An improved genetic sex test for Atlantic salmon (Salmo salar L.)

This is the final version. Available from the publisher via the DOI in this record.Accurate determination of sex ratios is an important metric for the conservation and management of wild Atlantic salmon populations. Previously published primers for a male-specific gene were shown to be unreliable at determining sex due to the presence of deletions in the forward primer-binding site. A new forward primer, used in conjunction with the existing reverse primer, greatly improved reliability of the genetic test, correctly assigning gender in samples of known sex. Using DNA extracted from both contemporary and archive tissues, comparison between the two primer sets screened on collections of unknown sex ratio showed significant discrepancies in the number of males identified. The new primer will help improve the management and conservation of Atlantic salmon by providing accurate sex ratios for the setting of Conservation Limits.European Union Interreg France England Channel programme project ‘Salmonid Management Around the Channel’ (SAMARCH)UK Department of Environment, Farming and Rural Affairs (DEFRA

Human mining activity across the ages determines the genetic structure of modern brown trout (Salmo trutta L.) populations.

PublishedJournal ArticleHumans have exploited the earth's metal resources for thousands of years leaving behind a legacy of toxic metal contamination and poor water quality. The southwest of England provides a well-defined example, with a rich history of metal mining dating to the Bronze Age. Mine water washout continues to negatively impact water quality across the region where brown trout (Salmo trutta L.) populations exist in both metal-impacted and relatively clean rivers. We used microsatellites to assess the genetic impact of mining practices on trout populations in this region. Our analyses demonstrated that metal-impacted trout populations have low genetic diversity and have experienced severe population declines. Metal-river trout populations are genetically distinct from clean-river populations, and also from one another, despite being geographically proximate. Using approximate Bayesian computation (ABC), we dated the origins of these genetic patterns to periods of intensive mining activity. The historical split of contemporary metal-impacted populations from clean-river fish dated to the Medieval period. Moreover, we observed two distinct genetic populations of trout within a single catchment and dated their divergence to the Industrial Revolution. Our investigation thus provides an evaluation of contemporary population genetics in showing how human-altered landscapes can change the genetic makeup of a species.Environment AgencyWest Country Rivers TrustUniversity of Exete

Development of SNP markers derived from RAD sequencing for Atlantic salmon (Salmo salar L.) inhabiting the rivers of southern England

This is the final version. Available on open access from Springer via the DOI in this recordData availability: SNP genotypes are available upon request from the lead author.The rivers of the Hampshire Basin, southern England contain a genetically unique group of Atlantic salmon that have suffered dramatic declines in numbers over the last 40 years. Knowledge of levels and patterns of genetic diversity is essential for effective management of these vulnerable populations. Using restriction site-associated DNA sequencing (RADseq) data, we describe the development and characterisation of a panel of 94 single nucleotide polymorphism (SNP) loci for salmon from this region and investigate their applicability and variability in both target (i.e. southern English) and non-target populations. The SNP loci will be useful for population genetic and assignment studies on Atlantic salmon within the UK and beyond.European UnionSouthern Wate

Historical processes and contemporary anthropogenic activities influence genetic population dynamics of Nassau grouper (Epinephelus striatus) within The Bahamas

This is the final version of the article. Available from Frontiers Media via the DOI in this record.Severe declines of endangered Nassau grouper (Epinephelus striatus) across The Bahamas and Caribbean have spurred efforts to improve their fisheries management and population conservation. The Bahamas is reported to hold the majority of fish spawning aggregations for Nassau grouper, however, the status and genetic population structure of fish within the country is largely unknown, presenting a major knowledge gap for their sustainable management. Between August 2014-February 2017, 464 individual Nassau grouper sampled from The Bahamas were genotyped using 15 polymorphic microsatellite loci to establish measures of population structure, genetic diversity and effective population size (N e ). Nassau grouper were characterized by mostly high levels of genetic diversity, but we found no evidence for geographic population structure. Microsatellite analyses revealed weak, but significant genetic differentiation of Nassau grouper throughout the Bahamian archipelago (Global FST 0.00236, p = 0.0001). Temporal analyses of changes in N e over the last 1,000 generations provide evidence in support of a pronounced historic decline in Bahamian Nassau grouper that appears to pre-date anthropogenic fishing activities. M-ratio results corroborate significant reductions in N e throughout The Bahamas, with evidence for population bottlenecks in three islands and an active fish spawning aggregation along with apparent signs of inbreeding at two islands. Current estimates of N e for Nassau grouper are considerably lower compared with historic levels. These findings represent important new contributions to our understanding of the evolutionary history, demographics and genetic connectivity of this endangered species, which are of critical importance for advancing their sustainable management.Molecular research was financially supported by the University of Exeter and research cruises were funded by the John G. Shedd Aquarium. Partial funding for KS was provided by the Shirley Oakes Butler Charitable Trust, Rotary Club of East Nassau and a private donation by I. de la Rocha

Atlantic salmon Salmo salar in the chalk streams of England are genetically unique.

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this recordRecent research has identified genetic groups of Atlantic salmon Salmo salar that show association with geological and environmental boundaries. This study focuses on one particular subgroup of the species inhabiting the chalk streams of southern England, U.K. These fish are genetically distinct from other British and European S. salar populations and have previously demonstrated markedly low admixture with populations in neighbouring regions. The genetic population structure of S. salar occupying five chalk streams was explored using 16 microsatellite loci. The analysis provides evidence of the genetic distinctiveness of chalk-stream S. salar in southern England, in comparison with populations from non-chalk regions elsewhere in western Europe. Little genetic differentiation exists between the chalk-stream populations and a pattern of isolation by distance was evident. Furthermore, evidence of temporal stability of S. salar populations across the five chalk streams was found. This work provides new insights into the temporal stability and lack of genetic population sub-structuring within a unique component of the species' range of S. salar.This research was funded by the Game & Wildlife Conservation Trust and the Atlantic Salmon Trust, with additional support from the Salmon and Trout Association, the Westcountry Rivers Trust and the University of Exeter

Small coastal streams - Critical reservoirs of genetic diversity for trout (Salmo trutta L.) in the face of increasing anthropogenic stressors

This is the final version. Available on open access from Wiley via the DOI in this recordWe used microsatellite markers to investigate levels and structuring of genetic diversity in trout (Salmo trutta L.) sampled from 16 rivers along the south coast of Cornwall in southwest England. This region is characterized by many small coastal streams with a few larger catchments. At a regional level, genetic structuring of contemporary populations has been influenced by a combination of events, including the last Ice Age and also more recent human activities over the last millennium. All populations are shown to have gone through strong genetic bottlenecks, coinciding with increased exploitation of mineral resources within catchments, beginning during the Medieval period. At more local levels, contemporary human-induced habitat fragmentation, such as weir and culvert construction, has disproportionally affected trout populations in the smaller catchments within the study area. However, where small catchments are relatively unaffected by such activities, they can host trout populations with diversity levels comparable to those found in larger rivers in the region. We also predict significant future loses of diversity and heterozygosity in the trout populations inhabiting small, isolated catchments. Our study highlights how multiple factors, especially the activity of humans, have and continue to affect the levels and structuring of genetic diversity in trout over long timescales.European Union 2007‐2013 Atlantic Area Programme INTERREG III B initiativeAtlantic Salmon TrustSalmonid Management Around the Channel (SAMARCH) projec

Has stocking contributed to an increase in the rod catch of anadromous trout (Salmo trutta L.) in the Shetland Islands, UK?

This is the final version. Available on open access from Wiley via the DOI in this recordThe stocking of hatchery-origin fish into rivers and lakes has long been used in fisheries management to try to enhance catches, especially for trout and salmon species. Frequently, however, the long-term impacts of stocking programmes have not been evaluated. In this study, the authors investigate the contribution of a stocking programme undertaken to support the rod catch of sea trout in the Shetland Islands, UK. Once a highly productive recreational fishery, Shetland sea trout catches crashed in the mid-1990s. Around the time that stocking began, increases in rod catches were also reported, with advocates of the stocking highlighting the apparent success of the programme. Using a suite of genetic markers (microsatellites), this study explores the contribution of the stocking programme to the Shetland sea trout population. The authors found that the domesticated broodstock and wild spawned brown trout from seven streams were genetically distinct. Despite extensive stocking, wild spawned brown trout dominated, even in those streams with a long history of supplementation. The majority of sea trout caught and analysed were of wild origin – only a single individual was of pure stocked origin, with a small number of fish being of wild × stocked origins. This study suggests that stocking with a domesticated strain of brown trout has made only a very limited contribution to the Shetland Islands rod catch, and that the revival of sea trout numbers appears to be driven almost exclusively by recovery of trout spawned in the wild.Atlantic Salmon TrustMarine Alliance Science Technology ScotlandScottish Funding Council/Research Grants Council Joint Research Schem

Evaluating the importance of accurate sex ratios on egg deposition targets and conservation limit compliance for Atlantic salmon (Salmo salar L.) in the River Tamar, south‐west England

This is the final version. Available on open access from Wiley via the DOI in this recordData availability statement: The data that support the findings of this study are available from the corresponding author upon reasonable request.Effective management of Atlantic salmon requires a suite of metrics that are fed into stock assessment models to assess stock compliance within individual rivers in relation to estimated conservation limits. Key among metrics required to assess compliance are the number of adult female spawners within each adult sea age class and their corresponding egg deposition rates. Owing to the current need to conserve salmon stocks, adult sex ratios used to calculate egg deposition estimates often depend on data derived from historic lethal sampling. Using non-invasive sampling and an accurate genetic sex test, we determined the proportion of female fish in two adult life history stages (one sea winter and two sea winter) of Atlantic salmon from the River Tamar, an Environment Agency (England) Monitored River. Our results suggested that phenotypic-based sexing of Tamar salmon was unreliable, especially for early run fish and that the proportion of female salmon has been under-estimated, thereby leading to consistent under-estimation of egg deposition rates.UK Department of Environment, Farming and Rural Affairs (DEFRA)Atlantic Salmon Trust (AST)UK Environment Agency (EA)European Union Interreg France England Channel Manche programm

Gender, economics and culture: diversity and the international evolution of smoking prevalence

Aims: To examine whether the observed diversity between national patterns of smoking prevalence could require modification of the World Health Organization (WHO) linear model for an international `smoking pandemic' (a worldwide epidemic) to address data from non-western countries. Method: We conducted secondary research using current measures in three publicly available databases: Globalink, the International Labour Organization and the World Bank (all internetaccessible). The measures we used are the separate percentage data for men and women on: smoking and employment and national income per capita (US$) and percentage growth per annum. Results: Regression analysis showed that women smokers were more frequent in countries with higher national income, but women were less likely to smoke in countries of rapid growth. Men were less likely to smoke in countries with higher national income, but more likely to smoke in countries of rapid growth. Two principle components together explained 62% of all the variance in the international data. The largest factor was positively correlated with the percentage of employed females, the percentage of female smokers and national income per capita, but negatively correlated with the percentage of male smokers and percentage annual growth. The effect of female employment was not continuous, but above a threshold of 51%, was associated with a higher prevalence of female smoking. The smaller, second factor was only weakly correlated with any smoking variables. Conclusions: In his 1994 model (subsequently adopted by the WHO) Lopez looked at historical trends in `stages' of smoking prevalence. These have been associated with `stages' of economic development. We extended this analysis to look at a dynamic change (% annual growth) and a social indicator (employment). Male and female smoking is affected differentially by economic change and by level of income. These are also strongly related to the percentage of women in employment. This has implications for workplace policies on smoking