A. F. Youngson

A critical review of adaptive genetic variation in Atlantic salmon: implications for conservation

Here we critically review the scale and extent of adaptive genetic variation in Atlantic salmon (Salmo salar L.), an important model system in evolutionary and conservation biology that provides fundamental insights into population persistence, adaptive response and the effects of anthropogenic change. We consider the process of adaptation as the end product of natural selection, one that can best be viewed as the degree of matching between phenotype and environment. We recognise three potential sources of adaptive variation: heritable variation in phenotypic traits related to fitness, variation at the molecular level in genes influenced by selection, and variation in the way genes interact with the environment to produce phenotypes of varying plasticity. Of all phenotypic traits examined, variation in body size (or in correlated characters such as growth rates, age of seaward migration or age at sexual maturity) generally shows the highest heritability, as well as a strong effect on fitness. Thus, body size in Atlantic salmon tends to be positively correlated with freshwater and marine survival, as well as with fecundity, egg size, reproductive success, and offspring survival. By contrast, the fitness implications of variation in behavioural traits such as aggression, sheltering behaviour, or timing of migration are largely unkown. The adaptive significance of molecular variation in salmonids is also scant and largely circumstantial, despite extensive molecular screening on these species. Adaptive variation can result in local adaptations (LA) when, among other necessary conditions, populations live in patchy environments, exchange few or no migrants, and are subjected to differential selective pressures. Evidence for LA in Atlantic salmon is indirect and comes mostly from ecological correlates in fitness‐related traits, the failure of many translocations, the poor performance of domesticated stocks, results of a few common‐garden experiments (where different populations were raised in a common environment in an attempt to dissociate heritable from environmentally induced phenotypic variation), and the pattern of inherited resistance to some parasites and diseases. Genotype × environment interactions occurr for many fitness traits, suggesting that LA might be important. However, the scale and extent of adaptive variation remains poorly understood and probably varies, depending on habitat heterogeneity, environmental stability and the relative roles of selection and drift. As maladaptation often results from phenotype‐environment mismatch, we argue that acting as if populations are not locally adapted carries a much greater risk of mismanagement than acting under the assumption for local adaptations when there are none. As such, an evolutionary approach to salmon conservation is required, aimed at maintaining the conditions necessary for natural selection to operate most efficiently and unhindered. This may require minimising alterations to native genotypes and habitats to which populations have likely become adapted, but also allowing for population size to reach or extend beyond carrying capacity to encourage competition and other sources of natural mortality.

Fine sediment influence on salmonid spawning habitat in a lowland agricultural stream: a preliminary assessment

Spawning habitat utilized by Atlantic Salmon (Salmo salar) and Sea Trout (Salmo trutta) was characterized in a 1.6-km reach of the Newmills Burn, a small, highly canalized tributary of the River Don in Aberdeenshire. The Newmills Burn is typical of the intensively farmed lower sub-catchments of the major salmon rivers on the east coast of Scotland. Such streams have substantial potential in providing spawning and juvenile habitat for salmonids, with high redd densities resulting in egg deposition rates of > 5 m2. However, in comparison with upland spawning tributaries draining less intensively managed catchments, canalization and intensive cultivation has seriously degraded the physical characteristics of aquatic habitats in many streams. In the Newmills Burn, spawning gravels have a relatively high (> 20% by mass) fine sediment (< 2 mm in size) content. The burn is characterized by hydraulic conditions that are suitable for salmonid spawning, with modal velocities of 0.50-0.65 m s(-1) and depths of 0.20-0.25 m. However, infiltration of fine sediments into gravels is rapid during hydrological events in the winter months. Thus, complete siltation of open gravel matrices (simulated redds) can occur within a week, and probably within a single moderate to large storm event. Appreciable, but small, deposition of organic and silt/clay particles can also affect spawning gravels. Egg mortalities in redds following spawning are variable, but can be as high as 86% in the Newmills Burn. This may be related to fine sediment infiltration, reduced permeability of spawning gravels and reduced oxygen supply to ova. It appears that the main cause of high influx is sediment loads mobilized from intensively managed land. It is suggested that fundamental changes to the management of agricultural land is required if fish habitats are to be improved and degraded streams are allowed to re-naturalize. The need for closely focused investigations of the causal relationships between fine sediment infiltration and egg survival is stressed.

Variation in river water temperatures in an upland stream over a 30-year period.

Stream water temperature data from the Girnock burn, a 30-km2 catchment in Scotland were examined for systematic variation across 30 years of record (1968-1997). The data suggest that there has been no change in mean annual temperature with time, but at a seasonal level there is some indication of an increase in mean daily maximum temperatures during the winter (December to February) and spring (March to May) seasons. For the spring season, there is also evidence that mean temperature has increased. There are no apparent or obvious changes in stream flow to account for this. The strong relationship between air and stream temperatures (r2 = 0.96) implies that changes in the stream are the result of changes in the climate. It is possible that this may occur as a result of the effect of increasing air temperatures which may have also reduced the influence of snow and snowmelt on the catchment during the winter and spring seasons.

Hydrological controls on nutrient concentrations and fluxes in agricultural catchments

Like many streams draining intensively farmed parts of lowland Scotland, water quality in the Newmills burn, Aberdeenshire, is characterized by relatively high nutrient levels; mean concentrations of NO3-N and NH3-N are 6.09 mg l(-1) and 0.28 mg l(-1), respectively, whilst average PO4-P concentrations reach 0.06 mg l(-1). Nutrient concentrations vary spatially and temporally with levels being highest under arable farming during the autumn and winter. Annual fluxes from the 14.5 km2 catchment are estimated at 25.67 and 1.26 kg ha(-1) a(-1) for NO3-N and NH3-N, respectively, and 0.26 kg ha(-1) a(-1) for PO4-P. Hydrological controls exert a strong influence on both nutrient concentrations and fluxes. Over short timescales nutrient concentrations and fluxes are greatest during storm events when P04-P and NH3-N are mobilized by overland flow in riparian areas, particularly where the soils have been compacted by livestock or farm machinery. Delivery of deeper soil water in subsurface storm flow, facilitated by agricultural under-drainage, provide large contributions of NO3-N on the recession limb of hydrological events. In contrast, groundwater inputs generally have lower NO3 concentrations implying that denitrification may be a pathway of N loss in the saturated zone. Approximately 75% of the N loss for the catchment occurs during the autumn and early winter when high flows dominate the hydrological regime. The close coupling of hydrological pathways and biogeochemical processes has major implications for catchment management strategies such as Nitrate Vulnerable Zones (NVZs) as it is likely that significant groundwater stores with long residence times will continue to cause N losses before water quality improvements become apparent.

Management of salmonid fisheries in the British Isles: towards a practical approach based on population genetics

The evidence for structuring of Atlantic salmon (Salmo salar) and brown trout (Salmo trutta) into distinct reproductive populations and for genetic differentiation and local adaptation is compelling. The effect of genetic variation among populations is demonstrably a factor determining the economic value of salmonid fisheries in the British Isles. Genetic considerations are, therefore, a matter of self-interest for fisheries managers and a shared interest with those advocating more general approaches to the conservation of diversity and variation. The local population is the basic unit of production and, therefore, the preferred unit of management. However, salmonid populations are numerous and many are small. These factors limit practical possibilities for management at the population level. We suggest that this difficulty can be addressed by combining populations in fisheries-biased management units that comprise interchangeable, nested groupings of populations that are both genetically and biologically meaningful. This population-based approach addresses the necessity of managing the fisheries in ways that are consistent with the conservation of adaptive potential in relation to the dynamic aspects of populations, their capacity to respond to changing environmental conditions, and the likelihood that salmonids will remain a worthwhile resource for the future.

Groundwater–surface water interactions in upland Scottish rivers: hydrological, hydrochemical and ecological implications

Synopsis Contrary to previous hydrogeological assumptions, we now know that drift deposits and fracture systems in crystalline rocks can constitute important aquifers in the Scottish Highlands and other montane environments. Groundwater from these aquifers usually has an important influence on the hydrology, hydrochemistry and ecology of upland river systems. Tracer-based research in the Girnock burn catchment in the Cairngorms revealed that groundwater comprises at least 30% of annual runoff. Groundwater often enters stream channels via drift deposits in valley bottom areas, which appear to be fed from recharge areas on the catchment interfluves. A range of groundwater sources exist in the catchment reflecting the complex solid and drift geology. These account for spatial differences in stream hydrochemistry and the spatial delineation of groundwater discharges to rivers and riparian zones. Areas where groundwaters enter the stream channel directly can have profound ecological implications. Most obvious are low rates of salmonid egg survival where chemically reduced groundwater discharges through the hyporheic zone. However, it is argued that only further research will reveal the full significance of groundwater–surface water interactions to the ecological status of Scottish rivers.

Frequency of occurrence of reared Atlantic salmon in Scottish salmon fisheries

Marine salmon farming in Scotland is restricted to sheltered inshore locations in four main geographical areas - the western coast, the Western Isles, the Orkney Islands, and the Shetland Islands. Rivers supporting runs of wild salmon are present on the western, northern, and eastern coasts of mainland Scotland and in the Western Isles. Since 1981, coastal fisheries and rivers have been monitored using a variety of methods to detect the presence of reared salmon, including those that have escaped from sea-cages. On the east coast and in the eastern rivers, reared salmon have not been detectable or have been detected only at low frequencies in catches - even in years when they were frequent among western coastal catches and when the progeny of females containing synthetic flesh colourant were widespread and sometimes frequent in western rivers. The eastern Scottish rivers are one of the principal world sources of early-running salmon and therefore include an important component of the phenotypic (and probably genetic) diversity associated with Atlantic salmon. In a European context, the eastern Scottish rivers constitute one of the greatest continuous units of wild salmon production that can be shown to have remained substantially free of escaped farmed salmon. 0 1997 International Council for the Exploration of the Sea

Divergent trends in anadromous salmonid populations in Norwegian and Scottish rivers.

The Atlantic salmon (Salmo salar) is a charismatic anadromous fish of high conservation and economic value. Concerns have been expressed regarding the long-term viability of fisheries throughout the speciess distributional range because of abundance variations that cannot currently be explained or predicted. Here, we analyse long-term catch data obtained over a wide geographical range and across a range of spatial subscales to understand more fully the factors that drive population abundance. We use rod catch data from 84 Norwegian rivers over 125 years (1876–2000) and 48 Scottish rivers over 51 years (1952–2002). The temporal correlation in catches is very long-term, with trends persisting over several decades. The spatial correlation is relatively short-range, indicating strong local-scale effects on catch. Furthermore, Scottish salmon populations exhibit recent negative trends in contrast to some more positive trends in Norway—especially in the north.

Process-based modelling of decadal trends in growth, survival, and smolting of wild salmon (Salmo salar) parr in a Scottish upland stream

This paper reports a new model of the freshwater stages of an anadromous fish, at the core of which is a stochastic description of the size-at-age dynamics of a growing cohort. Emigration is assumed to require the individual to exceed a threshold size at a critical time of year, thus making the distributions of survival to, and age at, smolting emergent properties of the model. The model is applied to a long-term data set on juvenile Atlantic salmon (Salmo salar) in the Girnock Burn, Scotland, to understand the role played by decadal temperature trends in generating changes in smolt production and age distribution. We conclude that changes in age at smolting are compatible with causation by shifts in the temperature regime. However, the large attenuation between a dramatic fall in spawner numbers and a relatively minor diminution in total smolt production does not result from the physiological effects of temperature but is rather a result of strongly density-dependent mortality between the deposition of o...

An approach to assessing hydrological influences on feeding opportunities of juvenile atlantic salmon (Salmo salar) : a case study of two contrasting years in a small, nursery stream

This case study sought to examine how temporal variability in hydrological and hydraulic conditions might affect the feeding opportunities of juvenile Atlantic salmon in two hydrologically contrasting years of 2002 and 2003, which were characterised by high and low flows respectively. Firstly, measures of hydraulic influence were calculated to define what might be ecologically meaningful disturbance periods during high flows. Secondly, for identifying such periods, the parameter Critical Displacement Velocity (CDV) was derived from a river discharge time series as a first approximation of the amount of time in two hydrologically extreme years when fish foraging strategies for specific age classes of juvenile Atlantic salmon (Salmo salar) might be disrupted by flows. The CDV estimates the threshold velocity above which juvenile salmon are unable to hold station and it is dependent upon fish size and stream temperature. In the wet year 2002, the CDV was exceeded on 18% and 21% of days for 0+ and 1+ fish respectively. In 2003 these respective numbers fell to 6% and 15%. The data suggest that hydrological conditions during certain times of the year have the potential to affect foraging behaviour. This in turn might have implications for recruitment and growth rates for juvenile salmon in upland streams.