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

Chen, Yuqing1; Kutsumi, Yuka1; Hare, Matthew P.1

Published Apr 28, 2026 on Dryad. https://doi.org/10.5061/dryad.08kprr5hv

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Abstract

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.