Across rather than between river genetic structure in Atlantic salmon Salmo salar in north-east Scotland, UK: potential causes and management implications.

The aim of this study was to examine the genetic structuring, based on c. 4300 single nucleotide polymorphic markers, of juvenile Atlantic salmon Salmo salar sampled from 11 rivers in north-east Scotland, which form part of a radial drainage system. Within this area, sites in the upper mountainous and lower coastal sections of the different rivers were more closely related than sites from the upper and lower sections of the same river. Differentiation between fish from upper and lower sections was related to both distance from the sea and elevation, which were themselves correlated. The occurrence of such cross-river genetic grouping appears to be the result of both similar selective pressures resulting in homologous adaptive differences within each river and also recent common ancestry between rivers. Examination of historical tagging information showed high rates (27·4%) of between-river straying in this region that may help to maintain the across rather than between-river structure. The existence of cross-river groupings highlights the complex structuring of S. salar populations and may confound genetic identification of single-river stocks. Furthermore, the results presented show that cross-river structuring should also be an important consideration in managing S. salar stocks.

Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.).

Microsatellite genotyping is a common DNA characterization technique in population, ecological and evolutionary genetics research. Since different alleles are sized relative to internal size-standards, different laboratories must calibrate and standardize allelic designations when exchanging data. This interchange of microsatellite data can often prove problematic. Here, 16 microsatellite loci were calibrated and standardized for the Atlantic salmon, Salmo salar, across 12 laboratories. Although inconsistencies were observed, particularly due to differences between migration of DNA fragments and actual allelic size ('size shifts'), inter-laboratory calibration was successful. Standardization also allowed an assessment of the degree and partitioning of genotyping error. Notably, the global allelic error rate was reduced from 0.05 ± 0.01 prior to calibration to 0.01 ± 0.002 post-calibration. Most errors were found to occur during analysis (i.e. when size-calling alleles; the mean proportion of all errors that were analytical errors across loci was 0.58 after calibration). No evidence was found of an association between the degree of error and allelic size range of a locus, number of alleles, nor repeat type, nor was there evidence that genotyping errors were more prevalent when a laboratory analyzed samples outside of the usual geographic area they encounter. The microsatellite calibration between laboratories presented here will be especially important for genetic assignment of marine-caught Atlantic salmon, enabling analysis of marine mortality, a major factor in the observed declines of this highly valued species.

Size-dependent growth of individual Atlantic salmon Salmo salar alevins from hatch to first feeding.

Variation in egg size, hatch timing and size at hatch, and their influence on individual growth rates of Atlantic salmon Salmo salar alevins up to first feeding were examined in pure strain and hybrid crosses of fish from Scotland and Canada. At the intra-female, intra-cross type and inter-cross type levels, specific growth rates prior to first feed were strongly size dependent, with smaller and later hatching alevins growing significantly faster. The magnitude of this size-dependent growth was greatest in the hybrid crosses. This resulted in a 40% reduction in the coefficient of variation (c.v.) in alevin size from post-hatch to first feeding at the intra-female level, and a reduction of both intra- and inter-cross differences in alevin sizes in the same period.