Complications of estimating hatchery introgression in the face of rapid divergence: A case study in brook trout (Salvelinus fontinalis)

Fish stocking has been utilized for over a century to offset extirpations
or declines in abundance of many native species. These historical declines
and hatchery contributions have led to uncertainty surrounding whether
many contemporary populations are native, introgressed with hatchery
sources, or entirely of hatchery origin. Such uncertainty is problematic
for the conservation of native biodiversity as it hampers management
agencies’ ability to prioritize the conservation of indigenous locally
adapted populations. Fortunately, genetic and genomic tools have allowed
researchers to investigate these questions, often through the use of
clustering or assignment approaches that are predicated on identifiable
and consistent divergence between native populations and hatchery sources.
Here, we apply these methods to genomic data from 643 brook trout
(Salvelinus fontinalis) originating from 13 wild populations and an
exogenous hatchery strain to investigate the extent of historical
extirpations, hatchery contributions, and processes affecting population
structure in a small area of the previously unglaciated Driftless Area of
Wisconsin, USA. Results from these analyses suggest that wild populations
in this region are genetically distinct even at small spatial scales, lack
hydrologically associated population structure, rarely exchange gene flow,
and have small effective population sizes. Further, wild populations are
substantially diverged from known hatchery strains and show minimal
evidence of introgression in clustering analyses. However, we demonstrate
through empirically informed simulations that distinct wild populations
may potentially be hatchery-founded and have since diverged through rapid
genetic drift. Collectively, the lack of hydrological population structure
and potential for rapid drift in the Driftless Area suggest that many
native populations may have been historically extirpated and refounded by
stocking events, and that commonly used genomic clustering methods and
their associated model selection criteria may result in underestimation of
hatchery introgression in the face of rapid drift.