A consensus microsatellite-based linkage map of the turbot (Scophthalmus maximus) was constructed from two unrelated families. The mapping panel was derived from a gynogenetic family of 96 haploid embryos and a biparental diploid family of 85 full-sib progeny with known linkage phase. A total of 242 microsatellites were mapped in 26 linkage groups, six markers remaining unlinked. The consensus map length was 1343.2 cM, with an average distance between markers of 6.5 ± 0.5 cM. Similar length of female and male maps was evidenced. However, the mean recombination at common intervals throughout the genome revealed significant differences between sexes, ∼1.6 times higher in the female than in the male. The comparison of turbot microsatellite flanking sequences against the Tetraodon nigroviridis genome revealed 55 significant matches, with a mean length of 102 bp and high sequence similarity (81–100%). The comparative mapping revealed significant syntenic regions among fish species. This study represents the first linkage map in the turbot, one of the most important flatfish in European aquaculture. This map will be suitable for QTL identification of productive traits in this species and for further evolutionary studies in fish and vertebrate species.

Variation in the internal transcribed spacer (ITS) of rDNA was examined throughout the range of the brown trout (Salmo trutta) to analyze the usefulness of this molecular marker for phylogeographic analysis. The results were compared with those previously obtained with mtDNA, a region exhaustively analyzed along the brown trout distribution. ITS2 was essentially conserved at all populations sampled, no informative characters being detected across the main lineages described in this species. Conversely, ITS1 showed a greater homogenization than other genetic markers at a microgeographic scale, with variation partitioning into several major phylogenetic groups. Phylogeographic patterns were partially congruent between both ITS1 and mtDNA. The main discrepancies were the detection of intra-individual variation and putative recombinant ITS1 sequences in hybridization areas between genetically different, yet historically overlapping, assemblages. Also, the existence of an ancient ITS1 sequence in the Mediterranean-southeastern area (rMEDA), not revealed by mtDNA analysis, was evidenced after rDNA ITS1 analysis.