Juvenile life history, migration, and habitat use of natural- versus hatchery-origin Chinook salmon
Data files
May 13, 2025 version files 149.73 MB
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0717_SrRatios.csv
792.85 KB
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1._Otolith_Data_Basic_Prep.R
11.49 KB
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1819_SrRatios.csv
467.10 KB
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2._Breakpoint_analysis.R
1.87 KB
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3._Habitat_Assignments.R
8.69 KB
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4._Merging_structure_and_chemistry_data.R
2.19 KB
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5._Summary_Stats.R
10.23 KB
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6._Microstructure_Summary_Stats.R
19.26 KB
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AllMicrochemistryData.csv
1.65 MB
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AllMicrostructure_data.csv
2.25 MB
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breakpoints.csv
30.27 KB
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CWTcodes.csv
110.20 KB
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Hatchery_Fish_IDs.csv
2.76 KB
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Interpolated_Microchemistry_2007.csv
1.44 MB
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Interpolated_Microchemistry_2008.csv
3.95 MB
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Interpolated_Microchemistry_2009.csv
3.44 MB
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Interpolated_Microchemistry_2015.csv
17.44 MB
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Interpolated_Microchemistry_2016.csv
10.42 MB
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Interpolated_Microchemistry_2017.csv
1.56 MB
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Interpolated_Microchemistry_2018.csv
12.58 MB
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Interpolated_Microchemistry_2019.csv
11.56 MB
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Interpolated_Microchemistry_with_Habitat_2007.csv
1.80 MB
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Interpolated_Microchemistry_with_Habitat_2008.csv
4.92 MB
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Interpolated_Microchemistry_with_Habitat_2009.csv
4.25 MB
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Interpolated_Microchemistry_with_Habitat_2015.csv
21.36 MB
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Interpolated_Microchemistry_with_Habitat_2016.csv
12.79 MB
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Interpolated_Microchemistry_with_Habitat_2017.csv
1.92 MB
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Interpolated_Microchemistry_with_Habitat_2018.csv
15.22 MB
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Interpolated_Microchemistry_with_Habitat_2019.csv
14.12 MB
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Microstructure_data_with_chemistry.csv
4.04 MB
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Microstructure_Measurements.csv
1.49 MB
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Ocean_entry_size.csv
21.16 KB
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README.md
36.10 KB
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SrV_adjustments.csv
643 B
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Transect_Angles.csv
6.57 KB
Abstract
Objectives: Our overall objective was to directly compare the early life history and migration patterns of hatchery and natural-origin fish and determine when hatchery fish provide good surrogates for natural-origin winter-run Chinook Salmon (Oncorhynchus tshawytscha) in the Sacramento River system. Specifically, our objectives were to compare the juvenile freshwater habitat use, residence time in freshwater habitats, and size-at-age and relative growth of juveniles.
Methods: Using otoliths collected from adult carcasses, we reconstructed the freshwater life history of hatchery and natural-origin fish through microstructural and chemical analyses. We analyzed the otolith strontium isotope chemistry and daily increment widths to characterize habitat use, migration timing, and growth.
Results: Following their hatchery rearing period, hatchery fish had much shorter residence times (11 days, SD = 16 days) in the river than natural-origin fish (129 days, SD = 37 days). Beyond the reduced duration of river residence, hatchery fish occupied fewer areas of the watershed during ocean outmigration. Despite these differences in outmigration behaviors, adults from both groups reached saltwater during their downstream outmigration at similar sizes (natural-origin: 633 µm, SD = 68 µm; hatchery-origin: 625 µm, SD = 63 µm) and ages (natural-origin: 161 days old, SD = 20 days; hatchery-origin: 165 days old, SD = 22 days) as juvenile smolts.
Conclusions: Considering differences in habitat use and timing between hatchery and natural-origin fish is critical to avoiding bias when applying data collected from hatchery fish to manage and conserve natural populations. Explicitly considering the presence of winter-run Chinook Salmon in habitats beyond the migratory corridor during habitat management is needed to promote and enable the contribution of multiple life histories for productivity, and resilience, and ultimately recovery.
Dataset DOI: 10.5061/dryad.47d7wm3rp
Description of the data and file structure
Files and variables
Scripts
1. Otolith Data Basic Prep.R – Preparing collected isotope ratio data and increment data for analysis. Interpolating Sr isotope ratios between measurements.
2. Breakpoint analysis.R – Identifying the breakpoint in SrV profile measurements.
3. Habitat Assignments.R – Assigning habitat associated with measurements along the otolith transects.
4. Merging structurey6t67t and chemistry data.R – Joining increment data information with associated strontium isotope and habitat information.
5. Summary stats.R – Summarizing information across samples to calculate metrics of habitat use and entry size into each habitat. Statistical tests of ocean entry size across years and origin.
6. Microstructure Summary Stats.R - Summarizing information across samples to calculate metrics of residence time and growth into each habitat. Statistical tests of ocean entry age across years and origin. Growth model.
1. Otolith Data Basic Prep.R
Data input
Microstructure Measurements.csv – Increment data collected for otolith samples in 2018 and 2019.
Column descriptions
Sample_ID – Unique identification code for each sample.
Escapement_Y – year in which sample was recovered.
Inc_no – Increment number starting from after the exogenous feeding check. EXOG = exogenous feeding check or increment number 0.
Inc_distance – recorded distance of increment from rightmost primordia of the otolith. Measurement is not corrected for angle between measurement transect and perpendicular transect.
Inc_confidence – confidence score of reader on a scale of 1 (least confident) to 5 (most confident).
Reader – initials of reader.
Transect Angles.csv – Angle between transect that measurements were taken and transect perpendicular towards the dorsal side of the otolith.
Column descriptions
lab_id – Unique identification code for each sample.
Transect angle – Angle between transect that measurements were taken and transect. perpendicular towards the dorsal side of the otolith. For samples in which there were different transect lines for different regions of the otolith, we note the increments in which the angle applies to.
0717 SrRatios.csv – Strontium isotope ratios measurements along transects of otoliths collected from 2007 to 2017.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current). NA values are “not available” because these were not recorded or were erroneously recorded.
Sr.V.notes – notes indicating secondary points or outliers in the SrV to exclude. Blank cells mean no notes.
Escap_yr – year in which sample was recovered
1819 SrRatios.csv – Strontium isotope ratios measurements along transects of otoliths collected from 2018 to 2019.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Sr.V.notes – notes indicating secondary points or outliers in the SrV to exclude
Escap_yr – year in which sample was recovered
CWTcodes.csv – CWT codes of hatchery samples, indicating they are of hatchery-origin
Column descriptions
Year – year in which sample was recovered
Sample.Number – Unique identification number for each sample
CWT.Code – batch number
Hatchery Fish IDs.csv– List of samples that have adipose fins intact but are assumed to be hatchery fish because of their strontium isotope ratio profiles.
Column descriptions
Sample_ID – Unique identification code for each sample
Data output
AllMicrostructure_data.csv – Increment data collected for all otolith samples (2018 and 2019). For *2. Breakpoint analysis.R *and 4. Merging structure and chemistry data.R
Column descriptions
Sample_ID – Unique identification code for each sample
Escapement_Y – year in which sample was recovered
Inc_no – Increment number starting from after the exogenous feeding check
Inc_distance – recorded distance in microns of increment from rightmost primordia of the otolith. Corrected for angle between measurement transect and perpendicular transect
Inc_confidence – confidence score of reader on a scale of 1 (least confident) to 5 (most confident). NAs are listed for points that were added in review.
Reader – initials of reader
Transect.angle - Angle between transect that measurements were taken and transect perpendicular towards the dorsal side of the otolith.
Between_inc_dist – distance between increment and previous increment in microns. There is no distance for the first point. Therefore those cells list NAs.
AllMicrochemistryData.csv – Strontium isotope ratio data collected for all otolith samples (2007-2019). For 3. Habitat Assignments.R
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Sr.V.notes – notes indicating secondary points or outliers in the SrV to exclude
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry 2007.csv – Strontium isotope ratio data collected for all otolith samples in 2007. For 3. Habitat Assignments.R
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry 2008.csv – Strontium isotope ratio data collected for all otolith samples in 2008. For 3. Habitat Assignments.R
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry 2009.csv – Strontium isotope ratio data collected for all otolith samples in 2009. For 3. Habitat Assignments.R
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry 2015.csv – Strontium isotope ratio data collected for all otolith samples in 2015. For 3. Habitat Assignments.R
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry 2016.csv – Strontium isotope ratio data collected for all otolith samples in 2016. For 3. Habitat Assignments.R
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry 2017.csv – Strontium isotope ratio data collected for all otolith samples in 2017. For 3. Habitat Assignments.R
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry 2018.csv – Strontium isotope ratio data collected for all otolith samples in 2018. For 3. Habitat Assignments.R
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry 2019.csv – Strontium isotope ratio data collected for all otolith samples in 2019. For 3. Habitat Assignments.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
2. Breakpoint analysis.R
Data input
AllMicrochemistryData.csv – Strontium isotope ratio data collected for all otolith samples (2007-2019). Generated in 1. Otolith Data Basic Prep.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Sr.V.notes – notes indicating secondary points or outliers in the SrV to exclude
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
SrV adjustments.csv – SrV breakpoints identified by eye for select samples due to error or misidentification using the breakpoint analysis.
Column descriptions
Sample_ID – Unique identification code for each sample
SrVbreak_adjusted – Identified SrV breakpoint along otolith transect (in microns)
Notes – reason for adjustment
Data output
breakpoints.csv – breakpoints for Sr8786 and SrV transect measurements identified through breakpoint analysis, except in 15 samples where SrV breakpoints were identified by eye due to error or misidentification through the breakpoint analysis. For 3. Habitat Assignments.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Sr8786break– Identified Sr8786 breakpoint along otolith transect (in microns)
SrVbreak– Identified SrV breakpoint along otolith transect (in microns)
3. Habitat Assignments.R
Data input
Interpolated Microchemistry 2007.csv – Strontium isotope ratio data collected for all otolith samples in 2007. Generated in 1. Otolith Data Basic Prep.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry 2008.csv – Strontium isotope ratio data collected for all otolith samples in 2008. Generated in 1. Otolith Data Basic Prep.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry 2009.csv – Strontium isotope ratio data collected for all otolith samples in 2009. Generated in 1. Otolith Data Basic Prep.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry 2015.csv – Strontium isotope ratio data collected for all otolith samples in 2015. Generated in 1. Otolith Data Basic Prep.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry 2016.csv – Strontium isotope ratio data collected for all otolith samples in 2016. Generated in 1. Otolith Data Basic Prep.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry 2017.csv – Strontium isotope ratio data collected for all otolith samples in 2017. Generated in 1. Otolith Data Basic Prep.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry 2018.csv – Strontium isotope ratio data collected for all otolith samples in 2018. Generated in 1. Otolith Data Basic Prep.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry 2019.csv – Strontium isotope ratio data collected for all otolith samples in 2019. Generated in 1. Otolith Data Basic Prep.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
breakpoints.csv – breakpoints for Sr8786 and SrV transect measurements identified through breakpoint analysis, except in 15 samples where SrV breakpoints were identified by eye due to error or misidentification through the breakpoint analysis. Generated in 2. Breakpoint analysis.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Sr8786break– Identified Sr8786 breakpoint along otolith transect (in microns)
SrVbreak– Identified SrV breakpoint along otolith transect (in microns)
Data output
Interpolated Microchemistry with Habitat 2007.csv – Strontium isotope ratio data collected for all otolith samples in 2007. For 5. Summary Stats.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry with Habitat 2008.csv – Strontium isotope ratio data collected for all otolith samples in 2008. For 5. Summary Stats.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry with Habitat 2009.csv – Strontium isotope ratio data collected for all otolith samples in 2009. For 5. Summary Stats.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry with Habitat 2015.csv – Strontium isotope ratio data collected for all otolith samples in 2015. For 5. Summary Stats.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry with Habitat 2016.csv – Strontium isotope ratio data collected for all otolith samples in 2016. For 5. Summary Stats.R
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry with Habitat 2017.csv – Strontium isotope ratio data collected for all otolith samples in 2017. For 5. Summary Stats.R
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry with Habitat 2018.csv – Strontium isotope ratio data collected for all otolith samples in 2018. For 4. Merging structure and chemistry data.R and 5. Summary Stats.R
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry with Habitat 2019.csv – Strontium isotope ratio data collected for all otolith samples in 2019. For 4. Merging structure and chemistry data.R and 5. Summary Stats.R
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
4. Merging structure and chemistry data.R
Data input
AllMicrostructure_data.csv – Increment data collected for all otolith samples (2018 and 2019). Generated in 1. Otolith Data Basic Prep.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Escapement_Y – year in which sample was recovered
Inc_no – Increment number starting from after the exogenous feeding check
Inc_distance – recorded distance in microns of increment from rightmost primordia of the otolith. Corrected for angle between measurement transect and perpendicular transect
Inc_confidence – confidence score of reader on a scale of 1 (least confident) to 5 (most confident). NAs are listed for points that were added in review.
Reader – initials of reader
Transect.angle - Angle between transect that measurements were taken and transect perpendicular towards the dorsal side of the otolith.
Between_inc_dist – distance between increment and previous increment in microns. There is no distance for the first point. Therefore those cells list NAs.
Interpolated Microchemistry with Habitat 2018.csv – Strontium isotope ratio data collected for all otolith samples in 2018. Generated in 3. Habitat Assignments.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry with Habitat 2019.csv – Strontium isotope ratio data collected for all otolith samples in 2019. Generated in 3. Habitat Assignments.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Data output
Microstructure data with chemistry.csv – Increment data collected for all otolith samples (2018 and 2019) with associated strontium isotope measurement and habitat assignment. For 6. Microstructure Summary Stats.R
Column descriptions
Sample_ID – Unique identification code for each sample
Escapement_Y – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Inc_no – Increment number starting from after the exogenous feeding check
Inc_distance – recorded distance in microns of increment from rightmost primordia of the otolith. Corrected for angle between measurement transect and perpendicular transect
Between_inc_dist – distance between increment and previous increment in microns.
Sr8786 – strontium isotope ratio standardized to global marine value of 0.70918
Habitat – Assigned region of the watershed or the ocean
5. Summary Stats.R
Data input
Interpolated Microchemistry with Habitat 2007.csv – Strontium isotope ratio data collected for all otolith samples in 2007. Generated in 3. Habitat Assignments.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry with Habitat 2008.csv – Strontium isotope ratio data collected for all otolith samples in 2008. Generated in 3. Habitat Assignments.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry with Habitat 2009.csv – Strontium isotope ratio data collected for all otolith samples in 2009. Generated in 3. Habitat Assignments.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry with Habitat 2015.csv – Strontium isotope ratio data collected for all otolith samples in 2015. Generated in 3. Habitat Assignments.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry with Habitat 2016.csv – Strontium isotope ratio data collected for all otolith samples in 2016. Generated in 3. Habitat Assignments.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry with Habitat 2017.csv – Strontium isotope ratio data collected for all otolith samples in 2017. Generated in 3. Habitat Assignments.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry with Habitat 2018.csv – Strontium isotope ratio data collected for all otolith samples in 2018. Generated in 3. Habitat Assignments.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Interpolated Microchemistry with Habitat 2019.csv – Strontium isotope ratio data collected for all otolith samples in 2019. Generated in 3. Habitat Assignments.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Distance_um - distance in microns from rightmost primordia of the otolith in which the measurement was taken. Corrected for angle between measurement transect and perpendicular transect
Sr8786_norm – strontium isotope ratio standardized to global marine value of 0.70918.
SrV – strontium voltage (relative changes in the 88Sr+ ion current)
Escap_yr – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Data output
Ocean_entry_size.csv – Otolith radius (um) at ocean entry. For 6. Microstructure Summary Stats.R
Column descriptions
Sample_ID – Unique identification code for each sample
Enter_Size – Otolith radius (in microns) at which samples transition from freshwater to saltwater.
6. Microstructure Summary Stats.R
Data input
Microstructure data with chemistry.csv – Increment data collected for all otolith samples (2018 and 2019) with associated strontium isotope measurement and habitat assignment. Generated in 4. Merging structure and chemistry data.R
Column descriptions
Sample_ID – Unique identification code for each sample
Escapement_Y – year in which sample was recovered
Origin – Source of sample. Hatchery or natural-origin.
Inc_no – Increment number starting from after the exogenous feeding check
Inc_distance – recorded distance in microns of increment from rightmost primordia of the otolith. Corrected for angle between measurement transect and perpendicular transect
Between_inc_dist – distance between increment and previous increment in microns.
Sr8786 – strontium isotope ratio standardized to global marine value of 0.70918
Habitat – Assigned region of the watershed or the ocean
Ocean_entry_size.csv – Otolith radius (um) at ocean entry. Generated in 5. Summary Stats.R.
Column descriptions
Sample_ID – Unique identification code for each sample
Enter_Size – Otolith radius (in microns) at which samples transition from freshwater to saltwater.
Access information
Other publicly accessible locations of the data: https://github.com/echenfishbitch/hatchery-versus-natural-juvenile-life-history