Genetic diversity of wild and farmed populations is crucial, both for conservation of fish resources and fish culture development. To infer the genetic diversity and population structure of Streaked prochilod Prochilodus lineatus, individuals were sampled between 2007-2009 from four fish farms and from the Upper Uruguay River Basin, both in southern Brazil. Population structure was identified in both farmed and wild individuals through seven microsatellite loci. Bayesian analysis indicated three main groups, including two from fish farms. Pairwise genetic differentiation showed spatial structure between and within wild and farmed populations; however, the sampling design did not allow testing temporal structure according to isolation-by-time (IBT), which means that populations can breed within the same geographic distribaution, but reproduce at different times. Cultivated individuals presented lower diversity, allelic richness and effective population size, but higher inbreeding rates, compared to wild populations. These characteristics constitute warning signs against indiscriminate restocking of natural Prochilodus lineatus populations, a species sensitive to fragmented habitats, with farmed fish.
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