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Preservation of corneous β-proteins in Mesozoic feathers

Nature Ecology & Evolution volume 7, pages 1706–1713 (2023)Cite this article

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Abstract

Fossil proteins are valuable tools in evolutionary biology. Recent technological advances and better integration of experimental methods have confirmed the feasibility of biomolecular preservation in deep time, yielding new insights into the timing of key evolutionary transitions. Keratins (formerly α-keratins) and corneous β-proteins (CBPs, formerly β-keratins) are of particular interest as they define tissue structures that underpin fundamental physiological and ecological strategies and have the potential to inform on the molecular evolution of the vertebrate integument. Reports of CBPs in Mesozoic fossils, however, appear to conflict with experimental evidence for CBP degradation during fossilization. Further, the recent model for molecular modification of feather chemistry during the dinosaur–bird transition does not consider the relative preservation potential of different feather proteins. Here we use controlled taphonomic experiments coupled with infrared and sulfur X-ray spectroscopy to show that the dominant β-sheet structure of CBPs is progressively altered to α-helices with increasing temperature, suggesting that (α-)keratins and α-helices in fossil feathers are most likely artefacts of fossilization. Our analyses of fossil feathers shows that this process is independent of geological age, as even Cenozoic feathers can comprise primarily α-helices and disordered structures. Critically, our experiments show that feather CBPs can survive moderate thermal maturation. As predicted by our experiments, analyses of Mesozoic feathers confirm that evidence of feather CBPs can persist through deep time.

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Fig. 1: Photographs of fossil specimens used in this study.
Fig. 2: Sulfur-XANES spectra for fossil feathers and untreated and experimentally degraded white (E. garzetta) and black (G. gallus) feathers.
Fig. 3: FTIR spectra for fossil feathers and untreated and experimentally degraded white (E. garzetta) and black (G. gallus) feathers.
Fig. 4: Deconvolution of the amide I + II region in FTIR data.
Fig. 5: Schematic representation of the hierarchical structure of feather CBPs and a taphonomic model for their degradation during fossilization.

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Data availability

Source data can be found on the Zenodo repository at https://doi.org/10.5281/zenodo.8161216.

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Acknowledgements

We thank S. Bone, V. Rossi, C. Rogers, T. Clements, L. McDonald and N. O’Reilly for assistance and V. Rhue for access to fossil material. Fossil soft tissue samples were collected and exported in a responsible manner and in accordance with relevant permits. This work was supported by European Research Council (ERC) Starting Grant H2020-ERC-2014-StG-637691-ANICOLEVO and ERC Consolidator Grant H2020-ERC-COG-101003293-Palaeochem awarded to M.E.M. and Irish Research Council (IRC) New Foundations awarded to T.S.S. Use of the Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory, is supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences under contract number DE-AC02-76SF00515. The SSRL Structural Molecular Biology Program is supported by the US Department of Energy Office of Biological and Environmental Research and by the National Institutes of Health, National Institute of General Medical Sciences (P30GM133894). The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of National Institute of General Medical Sciences or National Institutes of Health. SSRL beamtime was awarded under proposals SSRL-4274 and SSRL-5072 to M.E.M. and SSRL-5557 to T.S.S.

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Authors and Affiliations

  1. School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland

    Tiffany S. Slater & Maria E. McNamara

  2. Environmental Research Institute, University College Cork, Cork, Ireland

    Tiffany S. Slater & Maria E. McNamara

  3. Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA

    Nicholas P. Edwards & Samuel M. Webb

  4. Institute of Geology and Paleontology, Linyi University, Linyi, China

    Fucheng Zhang

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Contributions

M.E.M. and T.S.S. conceived the research and designed the study. T.S.S. and M.E.M. collected sulfur-XANES data with assistance from N.P.E., S.M.W. and F.Z.; T.S.S. collected FTIR data and processed and interpreted all spectral data. T.S.S. and M.E.M. wrote the manuscript with input from all other authors.

Corresponding authors

Correspondence to Tiffany S. Slater or Maria E. McNamara.

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Nature Ecology & Evolution thanks Quanguo Li, Liliana D’Alba and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Sulfur-XANES data for the sedimentary matrix of the fossil feathers analysed.

The low signal: noise ratio in spectra of host sediments reflects low sulfur concentrations in the sample. Spectra of fossil feathers are shown in grey; spectra for sedimentary matrix, in black. Data shown for sediment and Confuciusornis feather tissue are each from one spectrum; data for Sinornithosaurus and the Green River feather represent an average of three spectra.

Extended Data Fig. 2 FTIR data for the sedimentary matrix of the fossil feathers analysed.

Spectra for fossil feathers are shown in grey; spectra for sedimentary matrix, in black. The data shown for the Green River feather represent a Type 2 spectrum. Data shown represent an average of four spectra for Confuciusornis and Sinornithosaurus feather tissue, an average of three spectra for Sinornithosaurus host sediment, an average of two spectra for Green River feather host sediment and one spectrum each for Confuciusornis host sediment and Green River feather tissue.

Extended Data Fig. 3 Deconvolution of amide I and II regions in FTIR spectra of the sedimentary matrix associated with fossil feathers.

a, Green River feather (YPM VP 58657). b, Confuciusornis (IVPP V 13171). c, Sinornithosaurus (IVPP V 12811). The wavenumber (cm−1) on the x-axis differs slightly among spectra. Data shown represent an average of three spectra for Sinornithosaurus host sediment, an average of two spectra for Green River feather host sediment and one spectrum for Confuciusornis host sediment.

Extended Data Fig. 4

Sulfur-XANES data for analytical standards of selected S-bearing compounds.

Extended Data Fig. 5 SEM image of a transverse cross section of a feather barbule (Gallus gallus) matured at 200 °C.

Voids indicate the former positions of melanosomes; n = 3.

Extended Data Table 1 FTIR peak assignments for untreated and experimentally degraded black (Gallus gallus) and white (Egretta garzetta) feathers, fossil feathers and host sediment
Full size table
Extended Data Table 2 Deconvolution peak assignments for the amide region of spectra from untreated and experimentally degraded black (Gallus gallus) and white (Egretta garzetta) feathers, fossil feathers and sedimentary matrix
Full size table
Extended Data Table 3 Sulfur-XANES white line energies, oxidation state and chemical nature of analytical standards for selected S-bearing compounds
Full size table
Extended Data Table 4 Measurements of cortex thickness in feather barbules (Gallus gallus) matured at 200 °C
Full size table

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Slater, T.S., Edwards, N.P., Webb, S.M. et al. Preservation of corneous β-proteins in Mesozoic feathers. Nat Ecol Evol 7, 1706–1713 (2023). https://doi.org/10.1038/s41559-023-02177-8

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