Data and code from: Spatial and temporal admixture patterns from farm oysters supplementing wild population recruitment

Aquaculture is a fast-growing global industry providing important dietary
and economic benefits. Unlike other coastal aquaculture, bivalve
aquaculture diet depends on natural productivity rather than introduced
nutrients, avoiding detrimental environmental effects. In fact, farmed
bivalves provide ecosystem services during grow-out through their water
filtration, nutrient sequestration, and habitat provisioning. For
shellfish species that are farmed amidst declining wild conspecific
populations, recruitment supplementation has been hypothesized as an
additional ecosystem service, but there are also risks if domestication
has resulted in low relative fitness in the wild. This study uses
population genomics to contrast wild eastern oyster populations in regions
with and without aquaculture farming, providing the first documentation of
farm-source recruitment in an open-coast estuarine system.  Using
double-digest restriction-site associated DNA (ddRAD) with subsequent
confirmation and refinement based on low-coverage whole genome sequencing
(lcWGS) data, we find no admixture in most of the Hudson River (where
aquaculture is prohibited) but frequent low-level introgression among
individuals in western and central Long Island Sound. Almost all admixed
oysters are later-generation backcrosses, consistent with historical
recruitment supplementation from oyster spawning on farms and low recent
rates of immigration into wild stocks. We discuss both demographic
benefits and possible evolutionary impacts of this introgression from
domesticated oyster strains.