The physical arrangement of closely related individuals is expected to significantly influence the pattern of population genetic structure. For example, if related individuals are non-randomly distributed and included in samples, this may lead to exaggerated conclusions about genetic differentiation. In the present study, we compared population structure v. family relationships of brown trout (Salmo trutta L.) along a Mediterranean stream (Pyrenees) by using eight microsatellite loci. Results showed low levels of genetic (FST) differentiation between collections in a 6.5-km transect along the stream, and a significant correlation between genetic and geographical distance matrices, indicating a weak population structure associated with spatial distribution. Our data also indicated that geographical proximity of related individuals in the youngest (0+, 1+) cohorts probably was associated with limited dispersal of younger brown trout from spawning redds. Family relationships provided evidence, however, for movement of adult trout over distances of a few kilometres that probably contributed to the low observed differentiation. Dispersal of adult Mediterranean trout contrasts with the clustering of related older trout observed for some north European rivers and could be related to the reduced productivity in southern stream basins.

The Iberian Peninsula contains diverse populations of freshwater fish, with major river basins comprising differentiated biogeographic units. The Duero River flows through the North‐Western Iberian Peninsula and is one of the most important rivers within the Iberian glacial refuge. Brown trout (Salmo trutta) populate this whole basin, and studies using both allozyme and microsatellite loci have detected a geographically sorted distribution of genetic variation in this species. In this work, sequences of the mitochondrial control region obtained from 299 brown trout from the Duero River were compared with other Iberian and European datasets. Two differentiated haplotype groups were detected inside the Duero River basin. One of them was related to the Atlantic (AT) lineage that is present in Northern European populations, whereas the other comprised an unique group that was restricted to the inner region of the basin. The amount of divergence of this Duero group from the other brown trout populations studied is consistent with a new trout lineage (Duero, DU) that is endemic to this river basin and that diverged from other Atlantic populations during the Pleistocene. The distribution of the DU and AT quaternary lineages in the Duero River was consistent with the ichthyological pattern described in the basin that originated during the Miocene–Pliocene. Evidence of selective processes that favour the haplotypes of the DU lineage may explain this discrepancy.

Since the end of the 20th century, some headwaters of rivers in the eastern Pyrenees have been designated as genetic refuges to protect remaining native brown trout (Salmo trutta) diversity. The declaration was based on limited or no evidence of genetic impact from released non-native Atlantic hatchery fish. Hatchery releases were completely banned into the genetic refuges, but pre-existing fishing activities were maintained. Specific locations in each refuge have been monitored every 2–3 trout generations to update genetic information to accurately assess the contribution of these reservoirs to the preservation of native brown trout gene pools. This work updates genetic information to year 2014 in three of these locations (in Ter, Freser and Flamisell rivers). Previous studies identified hatchery introgressed populations within refuges and suggested discrepancies between the underlying intention of the genetic refuges and the gene pools detected. Therefore, we also examined genetic divergences among locations inside refuge river segments. Combined information at five microsatellite and the lactate dehydrogenase C (LDH-C*) loci showed reduced but significant temporal native allele frequency fluctuations in some of the above specific locations that did not modify overall levels of local diversity and river divergences. Bayesian clustering analyses confirmed the presence of differentiated native units within each genetic refuge. Some locations of the Freser River within the genetic refuge area showed high hatchery impact of non-native fish (over 20%). We discuss additional local actions (releases of native fish, selective removals and fishery reinforcement with sterile individuals) to improve the conservation objective of genetic refuge