Looking for a needle in a haystack: Discovery of indigenous Atlantic salmon ( Salmo salar L.) in stocked populations

Abstract

Microsatellite analysis of Atlantic salmon fromfive Danish rivers was performed to determinethe stocked or indigenous status ofindividuals. Genetic variation at six highlypolymorphic microsatellite loci was assayed andused for individual based analyses (assignmenttests). Contemporary samples of adult returningspawners and fry were compared to baseline datafrom: 1) historical DNA samples (from oldscales) representing the indigenouspopulations, 2) samples from another Danishpopulation (Skjern River) used for stocking,and 3) five exogenous populations used forstocking. Assignment power was high. Thepercent of stocked salmon correctly assigned topopulation of origin ranged from 83% to 99%and the percent of indigenous salmon correctlyassigned to population of origin ranged from83% to 90%. For two of the riverssignificantly more individuals were assigned tothe indigenous populations than expected frommisclassification alone, suggesting that someremains of the indigenous populations hadpersisted. Still, many fish were of exogenousorigin. Simulated hybrids among releasedexogenous salmon and between exogenous andreleased Danish salmon (Skjern River) revealedthat natural hybridisation among released fishwas not likely to be the source of the fryclassified as indigenous, however, thepossibility of hybridisation among indigenousand released fish could not be dismissed.Several full sib groups were found amongindigenous natural fry ruling out one or a fewmatings as the source of the indigenous fry.These results show that some native populationsmay persist even after years of introductionand environmental perturbation; geneticinformation can be used to identify thesepopulations and identify individualsrepresenting these populations for use inrestoration programs.