Beyond hybridization: the genetic impacts of non-reproductive ecological interactions of salmon aquaculture on wild populations

Cultured Atlantic salmon Salmo salar are of international socioeconomic value, and the process of domestication has resulted in significant behavioural, morphological, and allelic differences from wild populations. Substantial evidence indicates that direct genetic interactions or interbreeding between wild and escaped farmed Atlantic salmon occurs, genetically altering wild salmon and reducing population viability. However, genetic interactions may also occur through ecological mechanisms (e.g. disease, parasites, predation, competition), both in conjunction with and in the absence of interbreeding. Here we examine existing evidence for ecological and non-reproductive genetic interactions between domestic Atlantic salmon and wild populations and the potential use of genetic and genomic tools to resolve these impacts. Our review identified examples of genetic changes resulting from ecological processes, predominately through pathogen or parasite transmission. In addition, many examples were identified where aquaculture activities have either altered the selective landscape experienced by wild populations or resulted in reductions in population abundance, both of which are consistent with the widespread occurrence of indirect genetic changes. We further identify opportunities for genetic or genomic methods to quantify these impacts, though careful experimental design and pre-impact comparisons are often needed to accurately attribute genetic change to aquaculture activities. Our review indicates that ecological and non-reproductive genetic interactions are important, and further study is urgently needed to support an integrated understanding of aquaculture-ecosystem interactions, their implications for ecosystem stability, and the development of potential mitigation and management strategies

A microsatellite baseline for genetic stock identification of European Atlantic salmon (Salmo salar L.)

Atlantic salmon (Salmo salar L.) populations from different river origins mix in the North Atlantic during the marine life stage. To facilitate marine stock identification, we developed a genetic baseline covering the European component of the species’ range excluding the Baltic Sea, from the Russian River Megra in the north-east, the Icelandic Ellidaar in the west, and the Spanish Ulla in the south, spanning 3737 km North to South and 2717 km East to West. The baseline encompasses data for 14 microsatellites for 26 822 individual fish from 13 countries, 282 rivers, and 467 sampling sites. A hierarchy of regional genetic assignment units was defined using a combination of distance-based and Bayesian clustering. At the top level, three assignment units were identified comprising northern, southern, and Icelandic regions. A second assignment level was also defined, comprising eighteen and twenty-nine regional units for accurate individual assignment and mixed stock estimates respectively. The baseline provides the most comprehensive geographical coverage for an Atlantic salmon genetic data-set, and a unique resource for the conservation and management of the species in Europe. It is freely available to researchers to facilitate identification of the natal origin of European salmon

Short report: craniosynostosis, a late complication of nutritional rickets

OBJECTIVES: Nutritional rickets may be a preventable cause of craniosynostosis. This potential association is under-recognised. A late diagnosis of craniosynostosis may result in reduced brain growth, raised intracranial pressure and long-term psychosocial problems. CASE PRESENTATION: We present four cases of craniosynostosis associated with nutritional rickets. Those who had delayed presentation underwent emergency craniotomy. CONCLUSIONS: Treatment of nutritional rickets and early identification of craniosynostosis can reduce morbidity in these children

The early marine distribution of Atlantic salmon in the North-east Atlantic : A genetically informed stock-specific synthesis

The survival of Atlantic salmon (Salmo salar), an increasingly rare anadromous species, has declined dramatically during its marine phase, with disproportionate impacts on the poorly understood early post-smolt period. Logistical constraints on collecting oceanic data to inform this issue pose a formidable obstacle. To advance understanding of post-smolt distributional ecology in the North-east Atlantic, a comprehensive analysis of existing information was undertaken. Data were synthesized from 385 marine cruises, 10,202 individual trawls, and 9,269 captured post-smolts, spanning three decades and similar to 4.75 million km(2) of ocean, with 3,423 individuals genetically assigned to regional phylogeographic origin. The findings confirm major migrational post-smolt aggregations on the continental shelf-edge off Ireland, Scotland and Norway, and an important marine foraging area in the Norwegian Sea. Genetic analysis shows that aggregational stock composition does not simply reflect distance to natal rivers, with northern phylogeographic stock groups significantly under-represented in sampled high-seas aggregations. It identifies a key foraging habitat for southern European post-smolts located in international waters immediately west of the Voring Plateau escarpment, potentially exposing them to a high by-catch mortality from extra-territorial pelagic fisheries. Evidence of the differential distribution of regional stocks points to fundamental differences in their migration behaviours and may lead to inter-stock variation in responses to environmental change and marine survival. The study shows that understanding of post-smolt marine ecology, as regards to stock-specific variations in habitat utilization, biological performance and exposure to mortality factors, can be significantly advanced by data integration across studies and exploiting genetic approaches.Peer reviewe

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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s10709-011-9554-4) contains supplementary material, which is available to authorized users