DOI: 10.5061/dryad.51c59zwn4
title: Multi-isotope analysis of mammal bones provides environmental context for the adoption of agriculture in the Tehuacan Valley of Mexico

description: 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.
description: # Multi-isotope analysis of mammal bones provides environmental context
 for the adoption of agriculture in the Tehuacan Valley of Mexico Dataset
 DOI: [10.5061/dryad.51c59zwn4](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`.