006).

    Article  PubMed  Google Scholar 

  33. 33.

    Chaw, S.-M., Parkinson, C. L., Cheng, Y., Vincent, T. M. & Palmer, J. D. Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers. Proc. Natl Acad. Sci. USA 97, 4086–4091 (2000).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  34. 34.

    Morris, J. Remarks upon the recent and fossil cycadaceae. Ann. Mag. Nat. Hist. 7, 110–120 (1841).

    Google Scholar 

  35. 35.

    Delevoryas, T. Investigations of North American cycadeoids: cones of cycadeoidea. Am. J. Bot. 50, 45–52 (1963).

    Article  Google Scholar 

  36. 36.

    Kimura, T. & Sekido, S. Nilssoniocladus n. gen. (Nilssoniaceae, n. fam.), newly found from the early Lower Cretaceous of Japan. Palaeontographica B 153, 111–118 (1975).

    Google Scholar 

  37. 37.

    Pott, C., McLoughlin, S., Lindström, A., Wu, S.-Q. & Friis, E. M. Baikalophyllum lobatum and Rehezamites anisolobus: two seed plants with “cycadophyte” foliage from the Early Cretaceous of Eastern Asia. Int. J. Plant Sci. 173, 192–208 (2012).

    Article  Google Scholar 

  38. 38.

    Kustatscher, E. & van Konijenburg-van Cittert, J. H. A. Taxonomical and palaeogeographic considerations on the seedfern genus Ptilozamites with some comments on Anomozamites, Dicroidium, Pseudoctenis and Ctenozamites. Neues Jahrb. Geol. Paläontol. Abh. 243, 71–100 (2007).

    Article  Google Scholar 

  39. 39.

    Rees, P. M., Ziegler, A. M. & Valdes, P. J. Warm Climates in Earth History (eds Huber, B. T., Macleod, K. G. & Wing, S. L.) (Cambridge Univ. Press, 2000).

  40. 40.

    Liu, X.-Q., Li, C.-S. & Wang, Y.-F. Plants of Leptostrobus Heer (Czekanowskiales) from the Early Cretaceous and Late Triassic of China, with discussion of the genus. J. Integr. Plant Biol. 48, 137–147 (2006).

    Article  Google Scholar 

  41. 41.

    Chaw, S. M., Zharkikh, A., Sung, H. M., Lau, T. C. & Li, W. H. Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences. Mol. Biol. Evol. 14, 56–68 (1997).

    CAS  Article  PubMed  Google Scholar 

  42. 42.

    Ruhfel, B. R., Gitzendanner, M. A., Soltis, P. S., Soltis, D. E. & Burleigh, J. G. From algae to angiosperms—inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evol. Biol. 14, 23 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  43. 43.

    Wu, C.-S., Chaw, S.-M. & Huang, Y.-Y. Chloroplast phylogenomics indicates that Ginkgo biloba is sister to cycads. Genome Biol. Evol. 5, 243–254 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  44. 44.

    Wickett, N. J. et al. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc. Natl Acad. Sci. USA 111, E4859–E4868 (2014).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  45. 45.

    Jansson, I.-M., McLoughlin, S., Vajda, V. & Pole, M. An Early Jurassic flora from the Clarence-Moreton Basin, Australia. Rev. Palaeobot. Palynol. 150, 5–21 (2008).

    Article  Google Scholar 

  46. 46.

    Pattemore, G. A., Rigby, J. F. & Playford, G. Palissya: a global review and reassessment of eastern Gondwanan material. Rev. Palaeobot. Palynol. 210, 50–61 (2014).

    Article  Google Scholar 

  47. 47.

    Baker, M. J. et al. Using fourier transform IR spectroscopy to analyze biological materials. Nat. Protoc. 9, 1771–1791 (2014).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  48. 48.

    Madejová, J. & Komadel, P. Baseline studies of the clay minerals society source clays: infrared methods. Clays Clay Miner. 49, 410–432 (2001).

    Article  Google Scholar 

  49. 49.

    Domenighini, A. & Giordano, M. Fourier transform infrared spectroscopy of microalgae as a novel tool for biodiversity studies, species identification, and the assessment of water quality. J. Phycol. 45, 522–531 (2009).

    CAS  Article  PubMed  Google Scholar 

  50. 50.

    Bar-Joseph, Z., Gifford, D. K. & Jaakkola, T. S. Fast optimal leaf ordering for hierarchical clustering. Bioinformatics 17, S22–S29 (2001).

    Article  PubMed  Google Scholar 

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Acknowledgements

This research was financially supported by grants from Lund University, faculty funding for synchrotron-light-related projects for ESS and MAX IV to V.V., the Swedish Research Council (VR grant 2015-4264 to V.V., and VR grant 2014-5234 to S.M.), This research was further funded by the Swedish Research Council (VR) under grant LUCCI (Lund University Carbon Cycle Centre) and the Utrecht Network Young researchers’ grant to M.P. We thank the Botanical Garden of Lund University, Sweden for giving permission to sample plant leaves; M. Pole (Nanjing Institute of Geology and Paleontology, Nanjing, China) for providing fossil cuticles from New Zealand and Svend Visby Funder (Centre for GeoGenetics, Natural History Museum, Copenhagen, Denmark) for giving access to T. M. Harris’ fossil collections.

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V.V. and P.U. conceived and led the project, V.V. and S.M. recovered and prepared fossil cuticles, V.V. collected the modern cuticles. M.P., V.V. and A.E. carried out FTIR spectroscopy measurements, A.E., P.U. and J.H. provided expertise in infrared spectroscopy. Spectral analysis was performed by M.P., P.U. and J.H.S. All authors contributed to writing the paper.

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Correspondence to Vivi Vajda or Per Uvdal.

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1 Supplementary Table, 4 Supplementary Figures, Supplementary References and Supplementary details of analysis

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Vajda, V., Pucetaite, M., McLoughlin, S. et al. Molecular signatures of fossil leaves provide unexpected new evidence for extinct plant relationships. Nat Ecol Evol 1, 1093–1099 (2017). https://doi.org/10.1038/s41559-017-0224-5

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