Supplementary data for: Outmigrating central valley Chinook Salmon

Intraspecific diversity plays a critical role in the resilience of Chinook salmon populations. California’s Central Valley historically hosted one of the most diverse population complexes of Chinook salmon in the world. However, anthropogenic factors have dramatically decreased this diversity, with severe consequences for population resilience. Here we use next generation sequencing and an archive of thousands of tissue samples collected across two decades during the juvenile outmigration to evaluate phenotypic diversity between and within populations of Central Valley Chinook salmon. To account for highly heterogeneous sample qualities in the archive dataset, we develop and test an approach for population and subpopulation assignments of Central Valley Chinook salmon that allows inclusion of relatively low-quality samples while controlling error rates. We find significantly distinct outmigration timing and body size distributions for each population and subpopulation. Within the archiv..., , , # Outmigrating Central Valley Chinook Salmon

Access this data on Dryad (DOI: 10.5061/dryad.280gb5mxx)

This Dryad entry contains data files and scripts used for analyses in Thompson et al. 2024 (Evolutionary Applications). Briefly, the study examines outmigration characteristics of juvenile Chinook salmon collecte
d at Chipps Island in the Sacramento/San Joaquine Delta by assigning each sample to a population of origin. The analysis is broken down into three parts: 1) leave-one-out analyses to develop a population assignme
nt method and evaluate its expected efficacy; 2) validation of the assignment method using an independent dataset of known-origin samples; 3) population assignment of unknown-origin juvenile samples collected at
Chipps Island (and obtained from a tissue archive). This Dryad entry contains files and scripts necessary for that analysis, as well as the resulting output files.

## Data Files

The following are descriptions of all data files uploaded here.

(Note: the sin...