Agricultural and Biological Sciences, Aquatic Science, Ecology, Evolution, Behavior and Systematics, Animal Science and Zoology
66
Scopus Publications
Scopus Publications
Dams threaten salmonids by triggering temperature-dependent proliferative kidney disease Magnus Lauringson, Joacim Näslund, Lilian Pukk, Siim Kahar, Riho Gross, et al. Communications Biology, 2026 Dams provide different services for human society, but they also significantly disrupt ecosystems by altering natural flow and temperature regimes. Here, we describe a novel, unappreciated threat posed by reservoirs to one of the world’s most popular game fish, brown trout ( Salmo trutta ). We show that small river impoundments elevate downstream water temperature during summer, which increases the prevalence and abundance of Tetracapsuloides bryosalmonae parasite triggering proliferative kidney disease (PKD), an emerging disorder in salmonids across North America and Europe. Our study highlights the role of reservoirs in creating parasite and disease hotspots, while providing limited evidence that dams act as barriers to parasite spread. This makes downstream areas from reservoirs valuable sentinel sites for monitoring climate impacts on riverine ecosystems. Ultimately, the assessment of dams requires a more holistic approach, where the disease risks are included in the decision-making process balancing human needs with the health of aquatic ecosystems.
Pan-Continental Genomic Analysis of Eurasian Perch Uncovers Global Diversity Hotspots and Postglacial Recolonization Patterns Vitalii Lichman, Mikhail Ozerov, María‐Eugenia López, Kristina Noreikiene, Siim Kahar, et al. Ecology and Evolution, 2026 The contemporary distribution of genetic diversity in widespread freshwater species reflects a complex interplay between historical processes and recent demographic events. We investigated the postglacial recolonization history of the Eurasian perch ( Perca fluviatilis L.) across its native range spanning Europe and Western Siberia, aiming to understand how historical and recent demographic processes have shaped contemporary genetic diversity in a widespread freshwater species. Using an integrative genomic approach, we combined whole mitochondrial genome resequencing with nuclear SNP‐array genotyping (3660 SNPs) for 382 individuals from 188 locations to reconstruct patterns of lineage divergence, population structure, and admixture. We identified five highly divergent mitochondrial lineages, consistent with the existence of multiple glacial refugia across Southwestern, Southeastern, and Central Europe, as well as Siberia. Nuclear data (3660 SNPs) revealed three major genetic clusters corresponding to Western, Northern, and Southeastern Europe, along with strong regional admixture. The Baltic Sea region emerged as a contemporary hotspot of genetic diversity, likely resulting from the admixture and convergence of distinct maternal lineages during the postglacial recolonization of Northern Europe. Signals of isolation by distance were evident both within and across lineages, highlighting the role of limited dispersal in shaping current genetic patterns. The integration of mitochondrial and nuclear genomic data provided a comprehensive view of the evolutionary history of P. fluviatilis , revealing both deep historical divergence and recent admixture events. The existence of multiple glacial refugia and subsequent secondary contact underscores the complexity of postglacial recolonization processes in freshwater fauna. These findings advance our understanding of how historical and contemporary factors interact to shape biodiversity across Europe.
Spleen as an Alternative Tissue for Estimating Tetracapsuloides bryosalmonae Load, Prevalence and Its Relationship With Proliferative Kidney Disease in Brown Trout Magnus Lauringson, Lilian Pukk, Siim Kahar, Oksana Burimski, Riho Gross, et al. Journal of Fish Diseases, 2026 Accurate pathogen detection is essential in fish health management and disease prevention. Pathogens often target different host tissues, and monitoring alternative target organs can provide important insights into disease progression. We evaluated the spleen as an alternative to the kidney for estimating the load and prevalence of the myxozoan parasite Tetracapsuloides bryosalmonae (Tb) and its relationships with proliferative kidney disease (PKD) in juvenile brown trout. We sampled 238 brown trout across nine rivers and quantified parasite load in both tissues using qPCR. Parasite load showed a strong positive correlation between the two tissues for both raw and log10‐transformed data (Pearson's r = 0.60–0.71, Spearman's ρ = 0.78), with the spleen exhibiting, on average, 4.1‐fold lower parasite load compared to the kidney. Tb was found in 191 specimens, consisting of 167 spleen and 190 kidney detections. The relationships between parasite load and PKD symptoms (renal hyperplasia and anaemia) were comparable for both tissues, and segmented regression line analysis indicated that health parameters deteriorate faster after exceeding a certain parasite load threshold. In conclusion, these results suggest that the spleen may serve as a viable alternative to the kidney for Tb monitoring, providing useful insights into Tb presence, load, and PKD progression in salmonids.
Integrative Genomics Refines Tissues, Candidate Genes and Putative Regulatory Links Involved in the Humic Adaptation of Keystone Freshwater Fish M. Yu. Ozerov, K. Noreikiene, K. Taube, R. Gross, A. Vasemägi Molecular Ecology, 2025 Although population genomics approaches have been successful in identifying regions of the genome shaped by natural selection, progress in dissecting the molecular mechanisms of adaptive variants and traits has been slow. By integrating multi‐tissue (gill, spleen, olfactory rosette, whole eye, and liver) transcriptomes from 16 wild Eurasian perch (Perca fluviatilis) populations and previously identified footprints of selection, we prioritise tissues, candidate genes, and putative SNP‐gene expression associations potentially involved in the humic adaptation of this keystone freshwater fish. Over 5000 differentially expressed genes (DEGs) were discovered across the five tissues. A significant excess of outlier SNPs among DEGs found in the gill and spleen tissues indicated their potential involvement in humic adaptation. Next, we identified 2640 cis‐eQTLs, and observed significant enrichment of outliers among expression‐associated SNPs (eSNPs) in spleen and olfactory rosette tissues, as well as in all tissues combined. Several eQTLs were found in the regions showing the strongest signals of selection, which also harboured DEGs (chr. 5: PLAGL2, chr. 7: PPP1R8, TCHH). Thus, our integrative analyses enabled us to pinpoint specific organs that potentially play a key role in adaptation, prioritise candidate genes under divergent selection based on their expression patterns, and identify links between SNPs and transcript abundance variation. We expect that by combining evolutionary and functional genomics perspectives this work provides a practical framework for understanding the genetic basis of phenotypic diversification and adaptation across a wide range of species.
Parasite spillover rather than niche expansion explains infection of host brain by diplostomid eye flukes Alfonso Diaz-Suarez, Veljo Kisand, Siim Kahar, Riho Gross, Anti Vasemägi, et al. Proceedings of the Royal Society B Biological Sciences, 2025 Parasites often occupy specific sites within their host, which has important implications for host performance and parasite transmission. Nonetheless, parasitic infections can occur beyond their typical location within a host, significantly altering host–parasite interactions. Yet, the causes behind the atypical tissue tropism are poorly understood. Here, we focus on a ubiquitous group of diplostomid parasites that form diverse communities in fish eyes. We used targeted DNA metabarcoding (cytochrome c oxydase subunit 1, COX1, 250 bp) to evaluate potential mechanisms underlying eye parasite atypical tissue tropism to the brain of two widespread fish species (Eurasian perch and common roach). We found that the most common eye-infecting species ( Tylodelphys clavata , Diplostomum baeri ) are present in the brains of perch but not in roach. The bipartite network comprising 5 species and 24 mitochondrial haplotypes revealed no brain-specific haplotypes, indicating an apparent lack of genetic divergence between brain- and eye-infecting parasites. Instead, the prevalence, intensity and diversity of eye infections were positively correlated with brain infections. Thus, our results suggest that the most parsimonious mechanism underlying brain infection is density-dependent spillover rather than parasite divergence-driven niche expansion. We anticipate that ‘off-target’ infections are likely to be severely underestimated in nature with important ecological, evolutionary and medical implications.
Dynamic Outlier Slicing Allows Broader Exploration of Adaptive Divergence: A Comparison of Individual Genome and Pool-Seq Data Linked to Humic Adaptation in Perch María‐Eugenia López, Mikhail Ozerov, Lilian Pukk, Kristina Noreikiene, Riho Gross, et al. Molecular Ecology, 2025 How genetic variation contributes to adaptation at different environments is a central focus in evolutionary biology. However, most free‐living species still lack a comprehensive understanding of the primary molecular mechanisms of adaptation. Here, we characterised the targets of selection associated with drastically different aquatic environments—humic and clear water—in the common freshwater fish, Eurasian perch (Perca fluviatilis). By using whole‐genome sequencing (WGS) on a large population dataset (n = 42 populations) and analysing 873,788 SNPs, our primary aim was to uncover novel and confirm known footprints of selection. We compared individual and pooled WGS, and developed a novel approach, termed dynamic outlier slicing, to assess how the choice of outlier‐calling stringency influences functional and Gene Ontology (GO) enrichment. By integrating genome‐environment association (GEA) analysis with allele frequency‐based approaches, we estimated composite selection signals (CSS) and identified 2679 outlier SNPs distributed across 324 genomic regions, involving 468 genes. Dynamic outlier slicing identified robust enrichment signals in five annotation categories (upstream, downstream, synonymous, 5′UTR and 3′UTR) highlighting the crucial role of regulatory elements in adaptive evolution. Furthermore, GO analyses revealed strong enrichment of molecular functions associated with gated channel activity, transmembrane transporter activity and ion channel activity, emphasising the importance of osmoregulation and ion balance maintenance. Our findings demonstrate that despite substantial random drift and divergence, WGS of high number of population pools enabled the identification of strong selection signals associated with adaptation to both humic and clear water environments, providing robust evidence of widespread adaptation. We anticipate that the dynamic outlier slicing method we developed will enable a more thorough exploration of adaptive divergence across a diverse range of species.
Eggs on a plate: Population-dependent effects of humic substance rich water on perch egg size and hatching success Kristina Noreikiene, Karl‐Erik Aavik, Siim Kahar, Magnus Lauringson, Konrad Taube, et al. Freshwater Biology, 2024 The ability of fish to sustain environmental perturbations during fragile early‐life stages can be of vital importance for populations and species facing rapid global environmental change. One of the potential challenges for aquatic organisms, including teleost fish, is rising concentration of dissolved organic carbon (DOC) in freshwater environments, known as brownification, which causes a cascade of changes including a decreased visibility and pH. Conversely, humic substances are increasingly recognised for their potential antimicrobial and immunostimulant properties. The questions remain whether exposure to humic waters high in DOC during the development causes significant perturbation, and to what extent genetic and parental factors may maintain optimal development in such a possibly challenging environment. To address these questions, we generated pure and hybrid (inter‐population) crosses of Eurasian perch (Perca fluviatilis) originating from clear‐water and humic lakes. Fertilised eggs from each cross were exposed to natural humic and clear‐water lake water. Intra‐chorionic space diameter (embryo diameter) and hatching success were recorded. Perch embryos successfully developed even in a small volume of water (5 mL) and majority hatched (70%) by 13 day post‐fertilisation. Embryo diameter was influenced by the interaction between cross type and treatment where embryos with maternal clear‐water origin were smaller than embryos of humic water origin in both clear‐water and humic water treatments. The probability of hatching was not related to female size, but rather to embryo diameter at the eyed stage and the interaction between cross type and treatment, resulting in pure clear‐water crosses hatching earlier and at higher numbers. Our study shows that effects of humic water are not uniformally negative in perch and discloses population‐dependent responses to humic water exposure during development. Our experimental design also illustrates the utility of multi‐well plates for conducting complex high‐throughput experiments beyond traditional model species and opens new possibilities for testing perch genotype–environment associations in early‐life traits. Taken together, results of this study add to the growing evidence that humic substances may have complex effects on fish during early life, motivating further investigations on their role in shaping natural phenotypes and potential use in the applied sector.
Whole-genome analysis reveals phylogenetic and demographic history of Eurasian perch Vitalii Lichman, Mikhail Ozerov, María‐Eugenia López, Kristina Noreikiene, Siim Kahar, et al. Journal of Fish Biology, 2024 The contemporary diversity and distribution of species are shaped by their evolutionary and ecological history. This can be deciphered with the help of phylogenetic and demographic analysis methods, ideally combining and supplementing information from mitochondrial and nuclear genomes. In this study, we investigated the demographic history of Eurasian perch (Perca fluviatilis), a highly adaptable teleost with a distribution range across Eurasia. We combined whole‐genome resequencing data with available genomic resources to analyse the phylogeny, phylogeography, and demographic history of P. fluviatilis populations from Europe and Siberia. We identified five highly diverged evolutionary mtDNA lineages, three of which show a strong signal of admixture in the Baltic Sea region. The estimated mean divergence time between these lineages ranged from 0.24 to 1.42 million years. Based on nuclear genomes, two distinct demographic trajectories were observed in European and Siberian samples reflecting contrasting demographic histories ca. 30,000–100,000 years before the present. A comparison of mtDNA and nuclear DNA evolutionary trees and AMOVA revealed concordances, as well as incongruences, between the two types of data, most likely reflecting recent postglacial colonization and hybridization events. Overall, our findings demonstrate the power and usefulness of genome‐wide information for delineating historical processes that have shaped the genome of P. fluviatilis. We also highlight the added value of data‐mining existing transcriptomic resources to complement novel sequence data, helping to shed light on putative glacial refugia and postglacial recolonization routes.
Changes in the spatio-temporal genetic structure of Baltic sea trout (Salmo trutta L.) over two decades: direct and indirect effects of stocking Oksana Burimski, Anti Vasemägi, Riho Gross Conservation Genetics, 2024 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 (Nb) 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.
Biodiversity and Population Structure T. L. King, E. Verspoor, A. P. Spidle, R. Gross, R. B. Phillips, et al. Atlantic Salmon Genetics Conservation and Management, 2007
Use of genetic markers in growth testing of common carp, Cyprinus carpio L., carried out over 2 or 3 year cycles Aquaculture Fisheries Management, 1994
