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1.	Donadi, Serena, et al. (författare) Contrasting long-term trends in juvenile abundance of a widespread cold-water salmonid along a latitudinal gradient: effects of climate, stream size and migration strategy 2023 Ingår i: Ecography. - : Wiley. - 0906-7590 .- 1600-0587. Tidskriftsartikel (refereegranskat)abstract A changing climate reshapes the range distribution of many organisms, and species with relatively low thermal optima, like many salmonids, are increasingly expected to face local population extinctions at lower latitudes. Understanding where and how fast these changes are happening is of pivotal importance for successful mitigation and conservation efforts.We used an extensive electrofishing database to explore temporal trends of juveniles of brown trout Salmo trutta in 218 locations from 174 Swedish streams, over the last 30 years (1991-2020). We hypothesized that 1) declines in abundance have occurred predominately in the warmer, southern regions, while increases have occurred in the colder, northern regions, 2) larger stream sizes may partly offset negative effects of climate, and 3) migrating and resident populations are affected differently by a warming climate.We found that abundance of brown trout juveniles generally declined in warmer regions especially in smaller streams (<= 6 m wide), while the abundance increased in colder regions. In larger streams, negative effects of higher temperatures were seemingly buffered, as we found lower rates of decline or even positive trends. The rate of change (i.e. the slopes of the trends in abundance) was more pronounced towards the climate extremes, and was on average zero in regions with a normal annual air temperature (average temperature over 30 year period) around 5-6 degrees C. Warmer climate had stronger effects on migrating compared to resident populations, suggesting that climate-induced loss of stream connectivity could be an additional factor that hinders recruitment in anadromous populations in a changing climate.Considering predictions of increasing temperatures and frequency of summer droughts, management of cold-water salmonid populations should focus on conserving and restoring riparian vegetation, wetlands, climate and thermal refugia, and habitat integrity overall. Such measures may, however, not suffice for small streams at lower latitudes, unless hydrological connectivity is maintained.
2.	Karlsson, Erik, et al. (författare) Strong positive relationships between eDNA concentrations and biomass in juvenile and adult pike (Esox lucius) under controlled conditions: Implications for monitoring 2022 Ingår i: Environmental DNA. - : Wiley. - 2637-4943. ; 4, s. 881-893 Tidskriftsartikel (refereegranskat)abstract Reliable abundance information is the foundation for managing aquatic resources. Species with low catchability are, however, often overlooked in monitoring programmes. Thus, governing bodies lack the data necessary to make well-informed management decisions. Environmental DNA (eDNA) can produce quantitative estimates of fish abundances, but the precision varies greatly depending on the species and system. It is, therefore, necessary to evaluate its performance and investigate how fish biomass and density affects eDNA dynamics on a case-by-case basis before eDNA-based monitoring can be a viable option. Here, we evaluate how biomass and density of an ecologically and socioeconomically important top predator, the Northern pike (Esox lucius), relate to eDNA concentrations in controlled aquarium and mesocosm experiments. We carried out experiments using both juvenile and adult individuals and evaluated eDNA, biomass and density relationships at three different time points using a previously developed TaqMan assay, targeting the cytochrome oxidase I gene. We also evaluated the performance of multiple extraction methods (DNeasy Blood & Tissue kit, DNeasy PowerWater kit, and Chelex 100), and filtering systems (single- vs. double-membrane filters). The results from both pike experiments showed a strong positive linear relationship between eDNA concentration and pike biomass (R2 = 0.74 – 0.87). Levels of eDNA dropped drastically within the initial 24 h of juvenile pike being removed from the aquaria, and low levels were detectable for up to 308 h. Of the extraction methods, Chelex 100 yielded the highest DNA concentration, offering a quick and cost-effective alternative compared with existing widely used extraction methods. Using double membrane filters of different material showed no increase in DNA yield regardless of the extraction method but it allowed more water to be processed. Although several challenges remain, our results show that eDNA holds promise to become a useful tool for monitoring fish biomass in natural environments.
3.	López, María-Eugenia, et al. (författare) Are you ready for the heat? Phenotypic plasticity versus adaptation of heat tolerance in three-spined stickleback 2022 Ingår i: Ecosphere. - : Wiley. - 2150-8925. ; 13 Tidskriftsartikel (refereegranskat)abstract Heat waves constitute a challenge for aquatic ectotherms. However, the thermal tolerance of animals and their individual phenotypic plasticity to respond to heat waves may be influenced by thermal history. We tested these hypotheses by comparing the upper thermal tolerance and the individual capacities of three-spined sticklebacks from populations with different thermal histories to respond to heat waves. Two populations originated from thermally polluted nuclear power plant (NPP) habitats, while four locations represented geographically adjacent control areas. To disentangle the genetic adaptation from the phenotypic plastic response, we measured the individual upper thermal tolerance and the responses at molecular level in common-garden conditions before and after a laboratory-mimicked heat wave. We found that the sticklebacks exhibit considerable phenotypic plasticity in thermal tolerance since the heat wave increased fish upper thermal tolerance significantly. The individual plasticity to respond to the heat wave was also negatively correlated with initial thermal tolerance. On the other hand, neither the thermal tolerance nor the plastic responses differed between NPP and control sites despite detection of significant but low genome-wide divergence in 10 out of 15 pairwise comparisons. Our results suggest that five decades of NPP activity with warmer water have not resulted in a detectable evolutionary change in either the upper thermal tolerance or its plasticity in three-spined sticklebacks potentially rendering them sensitive to frequent heat waves.
4.	López, María-Eugenia, et al. (författare) Lack of panmixia of Bothnian Bay vendace-Implications for fisheries management 2022 Ingår i: Frontiers in marine science. - : Frontiers Media SA. - 2296-7745. ; 9 Tidskriftsartikel (refereegranskat)abstract Overexploitation of fisheries is recognized as a major environmental and socioeconomic problem that threats biodiversity and ecosystem functioning. Inappropriate management policies of fish stocks have been applied as a consequence of inadequate characterization of subtle genetic structure in many fish species. In this study, we aim to assess the extent of genetic differentiation and structure of vendace (Coregonus albula) collected from eight locations in the Bothnian Bay, the northernmost part of the Baltic Sea. Specifically, we test if this species forms a single panmictic population or is divided into several genetically distinct units. We used restriction site-associated DNA sequencing (RAD-seq) to identify 21,792 SNPs based on 266 individuals. We identified a clear pattern of genetic differentiation between River Kalix and the other sampling locations, and a weak structuring between samples from Swedish and Finnish coast. Outlier analysis detected 41 SNPs putatively under divergent selection, mainly reflecting the divergence between River Kalix and the other samples. The outlier SNPs were located within or near 25 genes, including voltage-dependent calcium channel subunit alpha-2 (CACNA2D2), cadherin 26 (CDH26) and carbonic anhydrase 4-like (CA4) that have earlier been associated with salt-tolerance and salinity stress. Our study provides the first genome-wide perspective on genetic structuring of Baltic Sea vendace and rejects the hypothesis of panmixia in the Bothnian Bay. As such, our work demonstrates the power of RAD-sequencing to detect low but significant genetic structuring relevant for fisheries management.
5.	Niu, Jingyao, et al. (författare) Decades of warming alters maturation and reproductive investment in fish 2023 Ingår i: Ecosphere. - : Wiley. - 2150-8925. ; 14 Tidskriftsartikel (refereegranskat)abstract How does warming affect maturation and reproductive investment in ectotherms? Younger age and smaller size at maturation, as well as altered reproduction processes, have been found in a few species subjected to elevated temperatures. These observations, however, come from studies that do not distinguish effects of warming on maturation from those on growth, are also restricted to single generation responses to warming, or have additional stressors besides warming in the study system. Here, we study warming effects on maturation and reproductive investment in wild, unexploited fish populations using a whole-ecosystem heating experiment. The experiment is conducted on Eurasian perch (Perca fluviatilis) in a heated and control area (with > 5 degrees C temperature difference) in the Baltic Sea. We compare female perch size at maturation using estimated probabilistic maturation reaction norms (PMRNs) and the gonado-somatic index over 17 years of heating, spanning approximately five to eight perch generations. Using the PMRN approach, we show that warming has substantial effects on maturation size independent of warming-induced changes in body growth. We found that young fish mature at a smaller size and invest more in developing their gonads in the heated population than in the unheated population. Our findings suggest that warming effects on reproductive investment may initially compensate for the cost of warming-induced decrease in maturation size caused by the trade-off between early maturation and size-dependent fecundity. After multiple additional generations of warming, maturation and reproduction traits in perch differed from those in the first generations following the onset of warming, which suggests that warming-induced evolution may have occurred. Our study is particularly relevant in the context of climate change because of the unusually large temperature difference between the areas and the fact that the heating occurred on an ecosystem level. We call for experimental studies resolving mechanisms of trait responses to warming across generations, complemented with genomic analyses, to aid understanding of organisms' long-term responses to climate change.
6.	Niu, Jingyao, et al. (författare) Multi-decadal warming alters predator's effect on prey community composition 2024 Ingår i: Proceedings of the Royal Society B: Biological Sciences. - 0962-8452 .- 1471-2954. ; 291 Tidskriftsartikel (refereegranskat)abstract Predator responses to warming can occur via phenotypic plasticity, evolutionary adaptation or a combination of both, changing their top-down effects on prey communities. However, we lack evidence of how warming-induced evolutionary changes in predators may influence natural food webs. Here, we ask whether wild fish subject to warming across multiple generations differ in their impacts on prey communities compared with their nearby conspecifics experiencing a natural thermal regime. We carried out a common garden mesocosm experiment with larval perch (Perca fluviatilis), originating from a heated or reference coastal environment, feeding on zooplankton communities under a gradient of experimental temperatures. Overall, in the presence of fish of heated origin, zooplankton abundance was higher and did not change with experimental warming, whereas in the presence of fish of unheated origin, it declined with experimental temperature. Responses in zooplankton taxonomic and size composition suggest that larvae of heated origin consume more large-sized taxa as the temperature increases. Our findings show that differences between fish populations, potentially representing adaptation to their long-term thermal environments, can affect the abundance, biomass, size and species composition of their prey communities. This suggests that rapid microevolution in predators to ongoing climate warming might have indirect cross-generational ecological consequences propagating through food webs.
7.	Ogonowski, Martin, et al. (författare) Temperature moderates eDNA-biomass relationships in northern pike 2023 Ingår i: Environmental DNA. - 2637-4943. ; 5, s. 750-765 Tidskriftsartikel (refereegranskat)abstract Support for eDNA as a quantitative monitoring tool is growing worldwide. Despite ad-vances, there are still uncertainties regarding the representability of the eDNA signal over varying spatiotemporal scales, the influence of abiotic forcing, and phenological changes affecting the behavior of the study organism, particularly in open environ-ments. To assess the spatiotemporal variability and predictive power of quantitative eDNA analysis, we applied species-specific real-time quantitative PCR on water fil-trates during two visits to 22 coastal bays in the Baltic Sea. Within bays, we col-lected water along four transects across each bay and compared the pooled eDNA concentration to temporally matched catches from standardized angling targeting the northern pike (Esox lucius), a species for which reliable monitoring data is lacking. We found the variability in eDNA concentrations between transects to be moder-ate (21%) but still considerably lower than across bays and visits (52%), suggesting small- scale spatial differences are of less importance during spring when pike spawn. Standardized angling catches, bay area, and water temperature together explained 48% of the variance in eDNA concentrations. DNA concentrations decreased with the increasing bay area, likely indicating a dilution effect. Notably, the relationship be-tween eDNA and standardized catches was positive but varied with temperature and the eDNA-abundance relationship was only significant at higher temperatures, which also coincided with a higher proportion of spawning/spent fish. We conclude that temperature is a key moderating factor driving changes in pike behavior and spring DNA- dynamics. We recommend that future surveys focus on larger spatiotemporal scales during times when the influence of changing temperatures is minimized.
8.	Olsson, Jens, et al. (författare) Generation of a neutral FST baseline for testing local adaptation on gill raker number within and between European whitefish ecotypes in the Baltic Sea basin 2015 Ingår i: Journal of Evolutionary Biology. - : Wiley. - 1010-061X .- 1420-9101. ; 28, s. 1170-1183 Tidskriftsartikel (refereegranskat)abstract Divergent selection at ecologically important traits is thought to be a major factor driving phenotypic differentiation between populations. To elucidate the role of different evolutionary processes shaping the variation in gill raker number of European whitefish (Coregonus lavaretus sensu lato) in the Baltic Sea basin, we assessed the relationships between genetic and phenotypic variation among and within three whitefish ecotypes (sea spawners, river spawners and lake spawners). To generate expected neutral distribution of F-ST and to evaluate whether highly variable microsatellite loci resulted in deflated F-ST estimates compared to less variable markers, we performed population genetic simulations under finite island and hierarchical island models. The genetic divergence observed among (F-CT=0.010) and within (F-ST=0.014-0.041) ecotypes was rather low. The divergence in gill raker number, however, was substantially higher between sea and river spawners compared to observed microsatellite data and simulated neutral baseline (P-CT>F-CT). This suggests that the differences in gill raker number between sea and river spawners are likely driven by divergent natural selection. We also found strong support for divergent selection on gill raker number among different populations of sea spawners (P-ST>F-ST), most likely caused by highly variable habitat use and diverse diet. The putative role of divergent selection within lake spawners initially inferred from empirical microsatellite data was not supported by simulated F-ST distributions. This work provides a first formal test of divergent selection on gill raker number in Baltic whitefish, and demonstrates the usefulness of population genetic simulations to generate informative neutral baselines for P-ST-F-ST analyses helping to disentangle the effects of stochastic evolutionary processes from natural selection.
9.	Ozerov, Mikhail, et al. (författare) Differential expression and alternative splicing analyses of multiple tissues reveal albinism-associated genes in the Wels catfish (Silurus glanis) 2024 Ingår i: Comparative Biochemistry and Physiology - Part B: Biochemistry and Molecular Biology. - 1096-4959 .- 1879-1107. ; 271 Tidskriftsartikel (refereegranskat)abstract Albinism is a widespread departure from a typical body colouration due to altered melanin production. The Wels catfish (Silurus glanis) is among the largest freshwater fish species in the world, and albino individuals occur both in the wild and in aquaculture. Here, we performed transcriptome-wide analysis of albino and normally pigmented S. glanis using four tissues (skin, dorsal fin, whole eye and liver) to identify genes associated with albinism by exploring patterns of differential expression (DE) and differential alternative splicing (DAS). Multitissue analyses revealed a large number of genes in skin (n = 1355) and fin (n = 614) tissue associated with the albino phenotype in S. glanis, while the number of DE genes in eye and liver tissues was lower (n = 188, n = 189, respectively). Several DE genes across multiple tissues were detected as the most promising candidates (e.g., hsp4, hsp90b1, raph1, uqcrfs1, adcy-family and wnt-family) potentially causally linked to the albino phenotype in Wels catfish. Moreover, our findings supported earlier observations of physiological differences between albino and normally pigmented individuals, particularly in energy metabolism and immune response. In contrast, there were only a few pigmentation-related genes observed among DAS genes (4 in skin, 2 in fin), the overlap between DAS and DE genes was low (n = 25) and did not include known pigmentation-related genes. This suggests that DAS and DE in Wels catfish are, to a large extent, independent processes, and the observed alternative splicing cases are probably not causally linked with albinism in S. glanis. This work provides the first transcriptome-wide multi-tissue insights into the albinism of Wels catfish and serves as a valuable resource for further understanding the genetic mechanisms of pigmentation in fish.
10.	Ozerov, Mikhail, et al. (författare) Distribution and prevalence of the myxozoan parasite Tetracapsuloides bryosalmonae in northernmost Europe: analysis of three salmonid species 2022 Ingår i: Diseases of Aquatic Organisms. - : Inter-Research Science Center. - 0177-5103 .- 1616-1580. ; 151, s. 37-49 Tidskriftsartikel (refereegranskat)abstract Global climate change is altering the abundance and spread of many aquatic parasites and pathogens. Proliferative kidney disease (PKD) of salmonids caused by the myxozoan Tetracapsuloides bryosalmonae is one such emerging disorder, and its impact is expected to increase with rising water temperature. Yet, the distribution and prevalence of T. bryosalmonae in Northern Europe remain poorly characterized. Here, we studied 43 locations in 27 rivers in northernmost Norway and Finland to describe T. bryosalmonae infection frequency and patterns in 1389 juvenile salmonids. T. bryosalmonae was discovered in 12 out of 27 rivers (44%) and prevalence ranged from 4.2 to 55.5% in Atlantic salmon and from 5.8 to 75% in brown trout among infected rivers. In sympatric populations, brown trout was more frequently infected with T. bryosalmonae than was salmon. Age-specific parasite prevalence patterns revealed that in contrast to lower latitudes, the infection of juvenile fish predominantly occurs during the second summer or later. Temperature monitoring over 2 yr indicated that the mean water temperature in June was 2.1 to 3.2 degrees C higher in rivers containing T. bryosalmonae compared to parasite-free rivers, confirming the important role of temperature in parasite occurrence. Temporal comparison in T. bryosalmonae prevalence over a 10 yr period in 11 rivers did not reveal any signs of contemporary parasite spread to previously uninfected rivers. However, the wide distribution of T. bryosalmonae in rivers flowing to the Barents Sea indicates that climate change and heat waves may cause new disease outbreaks in northern regions.
11.	Ozerov, Mikhail, et al. (författare) DNA metabarcoding reveals spatial and temporal variation of fish eye fluke communities in lake ecosystems 2024 Ingår i: International Journal for Parasitology. - 0020-7519 .- 1879-0135. ; 54, s. 33-46 Tidskriftsartikel (refereegranskat)abstract Eye flukes (Diplostomidae) are diverse and abundant trematode parasites that form multi-species communities in fish with negative effects on host fitness and survival. However, the environmental factors and host-related characteristics that determine species diversity, composition, and coexistence in such communities remain poorly understood. Here, we developed a cost-effective cox1 region-specific DNA metabarcoding approach to characterize parasitic diplostomid communities in two common fish species (Eurasian perch and common roach) collected from seven temperate lakes in Estonia. We found considerable inter- and intra-lake, as well as inter-host species, variation in diplostomid communities. Sympatric host species characterization revealed that parasite communities were typically more diverse in roach than perch. Additionally, we detected five positive and two negative diplostomid species associations in roach, whereas only a single negative association was observed in perch. These results indicate that diplostomid communities in temperate lakes are complex and dynamic systems exhibiting both spatial and temporal heterogeneity. They are influenced by various environmental factors and by hostparasite and inter-parasite interactions. We expect that the described methodology facilitates ecological and biodiversity research of diplostomid parasites. It is also adaptable to other parasite groups where it could serve to improve current understanding of diversity, distribution, and interspecies interactions of other understudied taxa.
12.	Ozerov, Mikhail, et al. (författare) Draft genome assembly of the freshwater apex predator wels catfish (Silurus glanis) using linked-read sequencing 2020 Ingår i: G3. - : Oxford University Press (OUP). - 2160-1836. ; 10, s. 3897-3906 Tidskriftsartikel (refereegranskat)abstract The wels catfish (Silurus glanis) is one of the largest freshwater fish species in the world. This top predator plays a key role in ecosystem stability, and represents an iconic trophy-fish for recreational fishermen. S. glanis is also a highly valued species for its high-quality boneless flesh, and has been cultivated for over 100 years in Eastern and Central Europe. The interest in rearing S. glanis continues to grow; the aquaculture production of this species has almost doubled during the last decade. However, despite its high ecological, cultural and economic importance, the available genomic resources for S. glanis are very limited. To fulfill this gap we report a de novo assembly and annotation of the whole genome sequence of a female S. glanis. The linked-read based technology with 10X Genomics Chromium chemistry and Supernova assembler produced a highly continuous draft genome of S. glanis: ∼0.8Gb assembly (scaffold N50 = 3.2 Mb; longest individual scaffold = 13.9 Mb; BUSCO completeness = 84.2%), which included 313.3 Mb of putative repeated sequences. In total, 21,316 protein-coding genes were predicted, of which 96% were annotated functionally from either sequence homology or protein signature searches. The highly continuous genome assembly will be an invaluable resource for aquaculture genomics, genetics, conservation, and breeding research of S. glanis.
13.	Ozerov, Mikhail, et al. (författare) Humic-acid-driven escape from eye parasites revealed by RNA-seq and target-specific metabarcoding 2020 Ingår i: Parasites and Vectors. - : Springer Science and Business Media LLC. - 1756-3305. ; 13 Tidskriftsartikel (refereegranskat)abstract Background: Next generation sequencing (NGS) technologies are extensively used to dissect the molecular mechanisms of host-parasite interactions in human pathogens. However, ecological studies have yet to fully exploit the power of NGS as a rich source for formulating and testing new hypotheses.Methods: We studied Eurasian perch (Perca fluviatilis) and its eye parasite (Trematoda, Diplostomidae) communities in 14 lakes that differed in humic content in order to explore host-parasite-environment interactions. We hypothesised that high humic content along with low pH would decrease the abundance of the intermediate hosts (gastropods), thus limiting the occurrence of diplostomid parasites in humic lakes. This hypothesis was initially invoked by whole eye RNA-seq data analysis and subsequently tested using PCR-based detection and a novel targeted metabarcoding approach.Results: Whole eye transcriptome results revealed overexpression of immune-related genes and the presence of eye parasite sequences in RNA-seq data obtained from perch living in clear-water lakes. Both PCR-based and targeted-metabarcoding approach showed that perch from humic lakes were completely free from diplostomid parasites, while the prevalence of eye flukes in clear-water lakes that contain low amounts of humic substances was close to 100%, with the majority of NGS reads assigned toTylodelphys clavata.Conclusions: High intraspecific diversity ofT. clavataindicates that massively parallel sequencing of naturally pooled samples represents an efficient and powerful strategy for shedding light on cryptic diversity of eye parasites. Our results demonstrate that perch populations in clear-water lakes experience contrasting eye parasite pressure compared to those from humic lakes, which is reflected by prevalent differences in the expression of immune-related genes in the eye. This study highlights the utility of NGS to discover novel host-parasite-environment interactions and provide unprecedented power to characterize the molecular diversity of cryptic parasites.
14.	Ozerov, Mikhail, et al. (författare) Temporally stable small-scale genetic structure of Northern pike (Esox lucius) in the coastal Baltic Sea 2022 Ingår i: Fisheries Research. - : Elsevier BV. - 0165-7836 .- 1872-6763. ; 254 Tidskriftsartikel (refereegranskat)abstract The Northern pike (Esox lucius) is an important predator in freshwater and brackish water environments. In the Baltic Sea, Northern pike follows isolation by distance pattern across wide geographical scale. However, relatively little is known about the fine-scale population divergence and temporal genetic variation of Baltic pike, especially for populations inhabiting the eastern part of the Baltic Sea. Here, we characterize the population genetic structure of Northern pike and its temporal stability in six freshwater and one brackish water locations on the Island of Saaremaa (Estonia). To accomplish this, we collected 274 young-of-the-year (YOY) of two consecutive cohorts and 218 older specimens that were genotyped using ten microsatellite loci. Our results indicate a temporally stable population differentiation between geographically close locations and reduced diversity of the north-western Saaremaa populations. Furthermore, the correspondence analysis and a discriminant analysis of principal components showed a clear differentiation between north-western and the Gulf of Riga spawning grounds. Our findings support the idea that natal homing behavior, limited dispersal and facultative anadromy in Baltic pike likely promotes the existence of temporally stable genetic divergence among different populations at small geographical scale, representing an essential prerequisite for development of local adaptations. Thus, conservation, management and restoration efforts of coastal Baltic Sea pike should preserve the existing genetic differences between different populations and avoid actions, which potentially increase genetic homogenization.
15.	Ozerov, Mikhail, et al. (författare) The strength and form of natural selection on transcript abundance in the wild 2021 Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 30, s. 2724–2737- Tidskriftsartikel (refereegranskat)abstract Gene transcription variation is known to contribute to disease susceptibility and adaptation, but we currently know very little about how contemporary natural selection shapes transcript abundance. Here, we propose a novel analytical framework to quantify the strength and form of ongoing natural selection at the transcriptome level in a wild vertebrate. We estimated selection on transcript abundance in a cohort of a wild salmonid fish (Salmo trutta) affected by an extracellular myxozoan parasite (Tetracapsuloides bryosalmonae) through mark-recapture field sampling and the integration of RNA-sequencing with classical regression-based selection analysis. We show, based on fin transcriptomes of the host, that infection by the parasite and subsequent host survival is linked to upregulation of mitotic cell cycle process. We also detect a widespread signal of disruptive selection on transcripts linked to host immune defence, host-pathogen interactions, cellular repair and maintenance. Our results provide insights into how selection can be measured at the transcriptome level to dissect the molecular mechanisms of contemporary evolution driven by climate change and emerging anthropogenic threats. We anticipate that the approach described here will enable critical information on the molecular processes and targets of natural selection to be obtained in real time.
16.	Ozerov, Mikhail, et al. (författare) Whole-genome sequencing illuminates multifaceted targets of selection to humic substances in Eurasian perch 2022 Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 31, s. 2367-2383 Tidskriftsartikel (refereegranskat)abstract Extreme environments are inhospitable to the majority of species, but some organisms are able to survive in such hostile conditions due to evolutionary adaptations. For example, modern bony fishes have colonized various aquatic environments, including perpetually dark, hypoxic, hypersaline and toxic habitats. Eurasian perch (Perca fluviatilis) is among the few fish species of northern latitudes that is able to live in very acidic humic lakes. Such lakes represent almost "nocturnal" environments; they contain high levels of dissolved organic matter, which in addition to creating a challenging visual environment, also affects a large number of other habitat parameters and biotic interactions. To reveal the genomic targets of humic-associated selection, we performed whole-genome sequencing of perch originating from 16 humic and 16 clear-water lakes in northern Europe. We identified over 800,000 single nucleotide polymorphisms, of which >10,000 were identified as potential candidates under selection (associated with >3000 genes) using multiple outlier approaches. Our findings suggest that adaptation to the humic environment may involve hundreds of regions scattered across the genome. Putative signals of adaptation were detected in genes and gene families with diverse functions, including organism development and ion transportation. The observed excess of variants under selection in regulatory regions highlights the importance of adaptive evolution via regulatory elements, rather than via protein sequence modification. Our study demonstrates the power of whole-genome analysis to illuminate the multifaceted nature of humic adaptation and provides the foundation for further investigation of causal mutations underlying phenotypic traits of ecological and evolutionary importance.
17.	Vasemägi, Anti (författare) Assessing freshwater fish biodiversity of Kumbe River, Papua (Indonesia) through environmental DNA metabarcoding 2023 Ingår i: Pacific Conservation Biology. - 1038-2097. ; 29, s. 340-350 Tidskriftsartikel (refereegranskat)abstract Context. The ability to accurately assess biodiversity is a critical first step towards effective conservation and management. However, assessment of biodiversity using conventional monitoring programs is often constrained by high cost and a lack of taxonomic expertise. Environmental DNA (eDNA) metabarcoding may be a useful tool to efficiently catalogue biodiversity in areas that cannot be easily assessed using other methods. Aims. Here, we evaluated the potential of eDNA metabarcoding for assessing fish biodiversity and distribution in the Kumbe River, Papua Province, Indonesia. Methods. We selected four sampling locations and collected seven eDNA samples from each location. We used eDNA metabarcoding of the Cytochrome-b gene to characterise the fish community. Key results. A total of 23 species were detected, three of which comprised 92% of sequence reads detected: Melanotaenia goldiei (32%), Craterocephalus randi (31%), and the invasive tilapia Oreochromis niloticus (29%). Only five species that were previously detected using conventional methods were detected by metabarcoding: M. goldiei, Craterocephalus stercusmuscarum, O. niloticus, Neoarius graeffei, and Arius arius. We detected 18 species (70% native) that have never been recorded from the Kumbe River. Conclusions. This work has demonstrated that fish biodiversity is substantially underestimated in the Kumbe River. Environmental DNA metabarcoding is a promising rapid, non-invasive and cost-effective method for assessing fish biodiversity in Papua. Implications. The findings support future investment in eDNA metabarcoding to characterise the fish biodiversity in Papua. This will assist in allocating the limited resources for conservation and management to areas most at risk from anthropogenic impacts.
18.	Vasemägi, Anti (författare) Association Mapping Based on a Common-Garden Migration Experiment Reveals Candidate Genes for Migration Tendency in Brown Trout 2019 Ingår i: G3. - : Oxford University Press (OUP). - 2160-1836. ; 9, s. 2887-2896 Tidskriftsartikel (refereegranskat)abstract A better understanding of the environmental and genetic contribution to migratory behavior and the evolution of traits linked to migration is crucial for fish conservation and fisheries management. Up to date, a few genes with unequivocal influence on the adoption of alternative migration strategies have been identified in salmonids. Here, we used a common garden set-up to measure individual migration distances of generally highly polymorphic brown trout Salmo trutta from two populations. Fish from the assumedly resident population showed clearly shorter migration distances than the fish from the assumed migratory population at the ages of 2 and 3 years. By using two alternative analytical pipelines with 22186 and 18264 SNPs obtained through RAD-sequencing, we searched for associations between individual migration distance, and both called genotypes and genotype probabilities. None of the SNPs showed statistically significant individual effects on migration after correction for multiple testing. By choosing a less stringent threshold, defined as an overlap of the top 0.1% SNPs identified by the analytical pipelines, GAPIT and Angsd, we identified eight candidate genes that are potentially linked to individual migration distance. While our results demonstrate large individual and population level differences in migration distances, the detected genetic associations were weak suggesting that migration traits likely have multigenic control.
19.	Vasemägi, Anti (författare) Beyond hybridization: the genetic impacts of non-reproductive ecological interactions of salmon aquaculture on wild populations 2020 Ingår i: Aquaculture environment interactions. - : Inter-Research Science Center. - 1869-215X .- 1869-7534. ; 12, s. 429-445 Forskningsöversikt (refereegranskat)abstract Cultured Atlantic salmon Salmo salar are of international socioeconomic value, and the process of domestication has resulted in significant behavioural, morphological, and allelic differences from wild populations. Substantial evidence indicates that direct genetic interactions or interbreeding between wild and escaped farmed Atlantic salmon occurs, genetically altering wild salmon and reducing population viability. However, genetic interactions may also occur through ecological mechanisms (e.g. disease, parasites, predation, competition), both in conjunction with and in the absence of interbreeding. Here we examine existing evidence for ecological and non-reproductive genetic interactions between domestic Atlantic salmon and wild populations and the potential use of genetic and genomic tools to resolve these impacts. Our review identified examples of genetic changes resulting from ecological processes, predominately through pathogen or parasite transmission. In addition, many examples were identified where aquaculture activities have either altered the selective landscape experienced by wild populations or resulted in reductions in population abundance, both of which are consistent with the widespread occurrence of indirect genetic changes. We further identify opportunities for genetic or genomic methods to quantify these impacts, though careful experimental design and pre-impact comparisons are often needed to accurately attribute genetic change to aquaculture activities. Our review indicates that ecological and non-reproductive genetic interactions are important, and further study is urgently needed to support an integrated understanding of aquaculture-ecosystem interactions, their implications for ecosystem stability, and the development of potential mitigation and management strategies.
20.	Vasemägi, Anti (författare) Changes in the spatio-temporal genetic structure of Baltic sea trout (Salmo trutta L.) over two decades: direct and indirect effects of stocking 2024 Ingår i: Conservation Genetics. - 1566-0621 .- 1572-9737. ; 25, s. 481–497- Tidskriftsartikel (refereegranskat)abstract Several countries have implemented stocking programmes to enhance abundance and fish production by releases of hatchery-reared fish. However, due to fluctuations in population size, stocking history, and potential indirect effects of straying of hatchery-reared fish, it is often difficult to predict how these factors will affect genetic diversity and differentiation patterns among wild populations. This study characterized the population genetic structure and temporal variability of four Estonian sea trout populations by evaluating the degrees of direct and indirect genetic impacts of stocking over two decades using 14 microsatellite loci. Our results demonstrate considerable temporal change combined with weak genetic structuring among studied sea trout populations. We found a reduction of the overall level of genetic differentiation combined with the tendency for increased genetic diversity, and an effective number of breeders (N-b) over the study period. Furthermore, we found that immigration rates (m) from hatchery stocks were highest in the population subjected to direct stocking and in non-stocked populations that were located geographically closer to the stocked rivers. This work suggests that hatchery releases have influenced the genetic diversity and structuring of studied sea trout populations. However, the impact of hatchery releases on the adaptive variation and fitness-related traits in wild trout populations remains to be revealed by more informative genetic markers. This study illustrates the dynamic nature of the population genetic structure of sea trout and the value of long-term genetic monitoring for management and conservation.
21.	Vasemägi, Anti (författare) Climate change-driven disease in sympatric hosts: Temporal dynamics of parasite burden and proliferative kidney disease in wild brown trout and Atlantic salmon 2021 Ingår i: Journal of Fish Diseases. - : Wiley. - 0140-7775 .- 1365-2761. ; 44, s. 689-699 Tidskriftsartikel (refereegranskat)abstract Global climate change is altering the abundance and spread of various parasites, which has important consequences not only for host-parasite interactions but also for the relationships between different host species. Here, we focus on the myxozoan endoparasite Tetracapsuloides bryosalmonae that causes temperature-dependent proliferative kidney disease (PKD) in salmonids. We characterized the temporal changes in the parasite load and the severity of PKD signs (renal hyperplasia, haematocrit) in two sympatric populations of wild brown trout (Salmo trutta) and Atlantic salmon (Salmo salar). We found that both the parasite load and disease signs vary considerably between individuals, species, rivers and sampling periods. We showed that Atlantic salmon was able to slow down the initial parasite proliferation rate and subsequently tolerate high parasite burden without obvious disease signs. In contrast, the initial parasite proliferation rate was much higher in brown trout, which was followed by the development of severe PKD signs. Thus, the speed of parasite proliferation, rather than the absolute number of the parasites in the host kidney, may play an important role in interspecific variation in PKD susceptibility. To conclude, this study illustrates the usefulness of temporal perspective for understanding host defence mechanisms and climate change-mediated impacts in the wild.
22.	Vasemägi, Anti (författare) Comparing RADseq and microsatellites for estimating genetic diversity and relatedness – implications for brown trout conservation 2019 Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 9, s. 2106-2120 Tidskriftsartikel (refereegranskat)abstract The conservation and management of endangered species requires information on their genetic diversity, relatedness and population structure. The main genetic markers applied for these questions are microsatellites and single nucleotide polymorphisms (SNPs), the latter of which remain the more resource demanding approach in most cases. Here, we compare the performance of two approaches, SNPs obtained by restriction-site-associated DNA sequencing (RADseq) and 16 DNA microsatellite loci, for estimating genetic diversity, relatedness and genetic differentiation of three, small, geographically close wild brown trout (Salmo trutta) populations and a regionally used hatchery strain. The genetic differentiation, quantified as F-ST, was similar when measured using 16 microsatellites and 4,876 SNPs. Based on both marker types, each brown trout population represented a distinct gene pool with a low level of interbreeding. Analysis of SNPs identified half- and full-siblings with a higher probability than the analysis based on microsatellites, and SNPs outperformed microsatellites in estimating individual-level multilocus heterozygosity. Overall, the results indicated that moderately polymorphic microsatellites and SNPs from RADseq agreed on estimates of population genetic structure in moderately diverged, small populations, but RADseq outperformed microsatellites for applications that required individual-level genotype information, such as quantifying relatedness and individual-level heterozygosity. The results can be applied to other small populations with low or moderate levels of genetic diversity.
23.	Vasemägi, Anti (författare) Comparison of Migratory and Resident Populations of Brown Trout Reveals Candidate Genes for Migration Tendency 2018 Ingår i: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 10, s. 1493-1503 Tidskriftsartikel (refereegranskat)abstract Candidate genes associated with migration have been identified in multiple taxa: including salmonids, many of whom perform migrations requiring a series of physiological changes associated with the freshwater-saltwater transition. We screened over 5,500 SNPs for signatures of selection related to migratory behavior of brown trout Salmo trutta by focusing on ten differentially migrating freshwater populations from two watersheds (the Koutajoki and the Oulujoki). We found eight outlier SNPs potentially associated with migratory versus resident life history using multiple (>= 3) outlier detection approaches. Comparison of three migratory versus resident population pairs in the Koutajoki watershed revealed seven outlier SNPs, of which three mapped close to genes ZNF665-like, GRM4-like, and PCDH8-like that have been previously associated with migration and smoltification in salmonids. Two outlier SNPs mapped to genes involved in mucus secretion (ST3GAL1-like) and osmoregulation (C14orf37-like). The last two strongly supported outlier SNPs mapped to thermally induced genes (FNTA1-like, FAM134C-like). Within the Oulujoki, the only consistent outlier SNP mapped close to a gene (EZH2) that is associated with compensatory growth in fasted trout. Our results suggest that a relatively small yet common set of genes responsible for physiological functions associated with resident and migratory life histories is evolutionarily conserved.
24.	Vasemägi, Anti (författare) First record of Tetracapsuloides bryosalmonae (Myxozoa; Malacosporea) in European whitefish (Coregonus lavaretus) 2018 Ingår i: European Association of Fish Pathologists Bulletin. - 0108-0288. ; 38, s. 171-176 Tidskriftsartikel (refereegranskat)abstract Proliferative kidney disease (PKD) is a temperature-dependent disorder of salmonids induced by the myxozoan parasite Tetracapsuloides bryosalmonae. In Europe, T. bryosalmonae has been reported in rainbow trout, Atlantic salmon, brown trout, Arctic char, brook trout and grayling. This study reports for the first time the presence of T. bryosalmonae in European whitefish (Coregonus lavaretus) while the parasite was not found in vendace (C. albula) and European smelt (Osmerus eperlanus).
25.	Vasemägi, Anti (författare) Genetic and morphological evidence of a single species of bronze featherback (Notopterus notopterus) in Sundaland 2024 Ingår i: Global Ecology and Conservation. - 2351-9894. ; 49 Tidskriftsartikel (refereegranskat)abstract The bronze featherback (Notopterus notopterus) is an iconic species of freshwater fish commonly found in South -East Asia and of great commercial and patrimonial importance. At present, the genus Notopterus comprises of two distinct species, Notopterus notopterus (Pallas, 1769) and Notopterus synurus (Bloch & Schneider 1801). On the Indonesian archipelago, genetic diversity and morphology of the bronze featherback were investigated for conservation purposes. The use of DNA -based species delimitation methods, applied to 165 Cytochrome oxidase I sequences of Notopteridae (121 belonging to N. notopterus), evidence a concordance between species and Molecular Operational Taxonomic Unit (MOTU) and the two species of Notopterus are recognized. In N. notopterus, 9 haplotypes are detected among the 121 sequences analyzed, and three are restricted to Sundaland. These three haplotypes had distinct geographic distribution with a haplotype observed in Java, Sumatra and Borneo, another haplotype restricted to South Sumatra and a third haplotype only found in Northern Sumatra. The analyze of 21 morphometric and 9 meristic variables revealed two groups within N. notopterus, which were only supported by subtle differences in measurements with overlapping distributions between groups. The present study supports the validity of Notopterus notopterus in Sundaland and the remarkable genetic continuity among populations across its range distribution.

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