Genetic structure in Atlantic brown trout (Salmo trutta L.) populations in the Iberian peninsula: evidence from mitochondrial and nuclear DNA analysis

Brown trout (Salmo trutta L.) was sampled in rivers belonging to three different Spanish basins in order to analyse the distribution of genetic variability. The genetic analysis was performed by using two systems and techniques: nuclear DNA was screened through random amplified polymorphic DNAs (screening 2 × 10⁵ bp of the whole genome), and mitochondrial DNA (mtDNA) through sequencing of the hypervariable control region. Genetic distances between the populations were similar using either analysis although some differences arise. For example, some populations of the Tajo basin were very close through nuclear analysis but more distant using mtDNA. Differences between the two DNA sources could be the result of a different evolutionary rate, and the fact that mtDNA is maternally transmitted and differences in sex migration rates will influence the patterns of genetic variation between the transmitted DNAs. Total variation was partitioned using amova showing a clear subdivision among basins although intrapopulation variation remained as high as 62%. A correspondence analysis defined the differences in a three‐dimensional way, clustering the populations according to their common basin. When mtDNA was sequenced, higher variability was noted in the segment between 400 and 600bp of the whole D‐loop sequence, suggesting that these 200bp improved the analysis of the variability more than sequencing the t‐RNA ends of the control region. A comparison was made between the t‐RNA^Pro ends of the 10 populations screened here and the rest of the published sequences found in the literature, leading to a concentration of these populations in group IV which includes all trouts which originate in the Atlantic. The analyses performed suggest that a high genetic variability is present in all populations and that although there has been a probable interference from stocked strains introduced to increase population density, this was only detectable through the variance between rivers which reflect different policies according to the region where the basin is located. However, the genetic analysis using the two approaches allows the control of the natural populations avoiding a loss of their genetic potential.