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.
As stream temperatures increase due to factors such as heated runoff from impervious surfaces, deforestation, and climate change, fish species adapted to cold water streams are forced to move to more ...suitable habitat, acclimate or adapt to increased thermal regimes, or die. To estimate the potential for adaptation, a (within individual) repeatable metric of thermal tolerance is imperative. Critical thermal maximum (CTmax) is a dynamic test that is widely used to measure thermal tolerance across many taxa and has been used in fishes for decades, but its repeatability in most species is unknown. CTmax tests increase water temperature steadily over time until loss of equilibrium (LOE) is achieved. To determine if CTmax is a consistent metric within individual fish, we measured CTmax on the same lab-held individually-marked adult brook trout Salvelinus fontinalis at three different times (August & September 2016, September 2017). We found that CTmax is a repeatable trait (Repeatability ± S.E.: 0.48 ± 0.14). CTmax of individuals males was consistent over time, but the CTmax of females increased slightly over time. This result indicates that CTmax is a robust, repeatable estimate of thermal tolerance in a cold-water adapted fish.
•Critical thermal maximum is a test that is widely used to measure thermal tolerance.•Within individual brook trout, critical thermal maximum was highly repeatable.•Critical thermal maximum of female brook trout increased slightly over time.•Fish size did not influence critical thermal maximum.•Cumulative degree minutes was a robust measure of critical thermal maximum.
A 5 year individual‐based data set was used to estimate size‐specific survival rates in a wild brook trout Salvelinus fontinalis population in a stream network encompassing a mainstem and three ...tributaries (1·5–6 m wetted width), western Massachusetts, U.S.A. The relationships between survival in summer and temperature and flow metrics derived from continuous monitoring data were then tested. Increased summer temperatures significantly reduced summer survival rates for S. fontinalis in almost all size classes in all four sites throughout the network. In contrast, extreme low summer flows reduced survival of large fish, but only in small tributaries, and had no significant effects on fish in smaller size classes in any location. These results provide direct evidence of a link between season‐specific survival and environmental factors likely to be affected by climate change and have important consequences for the management of both habitats and populations.
create is a Windows program for the creation of new and conversion of existing data input files for 52 genetic data analysis software programs. Programs are grouped into areas of sibship ...reconstruction, parentage assignment, genetic data analysis, and specialized applications. create is able to read in data from text, Microsoft Excel and Access sources and allows the user to specify columns containing individual and population identifiers, birth and death data, sex data, relationship information, and spatial location data. create's only constraints on source data are that one individual is contained in one row, and the genotypic data is contiguous. create is available for download at http://www.lsc.usgs.gov/CAFL/Ecology/Software.html.
Development in the southeastern US coastal plain generates the need for a better understanding of how survival and abundance of estuarine nekton respond to urbanization. Apparent survival and density ...of the dominant Atlantic coast salt marsh fish, the mummichog Fundulus heteroclitus, were estimated in four North Carolina tidal creeks using a model simultaneously fitted to mark-resight and mark-recapture data. Rates of weekly loss (mortality plus emigration) were high (~ 10 %). Sampling for tagged fish within and outside of study creeks showed high site fidelity to each creek, indicating that loss largely resulted from mortality rather than emigration. Estimated rates of apparent survival were lowest in the creek with the least instream-and watershed-level impacts. This creek has direct (non-culvert) access downstream to a larger waterbody, suggesting that enhanced access by predators and/or greater rates of permanent emigration may have contributed to lower apparent survival in this creek. There was a positive relation between minnow trap catch-per-unit-effort (CPUE) and density allowing the relationship between CPUE and habitat and urbanization to be examined in a total of six creeks. The largest CPUE estimates occurred early in each growing season and were associated with creeks possessing characteristics most representative of undisturbed salt marsh mosaics: high percentage of marsh coverage instream and downstream and high percentage of marsh edge. Given generally limited movement outside of creeks, differences in abundance among creeks likely result from different levels of recruitment that are related to salt marsh availability. Priority preservation of salt marsh habitats may be warranted by natural resource planners to maintain abundance levels of this trophically important species.
We evaluated the performance of small (12.5 mm long) passive integrated transponder (PIT) tags and custom detection antennas for obtaining fine-scale movement and demographic data of mummichog ...Fundulus heteroclitus in a salt marsh creek. Apparent survival and detection probability were estimated using a Cormack Jolly Seber (CJS) model fitted to detection data collected by an array of 3 vertical antennas from November 2010 to March 2011 and by a single horizontal antenna from April to August 2011. Movement of mummichogs was monitored during the period when the array of vertical antennas was used. Antenna performance was examined in situ using tags placed in wooden dowels (drones) and in live mummichogs. Of the 44 tagged fish, 42 were resighted over the 9 mo monitoring period. The in situ detection probabilities of the drone and live mummichogs were high (~80−100%) when the ambient water depth was less than ~0.8 m. Upstream and downstream movement of mummichogs was related to hourly water depth and direction of tidal current in a way that maximized time periods over which mummichogs utilized the intertidal vegetated marsh. Apparent survival was lower during periods of colder water temperatures in December 2010 and early January 2011 (median estimate of daily apparent survival = 0.979) than during other periods of the study (median estimate of daily apparent survival = 0.992). During late fall and winter, temperature had a positive effect on the CJS detection probability of a tagged mummichog, likely due to greater fish activity over warmer periods. During the spring and summer, this pattern reversed possibly due to mummichogs having reduced activity during the hottest periods. This study demonstrates the utility of PIT tags and continuously operating autonomous detection systems for tracking fish at fine temporal scales, and improving estimates of demographic parameters in salt marsh creeks that are difficult or impractical to sample with active fishing gear.
We present a simulation model in which individual adult migrant American shad (
Alosa sapidissima
) ascend the Connecticut River and spawn, and survivors return to the marine environment. Our ...approach synthesizes bioenergetics, reproductive biology, and behavior to estimate the effects of migratory distance and delays incurred at dams on spawning success and survival. We quantified both the magnitude of effects and the consequences of uncertainty in the estimates of input variables. Behavior, physiology, and energetics strongly affected both the distribution of spawning effort and survival to the marine environment. Delays to both upstream and downstream movements had dramatic effects on spawning success, determining total fecundity and spatial extent of spawning. Delays, combined with cues for migratory reversal, also determined the likelihood of survival. Spawning was concentrated in the immediate vicinity of dams and increased with greater migratory distance and delays to downstream migration. More research is needed on reproductive biology, behavior, energetics, and barrier effects to adequately understand the interplay of the various components of this model;; it does provide a framework, however, that suggests that provision of upstream passage at dams in the absence of expeditious downstream passage may increase spawning success but at the expense of reduced iteroparity.
Threats to aquatic biodiversity are expressed at broad spatial scales, but identifying regional trends in abundance is challenging owing to variable sampling designs and temporal and spatial ...variation in abundance. We compiled a regional data set of brook trout (Salvelinus fontinalis) counts across their southern range representing 326 sites from eight states between 1982 and 2014 and conducted a statistical power analysis using Bayesian state-space models to evaluate the ability to detect temporal trends by characterizing posterior distributions with three approaches. A combination of monitoring periods, number of sites and electrofishing passes, decline magnitude, and different revisit patterns were tested. Power increased with monitoring periods and decline magnitude. Trends in adults were better detected than young-of-the-year fish, which showed greater interannual variation in abundance. The addition of weather covariates to account for the temporal variation increased power only slightly. Single- and three-pass electrofishing methods were similar in power. Finally, power was higher for sampling designs with more frequent revisits over the duration of the monitoring program. Our results provide guidance for broad-scale monitoring designs for temporal trend detection.
Organisms that share the same genotype can develop into divergent phenotypes, depending on environmental conditions. In Atlantic salmon, young males of the same age can be found either as sneakers or ...immature males that are future anadromous fish. Just as the organism-level phenotype varies between divergent male developmental trajectories, brain gene expression is expected to vary as well. We hypothesized that rearing environment can also have an important effect on gene expression in the brain and possibly interact with the reproductive tactic adopted. We tested this hypothesis by comparing brain gene expression profiles of the two male tactics in fish from the same population that were reared in either a natural stream or under laboratory conditions. We found that expression of certain genes was affected by rearing environment only, while others varied between male reproductive tactics independent of rearing environment. Finally, more than half of all genes that showed variable expression varied between the two male tactics only in one environment. Thus, in these fish, very different molecular pathways can give rise to similar macro-phenotypes depending on rearing environment. This result gives important insights into the molecular underpinnings of developmental plasticity in relationship to the environment.
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