Multi-isotope analysis of mammal bones provides environmental context for the adoption of agriculture in the Tehuacan Valley of Mexico
Data files
Feb 21, 2026 version files 118.75 KB
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Data_S2.csv
26.40 KB
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Lat_Long_data_fauna_20250113.csv
20.83 KB
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MixSIAR_Paleoenvironment_20250818.R
3.07 KB
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README.md
4.79 KB
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SOURCE_IDEAL.csv
199 B
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Tables_stats_graphs_20260220.qmd
60.57 KB
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Tehuacan_Isotopes_GAM_01_30_25.Rmd
2.90 KB
Feb 24, 2026 version files 118.76 KB
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Data_S2.csv
26.40 KB
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Lat_Long_data_fauna_20250113.csv
20.83 KB
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MixSIAR_Paleoenvironment_20260220.R
3.06 KB
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README.md
4.79 KB
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SOURCE_IDEAL.csv
199 B
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Tables_stats_graphs_20260220.qmd
60.59 KB
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Tehuacan_Isotopes_GAM_01_30_25.Rmd
2.90 KB
Abstract
Understanding the environmental context in which agriculture emerged requires proxy records that capture local ecological conditions through time, yet long-term datasets from archaeologically well-dated contexts remain limited. We generated stable isotope measurements from archaeological faunal remains spanning the Late Pleistocene through Late Holocene sequence of the Tehuacan Valley of Puebla, Mexico, including deer (Odocoileus virginianus) and rabbit (Sylvilagus spp.) specimens recovered from multiple sites and cultural phases within the valley. The dataset includes δ13C and δ18O values from bone bioapatite and δ13C and δ15N values from bone collagen, together with specimen metadata, archaeological context information, and indicators of skeletal preservation and diagenesis used to assess data quality.
To facilitate interpretation and reproducibility, the repository also contains analytical workflows used to evaluate temporal variation in isotope values, including generalized additive modeling and a Bayesian stable isotope mixing approach used to estimate environmental composition through time. Reference isotope values for modeled environmental categories are provided to support replication and comparative applications. The data document temporal variation in vegetation structure and moisture conditions across major cultural transitions in the region and provide a comparative baseline for paleoenvironmental reconstruction and zooarchaeological research in other archaeological and ecological settings. All specimens derive from curated collections in Mexico that were analyzed with appropriate institutional permissions, and no sensitive information is included.
Dataset DOI: 10.5061/dryad.51c59zwn4
Description of the data and file structure
The submitted data file (Data S2.csv) includes the stable isotope values of deer and rabbit bones from archaeological sites within the Tehuacan Valley of Puebla, Mexico. Contextual and diagenesis information are presented in the data file alongside the isotopic data. Also included in the repository are the R scripts used to generate the images for publication and perform the statistical analyses of the data (see file Tables_stats_graphs_20260220.qmd). The code used to build the general additive models (GAM) to explore variation within the isotope values is presented in the file Tehuacan_Isotope_GAM_01_30_25.Rmd. The GAM script runs the locational and isotopic data that are presented in the file Lat_Long_data_fauna_20250113.csv. Finally, the script used to generate the Bayesian stable isotope mixing model with the MixSIAR package is included (MixSIAR_Paleoenvironment_20260220.R). In support of the isotope mixing model, a data table (SOURCE_IDEAL.csv) is included that specifies the expected isotope ratios of idealized environmental types (forest, desert, grassland) in rabbit bones. Cells are left empty if they interfere with a script or values not determined.
Files and variables
File: Data_S2.csv
Description:
This file contains the stable isotope data and diagenesis data generated by the research project from the analysis of deer and rabbit bones from the Tehuacan Valley of Puebla, Mexico. The data are presented alongside the contextual and temporal information of each bone.
Variables
- Specimen: Unique identifier of each specimen.
- Site_code: Unique identifier for each site location within the Tehuacan Valley.
- Site name: The name of each archaeological site from which mammal bones were sampled.
- Phase: The cultural phase associated with each bone sample. Phase designations were based on associated material culture, radiocarbon dates, and Bayesian modeling.
- Phase_code: Numerical code designating each cultural phase.
- Orientation: General spatial location within an archaeological site.
- Zone: Stratigraphic level of excavation.
- Prov_1: Provenience information associated with the bone sample.
- Prov_2: Additional provenience information associated with the bone sample.
- Animal: Common name for animal.
- Genus: Genus name of each animal.
- Species: Species-level taxonomic identification.
- Bone: Designating which skeletal element was sampled for analysis.
- Bone side: Anatomical left or right.
- Bone part: Specifying which part of the bone was sampled.
- Notes: Additional information.
- d13C: Stable carbon isotope (‰) value from bone apatite.
- d18O: Stable oxygen isotope (‰) value from bone apatite.
- d15N: Stable nitrogen isotope (‰) value from bone collagen.
- d13Ccol: Stable carbon isotope (‰) value from bone collagen.
- per_N: N%
- per_C: C%
- CN: Atomic ratio of C/N.
- FTIR_IR-SF: Infrared splitting factor value from Fourier transform infrared spectroscopy.
- FTIR_CP: Carbonate to phosphate ratio from Fourier transform infrared spectroscopy.
File: Tables_stats_graphs_20260220.qmd
Description: R scripts used for statistical analysis and to generate graphs for publication. The qmd file can be run and viewed in RStudio.
File: Tehuacan_Isotopes_GAM_01_30_25.Rmd
Description: R scripts to explore the patterning within the isotope data and run general additive models. The file should be run and viewed in RStudio.
File: Lat_Long_data_faun_20250113.csv
Description: This is the data file that includes the latitude, longitude, elevation (in m) and phase data for each site, in addition to the isotopic data for each specimen. These data were used in the general additive models that are run in the associated R script, "General_additive_models.Rmd".
File: MixSIAR_Paleoenvironment_20260220.R
Description: R code used to create a Bayesian stable isotope mixing model from rabbit bones using the MixSIAR package. The model can be run and viewed in R or RStudio.
File: SOURCE_IDEAL.csv
Description: A data table that specifies the expected stable isotope values (means and standard deviations) from rabbit bone collagen and apatite from idealized environmental types, including deserts, forests, and grasslands.
Code/software
Software requirements
- R (≥ 4.3.0)
- R packages (see
library()calls in theRmd and .qmd files), including but not limited to:
tidyverse,mgcv,ggplot2,ggpubr,viridis,dplyr,readr,knitr,quarto, MixSIAR.
Changes after Feb 21, 2026:
Uploaded a newer version of Table_stats_graphs_20260220.qmd. The new version now states that the file was last updated on February 20, 2026, replacing an older date of update.
Uploaded MixSIAR_Paleoenvironment_20260220.R, which replaced MixSIAR_Paleoenvironment_20250828.R. The new version includes the reference to Data S2.csv, instead of an older name of this file (Consumer_20250130.csv). This change was made to be consistent with the name of the primary data file for the manuscript and statistical analyses.