Contemporary divergence in early life history in grayling (Thymallus thymallus)

<p>Abstract</p> <p>Background</p> <p>Following colonization of new habitats and subsequent selection, adaptation to environmental conditions might be expected to be rapid. In a mountain lake in Norway, Lesjaskogsvatnet, more than 20 distinct spawning demes of grayling have been established since the lake was colonized, some 20-25 generations ago. The demes spawn in tributaries consistently exhibiting either colder or warmer temperature conditions during spawning in spring and subsequent early development during early summer. In order to explore the degree of temperature-related divergence in early development, a multi-temperature common-garden experiment was performed on embryos from four different demes experiencing different spring temperatures.</p> <p>Results</p> <p>Early developmental characters were measured to test if individuals from the four demes respond differently to the treatment temperatures. There was clear evidence of among-deme differences (genotype - environment interactions) in larval growth and yolk-to-body-size conversion efficiency. Under the cold treatment regime, larval growth rates were highest for individuals belonging to cold streams. Individuals from warm streams had the highest yolk-consumption rate under cold conditions. As a consequence, yolk-to-body-mass conversion efficiency was highest for cold-deme individuals under cold conditions. As we observed response parallelism between individuals from demes belonging to similar thermal groups for these traits, some of the differentiation seems likely to result from local adaptation</p> <p>Conclusion</p> <p>The observed differences in length at age during early larval development most likely have a genetic component, even though both directional and random processes are likely to have influenced evolutionary change in the demes under study.</p

The Chromosome-Level Genome Assembly of European Grayling Reveals Aspects of a Unique Genome Evolution Process Within Salmonids

Salmonids represent an intriguing taxonomical group for investigating genome evolution in vertebrates due to their relatively recent last common whole genome duplication event, which occurred between 80 and 100 million years ago. Here, we report on the chromosome-level genome assembly of European grayling (Thymallus thymallus), which represents one of the earliest diverged salmonid subfamilies. To achieve this, we first generated relatively long genomic scaffolds by using a previously published draft genome assembly along with long-read sequencing data and a linkage map. We then merged those scaffolds by applying synteny evidence from the Atlantic salmon (Salmo salar) genome. Comparisons of the European grayling genome assembly to the genomes of Atlantic salmon and Northern pike (Esox lucius), the latter used as a nonduplicated outgroup, detailed aspects of the characteristic chromosome evolution process that has taken place in European grayling. While Atlantic salmon and other salmonid genomes are portrayed by the typical occurrence of numerous chromosomal fusions, European grayling chromosomes were confirmed to be fusion-free and were characterized by a relatively large proportion of paracentric and pericentric inversions. We further reported on transposable elements specific to either the European grayling or Atlantic salmon genome, on the male-specific sdY gene in the European grayling chromosome 11A, and on regions under residual tetrasomy in the homeologous European grayling chromosome pairs 9A-9B and 25A-25B. The same chromosome pairs have been observed under residual tetrasomy in Atlantic salmon and in other salmonids, suggesting that this feature has been conserved since the subfamily split.Peer reviewe

Spatio-temporal patterns in pelvic reduction in threespine stickleback (Gasterosteus aculeatus L.) in Lake Storvatnet

Questions: The pelvic girdle with associated spines is an integrated anti-predator defence apparatus, and is assumed to protect against piscivores in the threespine stickleback. On the other hand, it might be costly to produce the pelvic apparatus in ion-poor and mineralchallenging freshwater. Hypothesis: Stickleback with a reduced pelvic apparatus should use more shelter and be more nocturnal, avoiding predation risk. In contrast, stickleback with a well-developed pelvic apparatus should have reduced mortality during ontogeny in encounters with piscivores and thus have a longer expected lifespan. Given these two life-history strategies, we expect assortative mating as a result of divergent selection. Organism: Marine and freshwater threespine stickleback (Gasterosteus aculeatus L.). Places and times: Two representative ancestral marine populations and 36 freshwater populations in northwestern Norway (Lake Storvatnet, the main focus of the study, and three lakes downstream of it). Material was collected from 2006 to 2009. Analytical methods: We categorized nominal pelvic apparatus development (CPS morphs) in all fish, and measured metrics associated with these categories in a subsample. We also studied temporal, spatial, and habitat variation in the distribution of pelvic morphs in Lake Storvatnet. In this population, and downstream populations, we contrasted the detailed pelvic morphology with the measured genetic diversity (microsatellites), also estimating gene flow. In Lake Storvatnet, we tested for genetic divergence and signs of potential build-up of reproductive isolation via assortative mating among the observed nominal categories of pelvic reduction (CPS). Results: Pelvic reduction was seen only in Lake Storvatnet, where more than 50% of fish had a reduced pelvis. The distribution of pelvic morphs was stable over time and did not differ between habitats. The proportion of fish with pelvic reduction decreased with age. Freshwater stickleback tended to have a smaller pelvis than marine fish. The Lake Storvatnet stickleback were genetically differentiated from the downstream Lake Gjerhaugsvatn population, and both of these were different from the marine populations, with little gene flow among populations. No apparent genetic structure was found between CPS morphs within Lake Storvatnet. However, genetic factorial correspondence axes were significantly correlated with pelvic principal component axes in Lake Storvatnet, suggesting some phenotype × genetic association. Conclusion: The weak association between phenotypes and genetic structure observed in this study may reflect the build-up of early steps of reproductive isolation. Given time, such mechanisms may lead to the evolution of assortative mating, which may drive adaptive pelvic morphs (niche peaks), further resulting in genetically divergent populations and pelvic morphs

Life history and demographic determinants of effective/census size ratios as exemplified by brown trout (Salmo trutta)

A number of demographic factors, many of which related to human-driven encroachments, are predicted to decrease the effective population size (Ne) relative to the census population size (N), but these have been little investigated. Yet, it is necessary to know which factors most strongly impact Ne, and how to mitigate these effects through sound management actions. In this study, we use parentage analysis of a stream-living brown trout (Salmo trutta) population to quantify the effect of between-individual variance in reproductive success on the effective number of breeders (Nb) relative to the census number of breeders (Ni). Comprehensive estimates of the Nb/N ratio were reduced to 0.16–0.28, almost entirely due to larger than binomial variance in family size. We used computer simulations, based on empirical estimates of age-specific survival and fecundity rates, to assess the effect of repeat spawning (iteroparity) on Ne and found that the variance in lifetime reproductive success was substantially higher for repeat spawners. Random family-specific survival, on the other hand, acts to buffer these effects. We discuss the implications of these findings for the management of small populations, where maintaining high and stable levels of Ne is crucial to extenuate inbreeding and protect genetic variability.publishedVersio

When phenology matters: age–size truncation alters population response to trophic mismatch

Climate-induced shifts in the timing of life-history events are a worldwide phenomenon, and these shifts can de-synchronize species interactions such as predator–prey relationships. In order to understand the ecological implications of altered seasonality, we need to consider how shifts in phenology interact with other agents of environmental change such as exploitation and disease spread, which commonly act to erode the demographic structure of wild populations. Using long-term observational data on the phenology and dynamics of a model predator–prey system (fish and zooplankton in Windermere, UK), we show that age–size truncation of the predator population alters the consequences of phenological mismatch for offspring survival and population abundance. Specifically, age–size truncation reduces intraspecific density regulation due to competition and cannibalism, and thereby amplifies the population sensitivity to climate-induced predator–prey asynchrony, which increases variability in predator abundance. High population variability poses major ecological and economic challenges as it can diminish sustainable harvest rates and increase the risk of population collapse. Our results stress the importance of maintaining within-population age–size diversity in order to buffer populations against phenological asynchrony, and highlight the need to consider interactive effects of environmental impacts if we are to understand and project complex ecological outcomes

Size- and stage-dependence in cause-specific mortality of migratory brown trout

Evidence‐based management of natural populations under strong human influence frequently requires not only estimates of survival but also knowledge about how much mortality is due to anthropogenic vs. natural causes. This is the case particularly when individuals vary in their vulnerability to different causes of mortality due to traits, life history stages, or locations. Here, we estimated harvest and background (other cause) mortality of landlocked migratory salmonids over half a century. In doing so, we quantified among‐individual variation in vulnerability to cause‐specific mortality resulting from differences in body size and spawning location relative to a hydropower dam. We constructed a multistate mark–recapture model to estimate harvest and background mortality hazard rates as functions of a discrete state (spawning location) and an individual time‐varying covariate (body size). We further accounted for among‐year variation in mortality and migratory behaviour and fit the model to a unique 50‐year time series of mark–recapture–recovery data on brown trout (Salmo trutta ) in Norway. Harvest mortality was highest for intermediate‐sized trout, and outweighed background mortality for most of the observed size range. Background mortality decreased with body size for trout spawning above the dam and increased for those spawning below. All vital rates varied substantially over time, but a trend was evident only in estimates of fishers' reporting rate, which decreased from over 50% to less than 10% throughout the study period. We highlight the importance of body size for cause‐specific mortality and demonstrate how this can be estimated using a novel hazard rate parameterization for mark–recapture models. Our approach allows estimating effects of individual traits and environment on cause‐specific mortality without confounding, and provides an intuitive way to estimate temporal patterns within and correlation among different mortality sources

Quantifying the Ocean, Freshwater and Human Effects on Year-to-Year Variability of One-Sea-Winter Atlantic Salmon Angled in Multiple Norwegian Rivers

Many Atlantic salmon, Salmo salar, populations are decreasing throughout the species' distributional range probably due to several factors acting in concert. A number of studies have documented the influence of freshwater and ocean conditions, climate variability and human impacts resulting from impoundment and aquaculture. However, most previous research has focused on analyzing single or only a few populations, and quantified isolated effects rather than handling multiple factors in conjunction. By using a multi-river mixed-effects model we estimated the effects of oceanic and river conditions, as well as human impacts, on year-to-year and between-river variability across 60 time series of recreational catch of one-sea-winter salmon (grilse) from Norwegian rivers over 29 years (1979–2007). Warm coastal temperatures at the time of smolt entrance into the sea and increased water discharge during upstream migration of mature fish were associated with higher rod catches of grilse. When hydropower stations were present in the course of the river systems the strength of the relationship with runoff was reduced. Catches of grilse in the river increased significantly following the reduction of the harvesting of this life-stage at sea. However, an average decreasing temporal trend was still detected and appeared to be stronger in the presence of salmon farms on the migration route of smolts in coastal/fjord areas. These results suggest that both ocean and freshwater conditions in conjunction with various human impacts contribute to shape interannual fluctuations and between-river variability of wild Atlantic salmon in Norwegian rivers. Current global change altering coastal temperature and water flow patterns might have implications for future grilse catches, moreover, positioning of aquaculture facilities as well as the implementation of hydropower schemes or other encroachments should be made with care when implementing management actions and searching for solutions to conserve this species

Slektskap og kolonisering hos ørekyt

Målet med dette prosjektet var å studere populasjonsgenetikken til ørekyt i Norge med sikte på å få økt kunnskap om artens spredningsmekanismer. Ørekyten utvider stadig sitt leveområde, og det er uklart hvordan spredningen skjer. Vi har kunnet fastslå at noen av de nyetablerte bestandene på Hardangervidda har en genetisk historie (en unik mitokondrie-DNA haplotype) som er svært forskjellig fra hva den naturlig utbredte ørekyten har. Innen det naturlige utbredelsesområdet finner vi bare en haplotype. Dette betyr at noe av spredningen trolig skyldes langtransport av levende fisk, dette kan skyldes bruk av levende agn (importert), eller utsetting av ikke kontrollert settefisk importert fra utlandet (med ørekyt som blindpassasjer). En del av den nyetablerte ørekyten har samme genetiske historie som naturlig utbredt ørekyt. I to vann (Legereidvann og Sandvatn) fant vi ørekyt med begge haplotypene; dette tyder på at ørekyten i disse vannene har blitt etablert som følge av to ulike spredningshendelser. Analysene av DNA-fingerprint viste at det var stor genetisk variasjon innen de ”naturlige” ørekytpopulasjonene. Det var som ventet mindre variasjon hos de nyetablerte populasjonene; noen av populasjonene oppviste imidlertid relativt høy genetisk variasjon. Den høye variasjonen i DNA-fingerprintdata hos ørekyt fra Sandvatn og Legereidvatn kan skyldes at det har forekommet minst to spredningshendelser (vi fant to ulike mitokondrie-DNA haplotyper). Også i de andre populasjonene hvor vi fant stor variasjon (Vinstri, Lesjaskogsvatn, Vålåsjøen) antar vi at årsaken er multiple spredningshendelser. Alle disse lokalitetene ligger i populære fiskeområder. Vi kan ikke fastslå i større detalj de ulike ørekytpopulasjonens opphav, til det trengs mer omfattende analyser

Data from: Short-term genetic changes: evaluating effective population size estimates in a comprehensively described brown trout (Salmo trutta) population

The effective population size (Ne) is notoriously difficult to accurately estimate in wild populations as it is influenced by a number of parameters that are difficult to delineate in natural systems. The different methods that are used to estimate Ne are impacted variously by different processes at the population level, such as the life-history characteristics of the organism, gene flow, population substructure, as well as by the frequency patterns of genetic markers used and the sampling design. Here, we compare Ne estimates obtained by different genetic methods and from demographic data, and elucidate how the estimates are impacted by various factors in an exhaustively sampled and comprehensively described natural brown trout (Salmo trutta) system. In general, the methods yielded rather congruent estimates, and we ascribe that to the adequate genotyping and exhaustive sampling. Effects of violating the assumptions of the different methods were nevertheless apparent. In accordance with theoretical studies, skewed allele frequencies would underestimate temporal allele frequency changes and thereby upwardly bias Ne if not accounted for. Overlapping generations and iteroparity would also upwardly bias Ne when applied to temporal samples taken over short time spans. Gene flow from a genetically not very dissimilar source population decreases temporal allele frequency changes and thereby acts to increase estimates of Ne. Our study reiterates the importance of adequate sampling, quantification of life-history parameters and gene flow, and incorporating these data into the Ne estimation