DOI: 10.5061/dryad.47d7wm3rp
title: Juvenile life history, migration, and habitat use of natural- versus hatchery-origin Chinook salmon

description: 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.
description: # Juvenile life history, migration, and habitat use of natural- versus
 hatchery-origin Chinook salmon Dataset DOI:
 [10.5061/dryad.47d7wm3rp](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](https://github.com/echenfishbitch/hatchery-versus-natural-juvenile-life-history)