Code and data associated with the article "Increasing control or biomineralization in conodont evolution"

Shirley, B., Leonhard, I., Murdock, D.J., Repetski, J., Świś, P., Bestmann, M., Trimby, P., Ohl, M., Plümper, O., King, H.E. and Jarochowska, E., 2024. Increasing control over biomineralization in conodont evolution. Nature Communications, 15(1), p.5273.

Authors

Bryan Shirley
Formerly: Utrecht University (2022-2023) and Fachgruppe Paläoumwelt, Friedrich-Alexander-Universität Erlangen-Nürnberg (2019-2022)
Current address: Carl Zeiss Ltd., Cambridge, UK
email: bryan.shirley [at] zeiss.com
ORCID: 0000-0002-8532-3890

Isabella Leonhard
Department of Palaeontology, Universität Wien
Formerly: Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw
email: isabella.leonhard [at] univie.ac.at

Duncan Murdock
Oxford University Museum of Natural History
email: duncan.murdock [at] oum.ox.ac.uk

John Repetski
US Geological Survey-Emeritus email: jrepetski [at] cox.net

Przemysław Świś
Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw
Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
email: swis.przemyslaw [at] gmail.com

Michel Bestmann
Department of Geology, Universität Wien
email: michel.bestmann [at] univie.ac.at

Pat Trimby
Formerly: Oxford Instruments, High Wycombe, UK
Current address: Carl Zeiss Ltd., Cambridge, UK
email: patrick.trimby [at] zeiss.com

Markus Ohl
Formerly: Utrecht University

Oliver Plümper
Utrecht University
email: O.Plumper [at] uu.nl

Helen King
Utrecht University
email: H.E.King [at] uu.nl

Emilia Jarochowska (maintainer)
Utrecht University
Formerly: Fachgruppe Paläoumwelt, Friedrich-Alexander-Universität Erlangen-Nürnberg
email: e.b.jarochowska [at] uu.nl
Web page: www.uu.nl/staff/EBJarochowska
ORCID: 0000-0001-8937-9405

Running instructions

EBSD datasets: Importing, postprocessing, plotting and calculations

Detailed instructions are in Conodont_Mtex_scripts/INSTRUCTION.md. In this step, datasets required for reproducing plots and tables used in the manuscript are produced. Datasets produced are also provided here as ready files, for users with no access to Matlab. Users without Matlab can reproduce the analysis of EBSD results by using R Studio:

Comparison of methods used to quantify crystallographic textures

In R Studio, run Texture methods comparison/Testing_Quant_Methods_extended.Rmd. It will download the data produced in Matlab, generate the plots and regression results presented in the manuscript. Run time on MacOS Sonoma 14.2.1 with 8 GB RAM: 9 s.

Analysis and plotting of Raman spectroscopy data

In R or R Studio, run Raman.R. It will download the data produced in Matlab, generate the plots and regression results presented in the manuscript. Run time on MacOS Sonoma 14.2.1 with 8 GB RAM: 8 s.

Dependencies

For manipulating EBSD data:

• MTEX 5.9, which uses the NFFT library
• MATLAB; the code was written in version 2023a

For plotting and calculations on datasets output from Matlab:

• R Software; the code was written in version 4.3.0
• R Studio, we used 2023.12.0
• Packages:
  • ggplot2 3.4.2
  • ggpubr 0.6.0
  • lmodel2 1.7-3
  • utils 4.3.1
  • osfr 0.2.9
  • knitr 1.42

The code has been tested and ran on Windows 10 and MacOS Sonoma 14.2.1. The loading and installation time were below 2 min for Matlab and instantaneous for all

Credits:

• R Core Team (2023). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/.
• Kassambara A (2023). ggpubr: 'ggplot2' Based Publication Ready Plots. R package version 0.6.0, https://CRAN.R-project.org/package=ggpubr.
• Legendre P (2018). lmodel2: Model II Regression. R package version 1.7-3, https://CRAN.R-project.org/package=lmodel2.
• H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.
• Wolen et al., (2020). osfr: An R Interface to the Open Science Framework. Journal of Open Source Software, 5(46), 2071, https://doi.org/10.21105/joss.02071

Citation

Shirley, B., Leonhard, I., Murdock, D.J.E., Repetski, J.E., Świś, P., Bestmann, M., Trimby, P., Ohl, M., Plümper, O., King, H., and Jarochowska, E., 2024, Code for Increasing control over biomineralization in conodont evolution: https://github.com/BryanShirl/Conodont_Crystals. https://github.com/BryanShirl/Conodont_Crystals/

@code{shirley_code_2024,
	title = {Code for Increasing control over biomineralization in conodont evolution},
	url = {https://github.com/BryanShirl/Conodont_Crystals},
	author = {Shirley, Bryan and Leonhard, Isabella and Murdock, Duncan J. E. and Repetski, John E. and Świś, Przemysław and Bestmann, Michel and Trimby, Pat and Ohl, Markus and Plümper, Oliver and King, Helen and Jarochowska, E.},
	year = {2024},
}

License

Code: Apache 2.0 License, see LICENSE file for license text.

Data: Creative Commons CC BY-SA 4.0 Attribution-ShareAlike 4.0 International

You are free to:

• Share — copy and redistribute the material in any medium or format for any purpose, even commercially.
• Adapt — remix, transform, and build upon the material for any purpose, even commercially.

Under the following terms:

• Attribution - You must give appropriate credit , provide a link to the license, and indicate if changes were made . You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
• ShareAlike - If you remix, transform, or build upon the material, you must distribute your contributions under the same license as the original.

Funding

• Deutsche Froschungsgemeinschaft grant to Emilia Jarochowska (project JA 2718/3-1)
• DAAD Scholarship to Bryan Shirley
• This publication results from work carried out under Trans-National Access action under the support of EXCITE - EC- HORIZON 2020 -INFRAIA 2020 Integrating Activities for Starting Communities under grant agreement N.101005611