Three decades of Mediterranean aquaculture expansion without detectable genetic effect in wild Gilthead seabream (Sparus aurata) populations

Marine fish farming in the Mediterranean has expanded rapidly in recent decades, raising concerns about the genetic impact of escapees from floating sea cages on wild fish populations. This study examined temporal changes in the population genetic structure of wild Gilthead seabream (Sparus aurata) in western Greece (eastern Ionian Sea) over the past three decades. Archived scales from historical samples (1994 – 1996), contemporary wild fish (2014 – 2018, 2024), and three reared populations from the Ionian and North Aegean Seas (as control samples) were analyzed. In total, 453 individuals were genotyped at fifteen polymorphic microsatellite loci. Results showed a temporally stable population structure (FST = -0.0044 to 0.0036, p > 0.05), consistently high genetic diversity across years, and large effective population sizes (Ne). No evidence of genetic drift was detected between 1994 and 2024. Reared fish exhibited reduced diversity and much smaller Ne, with moderate but significant differentiation from wild populations (FCT = 0.045; pairwise FST = 0.03 – 0.07, p < 0.05). Bayesian clustering and hybrid assignment analyses revealed no evidence of escapee ancestry or hybridization in wild individuals. Estimated migration rates from farmed to wild populations were very low (m = 0.0034 – 0.0089). Despite intensive and long-term aquaculture activity in a key farming hotspot, the combination of near panmictic natural population structure, with high connectivity as documented by genetic parameters, the modest wild–farm divergence, and the large wild Ne appears to buffer local populations against aquaculture-derived genetic effects. Consequently, no detectable temporal shifts in the genetic structure of wild Gilthead seabream were observed.