Fe and Mn K-edge XANES data for ferromanganese oxides mineralization in fossil shark teeth from the Rio Grande Rise (Southwest Atlantic), reference standards and analysis code

Fe and Mn K-edge XANES data for ferromanganese mineralization in fossil shark teeth from the Rio Grande Rise (Southwest Atlantic) and reference standards

Associated manuscript
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Felipe, T. C. et al. "Fossil shark teeth record a microscale pathway for ferromanganese oxide nucleation and Li–Ni enrichment in deep-sea biogenic substrates"
Manuscript published in Scientific Reports (2026). https://doi.org/10.1038/s41598-026-75019-9

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Dataset contents
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This repository contains raw Fe and Mn K-edge XANES measurements collected at the CARNAÚBA beamline of the Sirius synchrotron light source, Brazilian Synchrotron Light Laboratory (LNLS/CNPEM), together with reference-standard measurements used in the XANES analyses reported in the associated manuscript. The deposited files include zipped beamline HDF5 and DAT files, organized into separate sample and reference-standard archives. These data support the manuscript "Fossil shark teeth record a microscale pathway for ferromanganese oxide nucleation and Li–Ni enrichment in deep-sea biogenic substrates" published in Scientific Reports (2026). The reference-standard files contain XANES spectra of known Mn(IV), Mn(III), and Mn(II) reference compounds from the Chemistry Laboratory of the Brazilian Synchrotron Light Laboratory (LNLS-CNPEM), measured at the CARNAÚBA beamline.

The sample spectra contain spectra of mixed-valence manganates, one clay-rich spot and iron oxy(hydroxides) acquired from ferromanganese oxide mineralization preserved within dentin tubules of fossil shark tooth sample RGR4 from the Rio Grande Rise, southwestern Atlantic Ocean. 

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Mn sample spectra

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DAT

1. Three lithiophorite-bearing dentin-tubule spots:
- 20230317_XRFtubulo_zoom_XANESMn_1_Scan0.dat
- 20230317_XRFtubulo_zoom_XANESMn_3_Scan0.dat
- 20230317_XRFtubulo_zoom_XANESMn_3_Scan1.dat
- 20230318_XRFtubulozoom_XanesMn_1_Scan0.dat
- 20230318_XRFtubulozoom_XanesMn_1_Scan1.dat

2. One clay-rich spot:
- 20230318_XRFprocura_XANESMn_4_Scan0.dat

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HDF5

1. Three lithiophorite-bearing dentin-tubule spots:
   - 20230317_XRFtubulo_zoom_XANESMn_1.hdf5
   - 20230317_XRFtubulo_zoom_XANESMn_3.hdf5
   - 20230318_XRFtubulozoom_XanesMn_1.hdf5

2. One clay-rich spot:
   - 20230318_XRFprocura_XANESMn_4.hdf5

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Fe sample spectra
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The Fe K-edge analyses include spectra collected from Fe-rich dentin-tubule domains identified as goethite in sample RGR4, including:

DAT

20230317_XRFtubulo_XanesFe_Scan0.dat
20230317_XRFtubulo_zoom_XANESFe_1_Scan0.dat
20230317_XRFtubulo_zoom_XANESFe_1_Scan1.dat
20230317_XRFtubulo_zoom7_XANESFe_1_Scan0.dat
20230317_XRFtubulo_zoom7_XANESFe_1_Scan1.dat

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HDF5

- 20230317_XRFtubulo_XanesFe.hdf5
- 20230317_XRFtubulo_zoom_XANESFe_1.hdf5
- 20230317_XRFtubulo_zoom7_XANESFe_1.hdf5

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Reference standards
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The repository includes Fe and Mn reference-standard measurements acquired during the same beamtime:

Fe standards

- Fe foil
- FeO
- Fe2O3 / hematite
- goethite
- FeOOH
- magnetite

Mn standards

- Mn foil
- MnO
- Mn2O3
- Mn3O4
- MnO2

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This version of the repository also contains the Python source code used for XANES data reduction, energy calibration, Fe speciation, and Mn average oxidation-state (AOS) analysis reported in the associated manuscript.
The code is organized into six modules: config.py for dataset definition and calibration constants; xas.py for core Fe and Mn K-edge XANES reduction utilities; reduce.py for reduction, energy calibration and normalization; fe_speciation.py for Fe pre-edge analysis and linear-combination fitting; mn_db.py for Mn reference-database handling and Combo-fit routines; and mn_aos.py for Mn AOS analysis using derivative Combo-fit and normalized-spectrum linear-combination fitting.
A README.md file documents the required directory structure, dependencies, external reference database, execution order, and generated outputs. A requirements.txt file is also provided.
Data reduction and oxidation-state analysis were carried out in Python 3.12 using NumPy, SciPy, and xraydb. Matplotlib was used for figure generation. Claude was used to assist in developing and executing the Python-based computational workflow used for XANES data processing and fitting.
Mn AOS analysis uses the manganese K-edge reference database of Manceau et al. (2024), available separately at DOI 10.57745/ZW6KTP, and applies the derivative Combo-fit approach described by Manceau, Marcus & Grangeon (2012), together with normalized-spectrum linear-combination fitting.

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Data access
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The data and analysis code are publicly available under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.

Citation
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Please cite both the associated article and this Zenodo dataset when using these data.

Contact
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Thales C. Felipe
Oceanographic Institute, University of São Paulo (IO-USP)
E-mail: thales.felipe@usp.br