Juvenile life history, migration, and habitat use of natural- versus hatchery-origin Chinook salmon

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 dur..., , # 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 - Summ...,