DOI: 10.5061/dryad.3n5tb2rvw
title: Inter-method differences (SIMS vs. IRMS) in oxygen isotope fractionation: Insights from Chinook salmon otoliths

description: Stable oxygen isotopes (δ18O) in biogenic carbonates serve as a valuable
 proxy for reconstructing thermal history. Fish otoliths (ear stones) are
 particularly useful, as they precipitate continuously throughout life,
 creating a temporally resolved archive of water temperature. Here, we
 calibrate the temperature-dependent oxygen isotope fractionation equation
 for Chinook salmon (Oncorhynchus tshawytscha) using two analytical
 methods—secondary ion mass spectrometry (SIMS) and isotope ratio mass
 spectrometry (IRMS)—to evaluate method-dependent effects on fractionation
 equations and their implications for temperature reconstruction. Juvenile
 fish were reared for 15 weeks under controlled freshwater conditions
 (salinity &lt;0.1 ppt) with a stable ambient water δ18O of -5.54‰
 (VSMOW) (±0.10, 1 SD) at three temperatures (11, 16, 20 °C). Otolith δ18O
 values measured by SIMS showed a significant linear inverse relationship
 with ambient water temperature: 1000lnα=11.51(±1.39,1SE)×103T(K)−1 −
 10.94(±4.80,1SE) δ18Ootolith(VPDB) − δ18Owater(VSMOW) =
 −0.14(±0.02,1SE)×T(°C)+0.64(±0.27,1SE) Applying this equation yielded
 water temperature reconstructions with an accuracy of ± 1.97 °C and a
 precision of ± 0.70 °C (1 SD). A paired comparison revealed SIMS δ18O
 values were on average 1.97‰ lower than IRMS values, likely due to matrix
 effects and organic content. This offset produced large differences in
 equation intercepts, leading to reconstructed temperatures from IRMS-based
 equations that deviated ~10 °C from observed temperatures when applied to
 SIMS data. In contrast, the slopes (thermal sensitivity) of SIMS and IRMS
 equations were highly consistent, indicating that relative temperature
 changes can still be reliably inferred from SIMS δ¹⁸O values using
 IRMS-based equations. Greater variability in SIMS δ¹⁸O values compared to
 IRMS may partly reflect fine-scale isotopic heterogeneity within otoliths,
 suggesting that SIMS-based temperature reconstructions may require larger
 sample sizes or additional calibration tailored to specific contexts.
 Across-species comparison of fractionation equations revealed that
 inter-method differences exceeded inter-species differences, highlighting
 the need for method-matched equations for accurate absolute temperature
 reconstructions. Despite these challenges, once calibrated, SIMS-based
 otolith thermometry provides a powerful tool for reconstructing fine-scale
 fish thermal histories and assessing habitat refugia and resilience to
 climate change.
description: # Inter-method differences (SIMS vs. IRMS) in oxygen isotope
 fractionation: Insights from Chinook salmon otoliths DOI:
 10.5061/dryad.3n5tb2rvw This README was generated on 2025-11-14 by K.
 Arai. This README is in reference to the data sets and R codes (.Rmd)
 needed to recreate the figures and analyses in *“Inter-method differences
 (SIMS vs. IRMS) in oxygen isotope fractionation: insights from Chinook
 salmon otoliths”*, submitted by K. Arai. There are five major analyses
 within the manuscript. The first script `01_tank_2025-09-10.Rmd`
 summarizes the water temperature and stable oxygen isotopes (water δ¹⁸O)
 measured in the temperature treatment experiment for juvenile Chinook
 salmon. The second script `02_sims_fractionation_2025-09-10.Rmd ` fits a
 linear regression to Secondary Ion Mass Spectrometry (SIMS)-measured
 otolith stable oxygen isotopes for juvenile Chinook salmon to calibrate a
 temperature-dependent fractionation equation. The third script
 `03_irms_2025-09-10.Rmd` compares otolith δ¹⁸O values measured via SIMS
 and Isotope Ratio Mass Spectrometry (IRMS). The fourth script
 `04_equation_comparison_2025-09-10.Rmd ` compares fractionation equations
 for various fish species. The fifth script `05_ellipse _2025-09-10.Rmd`
 evaluates the relationship between the measured otolith area and
 within-individual variance (1 standard deviation) of SIMS δ¹⁸O otolith
 values. ## Description of the data and file structure Data list 1.
 `00_sims_raw_data_2025-09-23.csv` 2.
 `01_tank_temperature_data_2025-09-10.csv` 3.
 `01_tank_waterd18O_data_2025-09-10.csv` 4.
 `02_sims_d18O_data_all_2025-09-10.csv ` 5.
 `03_sims_irms_d18O_data_2025-09-10.csv` 6.
 `04_fractionation_equation_data_2025-09-10.csv` Script list 1.
 `01_tank_2025-09-10.Rmd` 2. `02_sims_fractionation_2025-09-10.Rmd` 3.
 `03_irms_2025-09-10.Rmd` 4. `04_equation_comparison_2025-09-10.Rmd` 5.
 `05_ellipse_2025-09-10.Rmd` ### Full raw SIMS stable oxygen isotope data
 (`00_sims_raw_data_2025-09-23.csv`) This dataset contains raw and
 instrument mass fractionation (IMF)-corrected measurements of otolith
 stable oxygen isotopes (δ¹⁸O) from juvenile Chinook salmon with known
 temperature histories. Measurements were obtained using Secondary Ion Mass
 Spectrometry (SIMS). The dataset also includes results from calcite
 standards (UWC3, UCLA C1 and C2) used for IMF correction and to assess
 instrument reproducibility. Missing or unavailable values are indicated by
 `NA`. Please note: The dataset includes measurements from all samples
 analyzed, including those not used in the associated manuscript (e.g.,
 spots excluded after quality control for surface artifacts or transfer
 line positioning). 1. Number of variables: 11 2. Number of cases/rows: 885
 3. Variable list: `session`: Unique SIMS analytical session ID (e.g.,
 “May2023”) `date`: Date of SIMS measurement `type`: Sample type (e.g.,
 Otolith, UWC3, UCLA_C1 and C2) `puck`: Unique sample puck ID used for
 mounting `fish_id_short`: Shortened fish ID (standards labeled as
 “standard”) `spot_seq`: Sequential SIMS spot number within each fish or
 standard `X_coord`: X coordinate of SIMS spot on mount (instrument
 reference frame, in µm) `Y_coord`: Y coordinate of SIMS spot on mount
 (instrument reference frame, in µm) `d18O_vsmow_raw`: Raw δ¹⁸O value (‰,
 relative to VSMOW) `d18O_vsmow_corrected`: IMF-corrected δ¹⁸O value (‰,
 relative to VSMOW) `d18O_vsmow_total_2se`: Total analytical uncertainty (2
 standard errors, ‰) ### Water temperature data from the tank experiment
 (`01_tank_temperature_data_2025-09-10.csv`) This dataset contains water
 temperature data from the temperature treatment experiment for juvenile
 Chinook salmon. Missing or unavailable values are indicated by `NA`. 1.
 Number of variables: 10 2. Number of cases/rows: 156174 3. Variable list:
 `DATE_TIME`: Date time of temperature measurement `TANK_ID`: Unique tank
 ID `TEMPERATURE`: Raw temperature measurements (°C) `LOGGER_TYPE`: Method
 of temperature measurement `NOTES`: Notes `DATE`: Date of temperature
 measurement `CORRECTION`: Temperature correction made based upon handheld
 probe `TEMP_CORR`: Corrected temperature (°C) `TARGET_TEMP`: Target
 treatment temperature (°C) `FEED_RATION`: Feeding level for the tank ###
 Water stable oxygen isotope data from the tank experiment
 (`01_tank_waterd18O_data_2025-09-10.csv`) This dataset contains water
 stable oxygen isotopes from the temperature treatment experiment for
 juvenile Chinook salmon. Missing or unavailable values are indicated by
 `NA`. 1. Number of variables: 4 2. Number of cases/rows: 124 3. Variable
 list: `ANALYSIS_ID`: Unique measurement ID `TANK_ID`: Unique tank ID
 `DATE`: Date of water sampling ` d18O`: Measured water δ¹⁸O value (‰,
 VSMOW scale) ### Known-temperature history juvenile Chinook salmon otolith
 stable oxygen isotope data measured with Secondary Ion Mass Spectrometry
 (`02_sims_d18O_data_all_2025-09-10.csv`) This dataset contains the otolith
 stable oxygen isotope data of known-temperature history juvenile Chinook
 salmon measured via Secondary Ion Mass Spectrometry (SIMS) along with the
 meta data of the fish. Missing or unavailable values are indicated by
 `NA`. 1. Number of variables: 16 2. Number of cases/rows: 521 3. Variable
 list: `temp`: Temperature treatment group (°C) `tank`: Rearing tank ID
 `collect_date`: Date of fish collection `fork_length`: Fork length of fish
 (mm) `fish_id_short`: Unique fish ID `session`: Unique SIMS analytical
 session ID `date`: Date of SIMS measurement `spot_seq`: SIMS spot number
 within each fish `X_coord`: X coordinate of SIMS spot (µm, instrument
 frame) `Y_coord`: Y coordinate of SIMS spot (µm, instrument frame)
 `d18O_vsmow_final`: IMF-corrected δ¹⁸O value (‰, VSMOW scale)
 `d18O_vsmow_final_1sd`: Standard deviation of δ¹⁸O value (‰)
 `d18O_vsmow_final_2se`: Standard error (2SE) of δ¹⁸O value (‰)
 `distance_from_core`: Standardized distance from otolith core (µm) `side`:
 The side (dorsal or ventral) of the otolith where the SIMS spots were
 measured `tank_dis`: Standardized otolith distance corresponding to the
 onset of tank treatments (i.e., “transfer line”) (µm) ### Juvenile Chinook
 salmon otolith stable oxygen isotope data measured with IRMS and SIMS
 (`03_sims_irms_d18O_data_2025-09-10.csv`) This dataset contains the
 otolith stable oxygen isotope data of known-temperature history juvenile
 Chinook salmon measured using both continuous-flow isotope ratio mass
 spectrometry (IRMS) and Secondary Ion Mass Spectrometry (SIMS). Missing or
 unavailable values are indicated by `NA`. 1. Number of variables: 13 2.
 Number of cases/rows: 60 3. Variable list: `temp`: Temperature treatment
 group (°C) `puck`: SIMS multi-mount puck ID `fish_id_short`: Unique fish
 ID (short format) `fish_id_order`: Unique fish order ID `tank`: Rearing
 tank ID `ration`: Feeding level (ration) of tank `collect_date`: Date of
 fish collection `fork_length`: Fork length of fish (mm)
 `d18O_vpdb_sims_mean`: Mean δ¹⁸O from SIMS (‰, VPDB scale)
 d18O_vpdb_sims_se_total`: Total standard error of SIMS δ¹⁸O (‰)
 `d18O_vpdb_irms`: δ¹⁸O from IRMS (‰, VPDB scale) `d18O_offset`: Offset
 between SIMS and IRMS δ¹⁸O values (‰) `sims_spots`: Number of SIMS spots
 measured per individual ### Fractionation equation slope and intercept
 coefficient data (`04_fractionation_equation_data_2025-09-10.csv`) This
 dataset contains the coefficient estimates of the oxygen isotope
 fractionation equation slope and intercept of various fish species, as
 reported in published studies. Missing or unavailable values are indicated
 by `NA`. 1. Number of variables: 19 2. Number of cases/rows: 11 3.
 Variable list: `author`: First author of original study `year`:
 Publication year `structure`: Biological structure analyzed (e.g.,
 otolith) `carbonate`: Type of carbonate measured `species_cap`: Common
 name of species `latin_name`: Scientific name of species `life_stage`:
 Life stage of species (e.g., juvenile, adult) `analy_method`:
 Instrumentation used for isotope analysis (SIMS or IRMS) `min_t`: Minimum
 experimental temperature (°C) `max_t`: Maximum experimental temperature
 (°C) `range`: Experimental temperature range (°C) `slope_1000lna`: Slope
 coefficient for general fractionation equation (1000·lnα) `int_1000lna`:
 Intercept coefficient for general fractionation equation (1000·lnα)
 `slope_1000lna_se`: Standard error of slope estimate (1000·lnα)
 `int_1000lna_se`: Standard error of intercept estimate (1000·lnα)
 `slope_d18O`: Slope coefficient for fractionation equation based on
 carbonate–water δ¹⁸O difference `int_d18O`: Intercept coefficient for
 fractionation equation based on carbonate–water δ¹⁸O difference
 `slope_d18O_se`: Standard error of slope estimate (carbonate–water δ¹⁸O)
 `int_d18O_se`: Standard error of intercept estimate (carbonate–water δ¹⁸O)
 ## Code/Software All analyses were conducted in `R`. The output assumes
 that the `.Rmd` scripts are placed in a `scripts` folder along with a
 `data` folder that contains the supplied data, a `figures` folder that is
 now empty but will contain output figures, and a `outputs` folder that is
 now empty but will contain outputs of the analyses. Please run the scripts
 in sequential order from 01 to 05.