Javier Lobón‐Cerviá

Species showing complex life cycles provide excellent opportunities to study the genetic associations between life cycle stages, as selective pressures may differ before and after metamorphosis. The European eel presents a complex life cycle with two metamorphoses, a first metamorphosis from larvae into glass eels (juvenile stage) and a second metamorphosis into silver eels (adult stage). We tested the hypothesis that different genes and gene pathways will be under selection at different life stages when comparing the genetic associations between glass eels and silver eels. We used two sets of markers to test for selection: first, we genotyped individuals using a panel of 80 coding-gene single nucleotide polymorphisms (SNPs) developed in American eel; second, we investigated selection at the genome level using a total of 153,423 RAD-sequencing generated SNPs widely distributed across the genome. Using the RAD approach, outlier tests identified a total of 2413 (1.57 %) potentially selected SNPs. Functional annotation analysis identified signal transduction pathways as the most over-represented group of genes, including MAPK/Erk signalling, calcium signalling and GnRH (gonadotropin-releasing hormone) signalling. Many of the over-represented pathways were related to growth, while others could result from the different conditions that eels inhabit during their life cycle. The observation of different genes and gene pathways under selection when comparing glass eels vs. silver eels supports the adaptive decoupling hypothesis for the benefits of metamorphosis. Partitioning the life cycle into discrete morphological phases may be overall beneficial since it allows the different life stages to respond independently to their unique selection pressures. This might translate into a more effective use of food and niche resources and/or performance of phase-specific tasks (e.g. feeding in the case of glass eels, migrating and reproducing in the case of silver eels).

Summary: 1. This study investigates when and where density dependence operates on the mortality rates of stream‐resident brown troutSalmo trutta. To this aim, I explored populations in habitats of different quality containing high, low or intermediate densities over broad scales of space and time. The study is based on census data of 170 cohorts quantified from recruitment to the total disappearance at 12 sites in four contrasting tributaries of the Rio Esva drainage (north‐western Spain), over the years 1986–2007.2. Log₁₀‐transformed survivor density over time highlighted a consistent pattern for the 170 cohorts characterised by the occurrence of only two life stages. An early stage starts at recruitment, lasts about half the lifetime and shows no or negligible mortality. A threshold time at 425–620 days after emergence preceded a second stage of continuous and constant mortality until the final disappearance of the cohorts. Consequently, in all scenarios, mortality only occurred in the adult component and no effect of season, year, age‐class and/or reproductive stage was detected.3. Substantial spatial and temporal variations typified both recruitment (rangeR = 0.01–1.62 ind m⁻²) and adults’ mortality rates (rangeZ = 0.03–0.38 day⁻¹). Nestedanovas revealed strong effects of site and year on both recruitment and mortality with sites interspersed along the stream gradients where recruitment and mortality were typically high relative to other sites located either nearby in the same stream or distant in another stream, where both recruitment and mortality rates were typically low or intermediate.4. Adult mortality rates plotted against recruitment for the 170 cohorts pooled revealed a continuous, positive power relationship that explained 45.3% of variation in mortality rates over the whole range of recruitment values. Similarly, highly significant power relationships were elucidated for site‐specific mortality rates averaged across years and for annual‐specific mortality rates averaged across sites against the corresponding mean recruitment averaged across years and sites, respectively. These relationships support the hypothesis that the operation of density dependence is scale independent and context independent but operates in a continuous manner across all scenarios examined.5. A chronic effect of density dependence on adult losses induces temporally persistent populations maintained by a low number of spawners. Apparently, the operation of density dependence adjusts the number of spawners to the availability of rearing and spawning habitat. This dynamic process may also help to explain the small effective population size (Ne) recently documented by genetic studies of stream‐living brown trout and other salmonids.

Summary: 1. We tested the hypothesis that lifetime mortality patterns and their corresponding rates and causal factors differ among populations of stream‐living salmonids. To this end, we examined the lifetime mortality patterns of several successive cohorts of two stream‐living brown trout (Salmo trutta) populations in Spain and Denmark.2. In the southern population, we observed a consistent two‐phase pattern, in which mortality was negligible during the first half of the lifetime and severe during the rest of the lifetime. In contrast, the northern population demonstrated a three‐phase pattern with an earlier phase varying from negligible to severe, followed by a second stage of weak mortality, and lastly by a third life stage of severe mortality.3. Despite substantial differences in the mortality patterns between the two populations, the combined effect of recruitment (as a proxy of the density‐dependent processes occurring during the lifetime) and mean body mass (as a proxy of growth experienced by individuals in a given cohort) explainedc.89% of the total lifetime mortality rates across cohorts and populations.4. A comparison with other published data on populations of stream‐living brown trout within its native range highlighted lifetime mortality patterns of one, two, three and four phases, but also suggested that common patterns may occur in populations that experience similar individual growth and population density.

The objective of this study was to elucidate the effects of density dependence on the individual size variation of brown trout (Salmo trutta) juveniles. Recruitment (the abundance of the youngest juveniles in May when they were 2 months old); the mean size attained by those individuals in September (6 months old) and the corresponding size variability around the mean size quantified with the coefficient of variation (CV) were examined in 22 year-classes at seven sites of two contrasting tributaries of the Rio Esva drainage (north-western Spain). Both mean size and CV tended to be site-specific but density dependence in the form of recruitment dependence affected both mean size and CV: the mean size depicted negative power relationships with increased recruitment whereas the CV increased positively with increased recruitment. However, this pattern differed among sites. At two out of seven sites, there was no obvious relationship between the mean size and recruitment. The CV increased positively with increased recruitment at all sites, although at several sites the CV described linear relationships and at others described power relationships. As a consequence, the stronger effects of density dependence on mean size occurred at low densities with minor effects at high densities, whereas density dependence operated on CV with continuous effects within the whole range of recruitment variation except at several sites where lower effects occurred at high densities. Thus, the occurrence, shape and intensity of competitive interactions underlying density dependence as a major cause of size variation differed across temporal and spatial scales.

Summary: 1. The objective was to assess the role of recruitment as a determinant of the production dynamics of stream‐resident brown trout (Salmo trutta) across replicate habitats of contrasting quality and population attributes. A total of 128‐year‐classes (YC) at 12 stream sites were examined along four tributaries of the Rio Esva drainage (northwestern Spain).2. A meta‐comparison revealed that growth, density, mortality and production were essentially site‐specific. However, when all data were pooled, recruitment (as a delayed density‐dependent process) affected both growth and mortality in a way such that individuals in YC with high recruitment grew less and had higher mortality.3. The value of total YC production recorded covered the global range of variation in the production of stream salmonids reported in the literature. Linear regressions of log‐transformed data revealed that 89.0%, 58.9% and 70.7% of the variation in YC density, biomass and production, respectively, were explained by variations in recruitment.4. The inclusion of growth and mortality, together with recruitment, into a multiple regression increased the variance explained of the total YC production by 13.3%, from 70.7% to 84.0%.5. The functional relationships between recruitment and the population attributes elucidated in this study appear to provide a useful tool for management applications, including forecasting population status.

Summary: 1. Around the year 2000, historically abundant populations of brown trout (Salmo trutta) and Atlantic salmon (S. salar) co‐occurring in rivers flowing along the Cantabrian corridor of north‐western Spain showed a dramatic decline to alarming levels. For one reason or another, fishing was not banned and fishing pressure continued to reduce the few survivors. Unexpectedly, the populations recovered ‘naturally’ in a very short time period to the extent that in 2004–06 numbers had attained population sizes comparable to those of the mid 1980s.2. The population of brown trout in Rio Chaballos showed a boom‐and‐bust pattern concurrent with those observed across broader geographical scales. This study revisits a 22‐year data set to explore the nature of the severe decline and rapid recovery of this population.3. Recruitment was related to stream discharge in March that covers the emergence period and the earliest search stages for food. Coefficients of variation for discharge and recruitment increased over the years and were highly correlated with each other, demonstrating that increased temporal variability in recruitment is strongly linked to increased variability in stream discharge. In turn, recruitment appears to be the major determinant of year‐class strength and hence, of population size.4. A number of factors appeared to operate as resilience mechanisms, permitting the population to increase rapidly when environmental conditions are optimal. These include strong recruitment‐discharge relationships, short life‐span, small stocks of eggs or offspring required to fill the amount of space suitable for the youngest juveniles and a few females surviving to spawn for a second time.5. Implications for fishery management and conservation are discussed in the context of the expectation that these populations will vary over the coming years within ranges similar to those in this study.

This study explored the extent to which variation in habitat factors related to growth and density influence self-thinning patterns in stream-living brown trout ( Salmo trutta ). Analysis of 110 cohorts at 12 sites of four contrasting streams revealed density–mass relationships in two phases. Density of survivors decreased little during the first half of their lifetime. A second phase commenced as individuals attained a threshold mass upon which density declined linearly with increased mass. The slopes of the second phase were greater than predicted by space and food demands. Among sites, these slopes were related to threshold densities at the beginning of the second phase. In turn, elevations, threshold densities, and slopes depicted concave trajectories against site depth, whereas threshold masses increased linearly. Apparently, cohorts remain below the carrying capacity during the first half of their lifetime and self-thin during the second half. Space-limited habitats impose site-specific carrying capacities and site-specific self-thinning coefficients, suggesting a common mechanism underlying self-thinning and an unanticipated, emerging property: two-phase patterns with far more variation in self-thinning coefficients. Variability in growth and density exhibited by brown trout and other salmonids across regions suggests that two-phase patterns may occur broadly, and self-thinning coefficients may vary widely.