Early-season brown trout (Salmo trutta) migrants grow and survive better at sea.

The timing of seaward migration is a key life-history trait for many anadromous fish species, with growth and survival at sea depending on a match/mismatch scenario between the timing of the sea entry and optimal conditions. Based on a 25-year study with 15,226 individually tagged brown trout (Salmo trutta) in a Norwegian river, we analysed how the within-season timing of sea migration impacted growth and survival. In both first-time and veteran migrants, marine growth was highest for early migrating individuals, large individuals, and those with a low condition factor when entering the sea. Survival was highest for individuals entering the sea early in the season. In first-time migrants, survival increased with body length. Survival also increased with the number of other smolts migrating simultaneously. As the early smolts were the most successful, it may seem strange that many smolts migrate later in the season. We suggest that late-migrating smolts may not be of a size and/or physiological state suitable for early marine conditions, and may make the best of a bad situation.

Introgression from farmed escapees affects the full life cycle of wild Atlantic salmon.

After a half a century of salmon farming, we have yet to understand how the influx of genes from farmed escapees affects the full life history of Atlantic salmon (Salmo salar L.) in the wild. Using scale samples of over 6900 wild adult salmon from 105 rivers, we document that increased farmed genetic ancestry is associated with increased growth throughout life and a younger age at both seaward migration and sexual maturity. There was large among-population variation in the effects of introgression. Most saliently, the increased growth at sea following introgression declined with the population's average growth potential. Variation at two major-effect loci associated with age at maturity was little affected by farmed genetic ancestry and could not explain the observed phenotypic effects of introgression. Our study provides knowledge crucial for predicting the ecological and evolutionary consequences of increased aquaculture production worldwide.

Joint temporal trends in river thermal and hydrological conditions can threaten the downstream migration of the critically endangered European eel.

Climate change is modifying the hydrological and thermal regimes of rivers worldwide, threatening the triggering of organisms' key life-cycle processes. European eel (Anguilla anguilla) is a critically endangered fish species that migrates over several thousand kilometres between its rearing habitats in continental waters of Europe and North Africa and its spawning area in the Sargasso Sea. Downstream migration of adult eels occurs during periods of decreasing river water temperature associated with high discharge but changes in these environmental cues may affected eel migratory conditions. An innovative multivariate method was developed to analyse long-term datasets of daily water temperature, discharge and eel passage in two European rivers. Over the past 50 years, water temperature and discharge increased in both rivers during the downstream migration period from August to November. Silver eels preferentially migrated at temperatures between 10 and 20 °C combined with high discharge. Environmental changes have resulted in the migration of silver eels under warmer water temperatures. This example illustrates how the changes in environmental cues have led to a growing mismatch between the migratory conditions preferentially selected and those actually used, which may threaten the completion of the eel's life cycle and ultimately the persistence of this already critically endangered species.

Selection against individuals from genetic introgression of escaped farmed salmon in a natural population of Atlantic salmon.

The viability of wild Atlantic salmon populations is threatened by genetic introgression from escaped farmed salmon. Farmed Atlantic salmon are genetically improved for important commercial traits and a life in captivity but are poorly adapted to the natural environment. The rate of gene flow from escaped farmed to wild salmon depends on their spawning success and on offspring survival at various life stages. We here investigate relative survival of introgressed juvenile Atlantic salmon (parr) in a river in northern Norway. The studied population has experienced genetic introgression from farmed salmon for about four generations (20 years). We followed two cohorts of parr from the year of hatching (0+) to the age of 2 years (2+). Farmed genetic introgression was quantified at the individual level and on a continuous scale using diagnostic SNPs. Population-level genetic introgression decreased from 0+ to 2+ by 64% (2011 cohort) and 37% (2013 cohort). This change was driven by a 70% (2011 cohort) and 49% (2013 cohort) lower survival from age 0+ to 2+ in introgressed parr compared to parr of wild origin. Our observations show that there is natural selection against genetic introgression with a potential cost of lower productivity.

Repeatable individual variation in migration timing in two anadromous salmonids and ecological consequences.

Consistent individual differences in behavior have been demonstrated for many animals, but there are few studies of consequences of such repeated behavior in the wild. We tested consistency in migration timing to and from the sea among anadromous Arctic char (Salvelinus alpinus) and brown trout (Salmo trutta), using data from a study period of about 25 years, including more than 27,000 uniquely Carlin-tagged individuals that migrated to sea for feeding in the spring and returned to the river in late summer for up to 13 successive years. Consistency was found between individuals across time in timing of the seaward migration. Individuals migrating early during their first migration tended to migrate early the following years, and late migrants tended to migrate late. The same pattern was found also at ascent to freshwater. Hence, this study demonstrated that individual fish in nature can differ in behavior related to migration timing and that these differences can be consistent during their lifetime. Early migrants increased their mass more than late migrants and had a higher specific growth rate. Early migrating Arctic char, but not brown trout, experienced a longer life after the first migration to sea than late migrants. In both species, maturity occurred earlier in individuals that migrated early. For brown trout, but not for Arctic char, fecundity was significantly correlated to the timing of smolt migration. Hence, the repeatable individual variation in migration timing seemed to have ecological and fitness consequences in terms of growth, longevity, timing of maturity, and lifetime fecundity.

Age of European silver eels during a period of declining abundance in Norway.

The European eel (Anguilla anguilla) is critically endangered throughout its range. Knowledge about age distribution of future spawners (silver eels) is essential to monitor the status and contribute to the recovery of this species. Determination of age in anguillid eels is challenging, especially in eels from the northern part of the distribution area where growth is slow and age at maturation can be up to 30 years or more. Eels from the river Imsa in Norway have been monitored since 1975, and this reference time series has been used to assess the stock at the European level. Population dynamics in this catchment were analyzed during the late 1980s by estimating ages on whole cleared otoliths. However, techniques for revealing annual increments on otoliths have evolved over the years sometimes yielding significant differences in age estimates. In this study, the historical otolith data were reanalyzed using a grinding and polishing method rather than reading the whole otolith. The new age estimates were considerably higher than the previous ones, sometimes by up to 29 years. Since the 1980s, mean age of silver eels only slightly increased (from 19 to 21 years in the 2010s). This was mainly due to the disappearance of younger silver eels (<15 years) in the 2010s. The new age estimates agreed with the steep decline in recruitment which occurred in the late 1980s in the Imsa catchment. Mean growth (30 mm/year, min-max: 16-64 mm/year) has not changed since the 1980s, although density in the catchment has decreased. Revealing and reading age of slow-growing eels remain a challenge but adding a measure of otolith reading uncertainty may improve age data collection and contribute to recovery measures for this species.

Supplementary stocking selects for domesticated genotypes.

Stocking of hatchery produced fish is common practise to mitigate declines in natural populations and may have unwanted genetic consequences. Here we describe a novel phenomenon arising where broodstock used for stocking may be introgressed with farmed individuals. We test how stocking affects introgression in a wild population of Atlantic salmon (Salmo salar) by quantifying how the number of adult offspring recaptured in a stocked river depend on parental introgression. We found that hatchery conditions favour farmed genotypes such that introgressed broodstock produce up to four times the number of adult offspring compared to non-introgressed broodstock, leading to increased introgression in the recipient spawning population. Our results provide the first empirical evidence that stocking can unintentionally favour introgressed individuals and through selection for domesticated genotypes compromise the fitness of stocked wild populations.

Environmental DNA filtration techniques affect recovered biodiversity.

Freshwater metazoan biodiversity assessment using environmental DNA (eDNA) captured on filters offers new opportunities for water quality management. Filtering of water in the field is a logistical advantage compared to transport of water to the nearest lab, and thus, appropriate filter preservation becomes crucial for maximum DNA recovery. Here, the effect of four different filter preservation strategies, two filter types, and pre-filtration were evaluated by measuring metazoan diversity and community composition, using eDNA collected from a river and a lake ecosystem. The filters were preserved cold on ice, in ethanol, in lysis buffer and dry in silica gel. Our results show that filters preserved either dry or in lysis buffer give the most consistent community composition. In addition, mixed cellulose ester filters yield more consistent community composition than polyethersulfone filters, while the effect of pre-filtration remained ambiguous. Our study facilitates development of guidelines for aquatic community-level eDNA biomonitoring, and we advocate filtering in the field, using mixed cellulose ester filters and preserving the filters either dry or in lysis buffer.

Gene flow from domesticated escapes alters the life history of wild Atlantic salmon.

Interbreeding between domesticated and wild animals occurs in several species. This gene flow has long been anticipated to induce genetic changes in life-history traits of wild populations, thereby influencing population dynamics and viability. Here, we show that individuals with high levels of introgression (domesticated ancestry) have altered age and size at maturation in 62 wild Atlantic salmon Salmo salar populations, including seven ancestral populations to breeding lines of the domesticated salmon. This study documents widespread changes to life-history traits in wild animal populations following gene flow from selectively bred, domesticated conspecifics. The continued high abundance of escaped, domesticated Atlantic salmon thus threatens wild Atlantic salmon populations by inducing genetic changes in fitness-related traits. Our results represent key evidence and a timely warning concerning the potential ecological impacts of the globally increasing use of domesticated animals.

Timing and pattern of annual silver eel migration in two European watersheds are determined by similar cues.

Many animals perform long-distance migrations in order to maximize lifetime reproductive success. The European eel migrates several thousand kilometers between their feeding habitats in continental waters (fresh-, brackish, and sea water) and their spawning area in the Sargasso Sea. Eels residing in freshwaters usually initiate their spawning migration as silver eels during autumn, triggered by diverse environmental cues. We analyzed the time series of silver eel downstream migration in Burrishoole, Ireland (1971-2015), and Imsa, Norway (1975-2015), to examine factors regulating the silver eel migration from freshwater to the sea. The migration season (90% of the run) generally lasted from 1 August to 30 November. Environmental factors acting in the months before migration impacted timing and duration of migration, likely through influencing the internal processes preparing the fish for migration. Once the migration had started, environmental factors impacted the day-to-day variation in number of migrants, apparently stimulating migration among those eels ready for migration. Both the day-to-day variation in the number of migrants and the onset of migration were described by nearly identical models in the two rivers. Variables explaining day-to-day variation were all associated with conditions that may minimize predation risk; number of migrants was reduced under a strong moon and short nights and increased during high and increasing water levels. Presence of other migrants stimulated migration, which further indicates that silver eel migration has evolved to minimize predation risk. The onset of migration was explained mainly by water levels in August. The models for duration of the migration season were less similar between the sites. Thus, the overall migration season seems governed by the need to reach the spawning areas in a synchronized manner, while during the actual seaward migration, antipredator behavior seems of overriding importance.

A standardized method for quantifying unidirectional genetic introgression.

Genetic introgression of domesticated to wild conspecifics is of great concern to the genetic integrity and viability of the wild populations. Therefore, we need tools that can be used for monitoring unidirectional gene flow from domesticated to wild populations. A challenge to quantitation of unidirectional gene flow is that both the donor and the recipient population may be genetically substructured and that the subpopulations are subjected to genetic drift and may exchange migrants between one another. We develop a standardized method for quantifying and monitoring domesticated to wild gene flow and demonstrate its usefulness to farm and wild Atlantic salmon as a model species. The challenge of having several wild and farm populations was circumvented by in silico generating one analytical center point for farm and wild salmon, respectively. Distributions for the probability that an individual is wild were generated from individual-based analyses of observed wild and farm genotypes using STRUCTURE. We show that estimates of proportions of the genome being of domesticated origin in a particular wild population can be obtained without having a historical reference sample for the same population. The main advantages of the method presented are the standardized way in which genetic processes within and between populations are taken into account, and the individual-based analyses giving estimates for each individual independent of other individuals. The method makes use of established software, and as long as genetic markers showing generic genetic differences between domesticated and wild populations are available, it can be applied to all species with unidirectional gene flow. Results from our method are easy to interpret and understand, and will serve as a powerful tool for management, especially because there is no need for a specific historical wild reference sample.

Combining counts and incidence data: an efficient approach for estimating the log-normal species abundance distribution and diversity indices.

Obtaining accurate estimates of diversity indices is difficult because the number of species encountered in a sample increases with sampling intensity. We introduce a novel method that requires that the presence of species in a sample to be assessed while the counts of the number of individuals per species are only required for just a small part of the sample. To account for species included as incidence data in the species abundance distribution, we modify the likelihood function of the classical Poisson log-normal distribution. Using simulated community assemblages, we contrast diversity estimates based on a community sample, a subsample randomly extracted from the community sample, and a mixture sample where incidence data are added to a subsample. We show that the mixture sampling approach provides more accurate estimates than the subsample and at little extra cost. Diversity indices estimated from a freshwater zooplankton community sampled using the mixture approach show the same pattern of results as the simulation study. Our method efficiently increases the accuracy of diversity estimates and comprehension of the left tail of the species abundance distribution. We show how to choose the scale of sample size needed for a compromise between information gained, accuracy of the estimates and cost expended when assessing biological diversity. The sample size estimates are obtained from key community characteristics, such as the expected number of species in the community, the expected number of individuals in a sample and the evenness of the community.

A multiple-site similarity measure.

Similarity measures are among the most intuitive and common measures for comparing two or more sites, or samples, with respect to their species overlap. A restriction of similarity measures is that they are limited to pairwise comparisons even in a multiple-site study. This work presents a multiple-site similarity measure that makes use of information on species shared by more than two sites and avoids the problem of covariance between pairwise similarities in a multiple-site study. Further, we show that our multiple-site similarity measure is related to beta-diversity measures such as Whittaker's beta-diversity. Similarity measures can also be used as descriptors of effective specialization of insects to host species by measuring similarity from host observations. Finally, we show that multiple-site similarity and host specificity are two sides of the same coin.

A General and Dynamic Species Abundance Model, Embracing the Lognormal and the Gamma Models.

One aspect of community ecology that has been given particular attention is the pattern of species abundances in a community. The species may have a wide range of abundances; some are very common and others rare. When species abundance models are fitted to observations, the lognormal model and one of the gamma models (e.g., the log-series model) are usually applied. The model that gives the best fit according to some goodness-of-fit test is then chosen. By applying a diffusion approximation for each species' dynamics with density regulation of the θ-logistic type, we here present a general species abundance model that embraces the two most widely applied species abundance models, the lognormal and the gamma. Our general model will, therefore, provide a better fit than the two special cases, except when it corresponds to one of them. In contrast to the classical models, ours is also dynamic, making it possible to evaluate the fluctuations in species abundance over time through both biotic and abiotic factors. The model is fitted to several species abundance data sets and our results compared to previous attempts to fit a model, usually either the lognormal or the log-series.