The signature of fine scale local adaptation in Atlantic salmon revealed from common garden experiments in nature

Understanding the extent, scale and genetic basis of local adaptation (LA) is important for conservation and management. Its relevance in salmonids at microgeographic scales, where dispersal (and hence potential gene flow) can be substantial, has however been questioned. Here, we compare the fitness of communally reared offspring of local and foreign Atlantic salmon Salmo salar from adjacent Irish rivers and reciprocal F-1 hybrid crosses between them, in the wild home\u27 environment of the local population. Experimental groups did not differ in wild smolt output but a catastrophic flood event may have limited our ability to detect freshwater performance differences, which were evident in a previous study. Foreign parr exhibited higher, and hybrids intermediate, emigration rates from the natal stream relative to local parr, consistent with genetically based behavioural differences. Adult return rates were lower for the foreign compared to the local group. Overall lifetime success of foreigners and hybrids relative to locals was estimated at 31% and 40% (mean of both hybrid groups), respectively. The results imply a genetic basis to fitness differences among populations separated by only 50km, driven largely by variation in smolt to adult return rates. Hence even if supplementary stocking programs obtain broodstock from neighbouring rivers, the risk of extrinsic outbreeding depression may be high

Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling:A power analysis

Background: Pedigree reconstruction using genetic analysis provides a useful means to estimate fundamental population biology parameters relating to population demography, trait heritability and individual fitness when combined with other sources of data. However, there remain limitations to pedigree reconstruction in wild populations, particularly in systems where parent-offspring relationships cannot be directly observed, there is incomplete sampling of individuals, or molecular parentage inference relies on low quality DNA from archived material. While much can still be inferred from incomplete or sparse pedigrees, it is crucial to evaluate the quality and power of available genetic information a priori to testing specific biological hypotheses. Here, we used microsatellite markers to reconstruct a multi-generation pedigree of wild Atlantic salmon (Salmo salar L.) using archived scale samples collected with a total trapping system within a river over a 10 year period. Using a simulation-based approach, we determined the optimal microsatellite marker number for accurate parentage assignment, and evaluated the power of the resulting partial pedigree to investigate important evolutionary and quantitative genetic characteristics of salmon in the system. Results: We show that at least 20 microsatellites (ave. 12 alleles/locus) are required to maximise parentage assignment and to improve the power to estimate reproductive success and heritability in this study system. We also show that 1.5 fold differences can be detected between groups simulated to have differing reproductive success, and that it is possible to detect moderate heritability values for continuous traits (h2 ~ 0.40) with more than 80% power when using 28 moderately to highly polymorphic markers. Conclusion: The methodologies and work flow described provide a robust approach for evaluating archived samples for pedigree-based research, even where only a proportion of the total population is sampled. The results demonstrate the feasibility of pedigree-based studies to address challenging ecological and evolutionary questions in free-living populations, where genealogies can be traced only using molecular tools, and that significant increases in pedigree assignment power can be achieved by using higher numbers of markers

The signature of fine scale local adaptation in Atlantic salmon revealed from common garden experiments in nature

Understanding the extent, scale and genetic basis of local adaptation (LA) is important for conservation and management. Its relevance in salmonids at microgeographic scales, where dispersal (and hence potential gene flow) can be substantial, has however been questioned. Here, we compare the fitness of communally reared offspring of local and foreign Atlantic salmon Salmo salar from adjacent Irish rivers and reciprocal F-1 hybrid crosses between them, in the wild home' environment of the local population. Experimental groups did not differ in wild smolt output but a catastrophic flood event may have limited our ability to detect freshwater performance differences, which were evident in a previous study. Foreign parr exhibited higher, and hybrids intermediate, emigration rates from the natal stream relative to local parr, consistent with genetically based behavioural differences. Adult return rates were lower for the foreign compared to the local group. Overall lifetime success of foreigners and hybrids relative to locals was estimated at 31% and 40% (mean of both hybrid groups), respectively. The results imply a genetic basis to fitness differences among populations separated by only 50km, driven largely by variation in smolt to adult return rates. Hence even if supplementary stocking programs obtain broodstock from neighbouring rivers, the risk of extrinsic outbreeding depression may be high

Chronic Kidney Disease Severity Is Associated With Selective Expansion of a Distinctive Intermediate Monocyte Subpopulation

Chronic kidney disease (CKD) affects 11–13% of the world's population and greatly increases risk of atherosclerotic cardiovascular disease (ASCVD) and death. It is characterized by systemic inflammation and disturbances in the blood leukocytes that remain incompletely understood. In particular, abnormalities in the numbers and relative proportions of the three major monocyte subsets—classical, intermediate, and non-classical—are described in CKD and end-stage renal disease. In this study, we characterized absolute numbers of blood leukocyte subtypes in adults with renal function varying from normal to advanced CKD. The primary aim was to identify monocyte subpopulations that associated most closely with current estimated glomerular filtration rate (eGFR) and subsequent rate of eGFR decline. Leucocyte and monocyte populations were enumerated by multi-color flow cytometry of whole blood and peripheral blood mononuclear cell (PBMC) samples from adults with CKD stage 1–5 (n = 154) and healthy adults (n = 33). Multiple-linear regression analyses were performed to identify associations between numbers of leucocyte and monocyte populations and clinical characteristics including eGFR and rate of eGFR decline with adjustment for age and gender. In whole blood, total monocyte and neutrophil, but not lymphocyte, numbers were higher in adults with CKD 1-5 compared to no CKD and were significantly associated with current eGFR even following correction for age. In PBMC, classical and intermediate monocyte numbers were higher in CKD 1-5 but only intermediate monocyte numbers were significantly associated with current eGFR in an age-corrected analysis. When intermediate monocytes were further sub-divided into those with mid- and high-level expression of class II MHC (HLA-DRmid and HLA-DRhi intermediate monocytes) it was found that only DRhi intermediate monocytes were increased in number in CKD 1-5 compared to no CKD and were significantly associated with eGFR independently of age among the total (No CKD + CKD 1-5) study cohort as well as those with established CKD (CKD 1-5 only). Furthermore, blood number of DRhi intermediate monocytes alone proved to be significantly associated with subsequent rate of renal functional decline. Together, our data confirm neutrophil and monocyte subset dysregulation in CKD and identify a distinct subpopulation of intermediate monocytes that is associated with higher rate of loss of kidney function

Inshore and offshore marine migration pathways of Atlantic salmon post-smolts from multiple rivers in Scotland, England, Northern Ireland, and Ireland

The migratory behavior of Atlantic salmon (Salmo salar) post-smolts in coastal waters is poorly understood. In this collaborative study, 1914 smolts, from 25 rivers, in four countries were tagged with acoustic transmitters during a single seasonal migration. In total, 1105 post-smolts entered the marine study areas and 438 (39.6%) were detected on a network of 414 marine acoustic receivers and an autonomous underwater vehicle. Migration pathways (defined as the shortest distance between two detections) of up to 575 km and over 100 days at sea were described for all 25 populations. Post-smolts from different rivers, as well as individuals from the same river, used different pathways in coastal waters. Although difficult to generalize to all rivers, at least during the year of this study, no tagged post-smolts from rivers draining into the Irish Sea were detected entering the areas of sea between the Hebrides and mainland Scotland, which is associated with a high density of finfish aquaculture. An important outcome of this study is that a high proportion of post-smolts crossed through multiple legislative jurisdictions and boundaries during their migration. This study provides the basis for spatially explicit assessment of the impact risk of coastal pressures on salmon during their first migration to sea

Maintenance of professional competence in Ireland: a national survey of doctors’ attitudes and experiences

Objectives Programmes to ensure doctors’ maintenance of professional competence (MPC) have been established in many countries. Since 2011, doctors in Ireland have been legally required to participate in MPC. A significant minority has been slow to engage with MPC, mirroring the contested nature of such programmes internationally. This study aimed to describe doctors’ attitudes and experiences of MPC in Ireland with a view to enhancing engagement.Participants All registered medical practitioners in Ireland required to undertake MPC in 2018 were surveyed using a 33-item cross-sectional mixed-methods survey designed to elicit attitudes, experiences and suggestions for improvement.Results There were 5368 responses (response rate 42%). Attitudes to MPC were generally positive, but the time, effort and expense involved outweighed the benefit for half of doctors. Thirty-eight per cent agreed that MPC is a tick-box exercise. Heavy workload, travel, requirement to record continuing professional development activities and demands placed on personal time were difficulties cited. Additional support, as well as higher quality, more varied educational activities, were among suggested improvements. Thirteen per cent lacked confidence that they could meet requirements, citing employment status as the primary issue. MPC was particularly challenging for those working less than full-time, in locum or non-clinical roles, and taking maternity or sick leave. Seventy-seven per cent stated a definite intention to comply with MPC requirements. Being male, or having a basic medical qualification from outside Ireland, was associated with less firm intention to comply.Conclusions Doctors need to be convinced of the benefits of MPC to them and their patients. A combination of clear communication and improved relevance to practice would help. Addition of a facilitated element, for example, appraisal, and varied ways to meet requirements, would support participation. MPC should be adequately resourced, including provision of high-quality free educational activities. Systems should be established to continually evaluate doctors’ perspectives

Spawning-related movements in a salmonid appear timed to reduce exposure to visually oriented predators

Animals often exhibit extensive flexibility in movement behaviours on a range of temporal and spatial scales in response to cues that reliably predict fitness outcomes. The annual timing of movements between distinct habitats can be crucial, particularly in seasonal environments with narrow ecological windows of opportunity. In polygamous species, sexual selection may further shape sex-specific phenology and movement behaviours. Here, we characterized seasonal, daily and diel movement patterns in adult brown trout, Salmo trutta, between a lake feeding habitat and two spawning streams in northwestern Ireland, using passive integrated transponder (PIT) telemetry. Antennae positioned at the inflow and outflow of the lake were used to monitor movements of 197 lake-tagged adults between lake and stream habitats. Across 2 years in both streams, movements were overwhelmingly nocturnal and exhibited distinct seasonality, with a peak in daily detections close to the winter solstice. In both streams, seasonal movement activity of males began and peaked before that of females (protandry). Daily detection probabilities for both sexes increased as the moon waned (decreasing lunar illumination) and as river depth increased, the latter being associated with reduced water clarity. These findings are consistent with fish favouring movement between fluvial and lacustrine habitats when light (both solar and lunar) or hydrological conditions decrease their exposure to visually oriented predators. The observed protandry also suggests a role for intrasexual male competition, whereby earlier male arrival could increase mating opportunities

Fitness reduction and potential extinction of wild populations of Atlantic salmon, Salmo salar, as a result of interactions with escaped farm salmon.

The high level of escapes from Atlantic salmon farms, up to two million fishes per year in the North Atlantic, has raised concern about the potential impact on wild populations. We report on a two-generation experiment examining the estimated lifetime successes, relative to wild natives, of farm, F(1) and F(2) hybrids and BC(1) backcrosses to wild and farm salmon. Offspring of farm and "hybrids" (i.e. all F(1), F(2) and BC(1) groups) showed reduced survival compared with wild salmon but grew faster as juveniles and displaced wild parr, which as a group were significantly smaller. Where suitable habitat for these emigrant parr is absent, this competition would result in reduced wild smolt production. In the experimental conditions, where emigrants survived downstream, the relative estimated lifetime success ranged from 2% (farm) to 89% (BC(1) wild) of that of wild salmon, indicating additive genetic variation for survival. Wild salmon primarily returned to fresh water after one sea winter (1SW) but farm and 'hybrids' produced proportionately more 2SW salmon. However, lower overall survival means that this would result in reduced recruitment despite increased 2SW fecundity. We thus demonstrate that interaction of farm with wild salmon results in lowered fitness, with repeated escapes causing cumulative fitness depression and potentially an extinction vortex in vulnerable populations

Doctors\u27 attitudes to, beliefs about, and experiences of the regulation of professional competence: A scoping review protocol

Background: Historically, individual doctors were responsible for maintaining their own professional competence. More recently, changing patient expectations, debate about the appropriateness of professional self-regulation, and high-profile cases of malpractice have led to a move towards formal regulation of professional competence (RPC). Such programmes require doctors to demonstrate that they are fit to practice, through a variety of means. Participation in RPC is now part of many doctors’ professional lives, yet it remains a highly contested area. Cost, limited evidence of impact, and lack of relevance to practice are amongst the criticisms cited. Doctors’ attitudes towards RPC, their beliefs about its objectives and effectiveness, and their experiences of trying to meet its requirements can impact engagement with the process. We aim to conduct a scoping review to map the empirical literature in this area, to summarise the key findings, and to identify gaps for future research. Methods: We will conduct our review following the six phases outlined by Arksey and O’Malley, and Levac. We will search seven electronic databases: Academic Search Complete, Business Source Complete, CINAHL, PsycINFO, PubMed, Social Sciences Full Text, and SocINDEX for relevant publications, and the websites of medical regulatory and educational organisations for documents. We will undertake backward and forward citation tracking of selected studies and will consult with international experts regarding key publications. Two researchers will independently screen papers for inclusion and extract data using a piloted data extraction tool. Data will be collated to provide a descriptive summary of the literature. A thematic analysis of the key findings will be presented as a narrative summary of the literature. Discussion: We believe that this review will be of value to those tasked with the design and implementation of RPC programmes, helping them to maximise doctors’ commitment and engagement, and to researchers, pointing to areas that would benefit from further enquiry. This research is timely; internationally existing programmes are evolving, new programmes are being initiated, and many jurisdictions do not yet have programmes in place. There is an opportunity for learning across different programmes and from the experiences of established programmes. Our review will support that learning. Systematic review registration: PROSPERO does not register scoping reviews