Data and source code for: Recent adaptation in a threatened salmonid revealed by museum genomics

Steelhead/rainbow trout (Oncorhynchus mykiss) is an imperiled salmonid
with two main life history strategies: migrate to the ocean or remain in
freshwater. Domesticated hatchery forms of this species have been stocked
into almost all California waterbodies, possibly resulting in
introgression into natural populations and altered population
structure.  We compared whole-genome sequence data from
contemporary populations against a set of museum population samples of
steelhead from the same locations that were collected prior to most
hatchery stocking.  We observed minimal introgression and few
steelhead-hatchery trout hybrids despite a century of extensive stocking.
Our historical data show signals of introgression with a sister species
and indications of an early hatchery facility. Finally, we found that
migration-associated haplotypes have become less frequent over time, a
likely adaptation to decreased opportunities for migration. Since
contemporary migration-associated haplotype frequencies have been used to
guide species management, we consider this to be a rare example of
shifting baseline syndrome that has been validated with historical
data.  We suggest cautious optimism that a century of hatchery
stocking has had minimal impact on California steelhead population genetic
structure, but we note that continued shifts in life history may lead to
further declines in the ocean-going form of the species.