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 archive
dataset, spring run individuals that assigned to the Mill and Deer Creeks
subpopulation exhibited an earlier and broader outmigration distribution
as well as larger body sizes than individuals that assigned to the Butte
Creek subpopulation. Within the fall run population, individuals that
assigned to the late-fall run subpopulation also exhibited an earlier and
broader outmigration distribution and larger body sizes than other fall
run fish in our dataset. These results highlight the importance of
distinct subpopulations for maintaining remaining diversity in Central
Valley Chinook salmon, and demonstrates the power of genomics-based
population assignments to aid the study and management of intraspecific
diversity.