Data from: Preservation of stable isotope niche dynamics in squamate museum specimens
Data files
May 15, 2026 version files 51.10 KB
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ebv_isotope_data_ALL.csv
34.20 KB
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ebv_museum_metaData.csv
4.43 KB
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MVZ_thamnophis_isotopes.csv
2.23 KB
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README.md
3.56 KB
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RNAlater_bias_correction_data.csv
6.68 KB
Abstract
Natural history museums are invaluable resources for large-scale ecological and evolutionary studies, but certain ecological traits can be challenging to recover, particularly from fluid preserved specimens. Stable isotope analysis is an elegant method for reconstructing the dietary niche over integrated timescales, and recovering this information from museum specimens can provide a critical axis of ecological information for studies of population dynamics through time and space. However, isotope ratios of tissues are known to be altered by extended contact with formalin and ethanol. Here, we assess whether intra- and interspecific variation in isotopic signature, which represent critical data used to assess metrics of niche diversity, can be reliably recovered following fluid preservation. We use a broad taxonomic distribution of squamates to compare niche metrics prior to and eight weeks following a standard museum preservation process. We could not recover intraindividual metrics of niche diversity but found that between-individual variation was not significantly altered, allowing for the reconstruction of community niche characteristics. We present an example isotopic analysis from museum specimens representing generalist and specialist Thamnophis garter snake populations that aligns with empirical estimates of niche width. We also present several additional analyses on tissue-specific effects, delipification, and buffer storage, with useful insights for field collection and downstream analysis decisions.
Dataset DOI: 10.5061/dryad.k98sf7mmr
Description of the data and file structure
The provided data files represent carbon and nitrogen stable isotope ratios from animal tissues that were flash frozen or stored in RNAlater salt buffer.
Files and variables
File: ebv_museum_metaData.csv
Description: Metadata for East Bay Vivarium squamate specimens including Museum of Vertebrate Zoology accession numbers.
Variables
- sample_ID: identification given to the specimen for use in the study
- museum_ID: accession number given to the specimen for housing at the Museum of Vertebrate Zoology
- genus: genus of the specimen
- species: species of the specimen
- ebv_diet: diet items fed to specimen while alive at the East Bay Vivarium
- SVL (mm): snout-vent length of specimen in millimeters
- tail (mm): tail length of specimen in millimeters
- weight (g): weight of specimen in grams following thawing
- donation_date: date specimen was donated to the MVZ (format: MM/DD/YYYY or YYYY)
- location_found: location data used by MVZ
- date_found: date range used by MVZ (format: Mon-Year or YYYY)
- circumstances: origin of specimen upon arrival to EBV
- fixed: date specimen was placed in formalin (format: MMDDYYYY)
- etoh_transfer: date specimen was transferred to ethanol (format: MMDDYYYY)
- days_in_formalin: days specimen spent in formalin to ensure fixation
File: RNAlater_bias_correction_data.csv
Description: Stable isotope ratios from paired samples for analysis of effect of RNAlater storage buffer.
Variables
- sample: identification given to the specimen for use in the study
- genus: genus of specimen
- tissue: tissue type used for stable isotope analysis
- d15N: delta nitrogen signature of flash frozen tissue
- d15N_treatment: delta nitrogen signature of tissue stored in RNAlater
- d13C: delta carbon signature of flash frozen tissue
- d13C_treatment: delta carbon signature of tissue stored in RNAlater
- bias_N: nitrogen bias between flash frozen and buffer-stored tissue
- bias_C: carbon bias between flash frozen and buffer-stored tissue
File: MVZ_thamnophis_isotopes.csv
Description: Stable isotope ratios from historical MVZ Thamnophis specimens.
Variables
- sample_id: sample_name plus tissue type code
- sample_name: name of specimen based on MVZ accession number
- N: percent nitrogen
- d15N: delta nitrogen signature
- C: percent carbon
- d13C: delta carbon signature
- species: species of specimen
- tissue: tissue type used for stable isotope analysis
File: ebv_isotope_data_ALL.csv
Description: Stable isotope ratios from East Bay Vivarium squamate specimens representing time series and effect of delipification analysis.
Variables
- sample_id: sample_name plus timepoint and tissue type code
- timepoint: timepoint sample was taken during preservation process
- tissue: tissue type used for stable isotope analysis
- delipified: TRUE if tissue was subjected to delipification
- flashfrozen: TRUE if tissue was flash frozen (vs. stored in RNAlater buffer)
- 15N: delta nitrogen signature
- 13C: delta carbon signature
- genus: genus of specimen
- species: species of specimen
Missing Values
Values represented by NA indicate missing data (i.e. metadata not available for specimens or samples that failed during isotope analysis)
Code/software
All data were analyzed in the R programming environment.