Lasse Fast Jensen

Local adaptation in brown trout early life-history traits: implications for climate change adaptability

Knowledge of local adaptation and adaptive potential of natural populations is becoming increasingly relevant due to anthropogenic changes in the environment, such as climate change. The concern is that populations will be negatively affected by increasing temperatures without the capacity to adapt. Temperature-related adaptability in traits related to phenology and early life history are expected to be particularly important in salmonid fishes. We focused on the latter and investigated whether four populations of brown trout (Salmo trutta) are locally adapted in early life-history traits. These populations spawn in rivers that experience different temperature conditions during the time of incubation of eggs and embryos. They were reared in a common-garden experiment at three different temperatures. Quantitative genetic differentiation (QST) exceeded neutral molecular differentiation (FST) for two traits, indicating local adaptation. A temperature effect was observed for three traits. However, this effect varied among populations due to locally adapted reaction norms, corresponding to the temperature regimes experienced by the populations in their native environments. Additive genetic variance and heritable variation in phenotypic plasticity suggest that although increasing temperatures are likely to affect some populations negatively, they may have the potential to adapt to changing temperature regimes.

Gene flow, effective population size and selection at major histocompatibility complex genes: brown trout in the Hardanger Fjord, Norway

Brown trout populations in the Hardanger Fjord, Norway, have declined drastically due to increased exposure to salmon lice from salmonid aquaculture. We studied contemporary samples from seven populations and historical samples (1972 and 1983) from the two largest populations, one of which has declined drastically whereas the other remains stable. We analysed 11 microsatellite loci, including one tightly linked to the UBA gene of the major histocompatibility class I complex (MHC) and another locus linked to the TAP2A gene, also associated with MHC. The results revealed asymmetric gene flow from the two largest populations to the other, smaller populations. This has important conservation implications, and we predict that possible future population recoveries will be mediated primarily by the remaining large population. Tests for selection suggested diversifying selection at UBA, whereas evidence was inconclusive for TAP2A. There was no evidence for temporally fluctuating selection. We assessed the distribution of adaptive divergence among populations. The results showed the most pronounced footprints of selection between the two largest populations subject to the least immigration. We suggest that asymmetric gene flow has an important influence on adaptive divergence and constrains local adaptive responses in the smaller populations. Even though UBA alleles may not affect salmon louse resistance, the results bear evidence of adaptive divergence among populations at immune system genes. This suggests that similar genetic differences could exist at salmon louse resistance loci, thus rendering it a realistic scenario that differential population declines could reflect differences in adaptive variation.

Sibship within samples of brown trout (Salmo trutta) and implications for supportive breeding

We analysed family relationships among brown trout from two small tributary populations that have been suggested as a source of individuals for supportive breeding, using variation at eight microsatellite loci. As a control, we analysed a sample of supposedly unrelated individuals representing a large anadromous population, and we simulated unrelated individuals based on the allelic distributions in all three samples. Two different approaches were used: (1) pairwise estimates of relatedness between individuals and (2) a method for partitioning individuals into half-sib and full-sib families. The anadromous population did not show evidence of a significant number of closely related individuals. In both tributary populations, however, the distributions of pairwise relatedness estimates suggested the presence of several related individuals, and sibship reconstruction suggested fewer families consisting of more individuals than were observed for the simulated individuals. The expected increase of inbreeding coefficient in the two samples due to family structure was 0.026 and 0.030 respectively. Moreover, tests for recent bottlenecks yielded significant outcomes in both populations suggesting a history of low effective population sizes. Depending on the effective population size of captive spawners and past effective population sizes in the populations it could be beneficial to conduct sib-avoidance matings, though this cannot eliminate inbreeding but only delay it. Alternatively, individuals from different populations could be crossed. Sibship reconstruction provided the clearest evidence for family structure, but pairwise relatedness is the best measure for designing mating schemes, as it allows for mating as unrelated individuals as possible rather than just avoiding mating between sibs.

Stocking impact and temporal stability of genetic composition in a brackish northern pike population ( Esox lucius L.), assessed using microsatellite DNA analysis of historical and contemporary samples

During the last decade, brackish northern pike populations in Denmark have been subject to stocking programmes, using nonindigenous pike from freshwater lakes, in order to compensate for drastic population declines. The present study was designed to investigate the genetic impact of stocking freshwater pike into a brackish pike population in Stege Nor, Denmark. We analysed polymorphism at eight microsatellite loci in samples representing the indigenous Stege Nor population prior to stocking (ie from 1956 to 1957), along with a sample of the contemporary Stege Nor population and samples from the three populations used for stocking. Despite large numbers of stocked fry, the results from both individual and population level admixture analyses demonstrated extremely poor performance and <1% introgression of stocked freshwater pike into the brackish pike population. Furthermore, pairwise FST estimates between samples demonstrated close genetic relationship among temporal samples from Stege Nor, indicating temporal stability over the last 45 years. We also estimated the effective population size (Ne) of pike in Stege Nor and applied a test for recent population bottlenecks. The harmonic mean of Ne was relatively high (>250), but there were indications of bottlenecks in all samples and populations. We ascribe this finding to historical rather than recent bottlenecks, possibly dating back to founder events associated with postglacial recolonisation.

Spatially and temporally fluctuating selection at non-MHC immune genes: evidence from TAP polymorphism in populations of brown trout ( Salmo trutta , L.)

Temporal samples of Danish brown trout (Salmo trutta) from populations representing varying geographical scales were analysed using eight putatively neutral microsatellite loci and two microsatellite loci embedded in TAP genes (Transporter associated with Antigen Processing). These genes encode molecules that are central to the major histocompatibility complex (MHC) class I restricted antigen presentation and thus integral components in the adaptive immune system. As such, they could be influenced by selection, driven by pathogens and parasites in a manner similar to MHC genes. Analysis of allele frequencies at presumably neutral microsatellite loci revealed a temporally unstable population structure within regions, while the population structure was stable over time among regions. Analyses of the two TAP markers indicated an effect of selection at both a regional and micro-geographical spatial scale. Moreover, signals of divergent selection among temporal samples within localities suggest that selection also might fluctuate at a temporal scale. These results suggest that immune genes other than the classical MHC class I and II might be subject to selection and warrant further studies of functional polymorphism of such genes in natural populations.

The Stranding Anomaly as Population Indicator: The Case of Harbour Porpoise Phocoena phocoena in North-Western Europe

Ecological indicators for monitoring strategies are expected to combine three major characteristics: ecological significance, statistical credibility, and cost-effectiveness. Strategies based on stranding networks rank highly in cost-effectiveness, but their ecological significance and statistical credibility are disputed. Our present goal is to improve the value of stranding data as population indicator as part of monitoring strategies by constructing the spatial and temporal null hypothesis for strandings. The null hypothesis is defined as: small cetacean distribution and mortality are uniform in space and constant in time. We used a drift model to map stranding probabilities and predict stranding patterns of cetacean carcasses under H0 across the North Sea, the Channel and the Bay of Biscay, for the period 1990–2009. As the most common cetacean occurring in this area, we chose the harbour porpoise Phocoena phocoena for our modelling. The difference between these strandings expected under H0 and observed strandings is defined as the stranding anomaly. It constituted the stranding data series corrected for drift conditions. Seasonal decomposition of stranding anomaly suggested that drift conditions did not explain observed seasonal variations of porpoise strandings. Long-term stranding anomalies increased first in the southern North Sea, the Channel and Bay of Biscay coasts, and finally the eastern North Sea. The hypothesis of changes in porpoise distribution was consistent with local visual surveys, mostly SCANS surveys (1994 and 2005). This new indicator could be applied to cetacean populations across the world and more widely to marine megafauna.

Behaviour of rainbow trout Oncorhynchus mykiss presented with a choice of normoxia and stepwise progressive hypoxia.

The objective of this study was to identify behavioural adjustments leading to avoidance of hypoxia. Using the oxygen-sensitive species rainbow trout Oncorhynchus mykiss as a model, individual fish were recorded while moving freely between two sides of a test arena: one with normoxia and one with stepwise progressive hypoxia [80-30% dissolved oxygen (DO) air saturation]. The results demonstrated a gradual decrease in the total time spent in hypoxia starting at 80% DO air saturation. At this DO level, the avoidance of hypoxia could not be attributed to changes in spontaneous swimming speed, neither in normoxia nor in hypoxia. Reducing the DO level to 60% air saturation resulted in decreased spontaneous swimming speed in normoxia, yet the number of trips to the hypoxic side of the test arena remained unchanged. Moreover, data revealed increased average residence time per trip in normoxia at DO levels ≤60% air saturation and decreased average residence time per trip in hypoxia at DO levels ≤50% air saturation. Finally, the spontaneous swimming speed in hypoxia increased at DO levels ≤40% air saturation and the number of trips to hypoxia decreased at the 30% DO air saturation level. Thus, avoidance of the deepest hypoxia was connected with a reduced number of trips to hypoxia as well as decreased and increased spontaneous swimming speed in normoxia and hypoxia, respectively. Collectively, the data support the conclusions that the mechanistic basis for avoidance of hypoxia may (1) not involve changes in swimming speed during mild hypoxia and (2) depend on the severity of hypoxia.

Possible Causes of a Harbour Porpoise Mass Stranding in Danish Waters in 2005

An unprecedented 85 harbour porpoises stranded freshly dead along approximately 100 km of Danish coastline from 7–15 April, 2005. This total is considerably above the mean weekly stranding rate for the whole of Denmark, both for any time of year, 1.23 animals/week (ranging from 0 to 20 during 2003–2008, excluding April 2005), and specifically in April, 0.65 animals/week (0 to 4, same period). Bycatch was established as the cause of death for most of the individuals through typical indications of fisheries interactions, including net markings in the skin and around the flippers, and loss of tail flukes. Local fishermen confirmed unusually large porpoise bycatch in nets set for lumpfish (Cyclopterus lumpus) and the strandings were attributed to an early lumpfish season. However, lumpfish catches for 2005 were not unusual in terms of season onset, peak or total catch, when compared to 2003–2008. Consequently, human activity was combined with environmental factors and the variation in Danish fisheries landings (determined through a principal component analysis) in a two-part statistical model to assess the correlation of these factors with both the presence of fresh strandings and the numbers of strandings on the Danish west coast. The final statistical model (which was forward selected using Akaike information criterion; AIC) indicated that naval presence is correlated with higher rates of porpoise strandings, particularly in combination with certain fisheries, although it is not correlated with the actual presence of strandings. Military vessels from various countries were confirmed in the area from the 7th April, en route to the largest naval exercise in Danish waters to date (Loyal Mariner 2005, 11–28 April). Although sonar usage cannot be confirmed, it is likely that ships were testing various equipment prior to the main exercise. Thus naval activity cannot be ruled out as a possible contributing factor.

Shift of grey seal subspecies boundaries in response to climate, culling and conservation

Identifying the processes that drive changes in the abundance and distribution of natural populations is a central theme in ecology and evolution. Many species of marine mammals have experienced dramatic changes in abundance and distribution due to climatic fluctuations and anthropogenic impacts. However, thanks to conservation efforts, some of these species have shown remarkable population recovery and are now recolonizing their former ranges. Here, we use zooarchaeological, demographic and genetic data to examine processes of colonization, local extinction and recolonization of the two northern European grey seal subspecies inhabiting the Baltic Sea and North Sea. The zooarchaeological and genetic data suggest that the two subspecies diverged shortly after the formation of the Baltic Sea approximately 4200 years bp, probably through a gradual shift to different breeding habitats and phenologies. By comparing genetic data from 19th century pre‐extinction material with that from seals currently recolonizing their past range, we observed a marked spatiotemporal shift in subspecies boundaries, with increasing encroachment of North Sea seals on areas previously occupied by the Baltic Sea subspecies. Further, both demographic and genetic data indicate that the two subspecies have begun to overlap geographically and are hybridizing in a narrow contact zone. Our findings provide new insights into the processes of colonization, extinction and recolonization and have important implications for the management of grey seals across northern Europe.

Partitioning the metabolic scope: the importance of anaerobic metabolism and implications for the oxygen- and capacity-limited thermal tolerance (OCLTT) hypothesis

Climate change is predicted to affect the aerobic capacity available for sustainable performances and fitness in fishes. This study reveals trade-offs between aerobic and anaerobic components of swimming performance and metabolic scope, and highlights the possibility of overestimating sustainable aerobic performances of fishes in relation to climate change.