AquaGenomics: linking genes and genomes to population and ecosystem health in a changing world

Our research

Our research aims to inform sustainable fisheries management and conservation of aquatic organisms by developing science-based solutions that support healthy fish populations, safeguard aquatic biodiversity, and promote the long-term sustainability of ecosystems in the face of global environmental challenges. 

• Population genomics – analysis of genetic diversity and structuring at different spatial and temporal scales.
• Ecological & functional genomics – linking genes to function, adaptation and environmental variables.
• Environmental DNA (eDNA) – Developing tools to detect and quantify aquatic biodiversity using molecular approaches.
• Emerging infectious diseases – Studying pathogens dynamics in cold-water salmonids and their ecological impacts. 
• Conservation genetics – Disentangling connectivity patterns and reconstructing demographic past.
• Effect of habitat alterations population genetic structuring of riverine fish – linking landscape features to genome-wide patterns.
• Genomic and plastic responses to humic substances – Exploring how keystone freshwater fish respond to brownification. 
• Host–parasite interactions and ecosystem change – Hidden consequences of parasitism associated with expanding ecosystem engineers projects.

Research team

Anti Vasemägi, Professor 

Anti is an evolutionary biologist interested in how genomic diversity translates into phenotypic variation and is shaped by both adaptive and non-adaptive processes, with a focus on aquatic species. Much of his work is focused on fish and their parasites, combining population genetic, environmental DNA, -omics and ecological approaches to understand the mechanisms of how aquatic organisms interact, disperse and adapt. 

María-Eugenia López, Researcher

María-Eugenia is a population geneticist using advanced genomic and bioinformatic tools to investigate evolutionary dynamics, population-level genomic variation, and the functional basis of adaptation. She has a strong interest in understanding how small and vulnerable populations respond to environmental change. Her research combines high-throughput DNA sequencing and array-based genotyping with population genetic theory and computational analyses to support the conservation and sustainable management of aquatic biodiversity.

Kristel Panksep, Postdoctoral fellow

Kristel is a hydrobiologist with a wide interest in aquatic ecosystems and ecology. She has a strong background in eDNA and metabarcoding to identify and quantify species in complex environmental samples.

Duncan Philpott, PhD-student

Duncan is an aquatic ecologist interested in drivers and impacts of temperature-dependent disease on wild salmonids.

Alfonso Diaz Suarez, PhD-student

Alfonso has keen interest in population genetics of hosts and parasites at different scales, from individuals to populations and communities. Currently, he is studying the diversity of eye fluke parasites in fish and its consequences to fish health.

Konrad Taube, PhD-student

Konrad’s research interests are centred on understanding how animals adapt to their environments, with an emphasis on genomic and phenotypic diversity, bioinformatics, and biogeography. He is currently investigating the adaptive significance of regulatory variation in Eurasian perch. 

Vitalii Lichman, PhD-student

Vitalii is a PhD student passionate about population genetics and genomics, with a particular focus on uncovering evolutionary patterns across diverse spatial scales. His expertise lies in phylogenomics, integrating data from local to global levels to explore the dynamics of genetic diversity and structure in space and time.

Adaptation and Biodiversity in a Changing World

Fresh- and brackish-water habitats are among the most threatened and over-exploited ecosystems on the planet, facing accelerating pressures from climate change, pollution, habitat fragmentation, invasive species, and emerging pathogens. Most of our work focuses on studying the genetic variation and adaptive potential of fish and their parasites to develop strategies for maintaining healthy fish populations. Through the use of cutting-edge genomic methodologies, environmental DNA tools, and robust computational analyses, my research group seeks to build a deeper understanding of population vulnerability and ecosystem resilience. Our goal is to develop practical, science-based solutions that support healthy fish populations, safeguard genetic diversity and biodiversity, and promote the long-term sustainability of aquatic ecosystems.

Alumni

• Jingyao Niu, PhD student 2020-2025 
• Erik Karlsson, PhD-student 2019-2024 
• Magnus Lauringson, PhD student 2018-2024 
• Freed Ahmad, PhD student 2015-2023 
• Kristina Noreikiene, Post-doc 2018-2020
• Mikhail Ozerov, Post-doc 2013-2018

Research Interns

• Aidana Bekitayeva, 2024-2025
• Boris Depoortere, 2023

Our Publications (from 2018)

Lauringson M, Pukk L, Kahar S, Burimski O, Gross R, Kisand V, Vasemägi A (2025) Spleen as an alternative tissue for estimating Tetracapsuloides bryosalmonae load, prevalence and its relationship with proliferative kidney disease in brown trout. Journal of Fish Diseases, 0:e14148. https://doi.org/10.1111/jfd.14148

Ozerov YM, Noreikiene K, Taube K, Gross R, Vasemägi A (2025) Integrative genomics refines tissues, candidate genes and putative regulatory links involved in the humic adaptation of keystone freshwater fish. Molecular Ecology, 0:e17698. https://doi.org/10.1111/mec.17698 

Philpott D, Näslund J, Donadi S, Burimski O, Lauringson M, Pukk L, Vasemägi A (2025) Effects of different preservatives during ecological monitoring of myxozoan parasite Tetracapsuloides bryosalmonae causing proliferative kidney disease (PKD) in salmonids. Journal of Fish Diseases, e14095. doi: 10.1111/jfd.14095. 

López M-E, Ozerov M, Noreikiene K, Pukk L, Gross R, Vasemägi A (2025) Dynamic outlier slicing allows broader exploration of adaptive divergence: a comparison of individual genome and pool-seq data linked to humic adaptation in perch Molecular Ecology, 34, 4: e17659 DOI: 10.1111/mec.17659

Diaz-Suarez A,  Kisand V, Kahar S, Gross R, Vasemägi A, Noreikiene K (2025) Parasite spillover rather than niche expansion explains infection of host brain by diplostomid eye flukes. Proceedings of the Royal Society B, 29220242648. https://doi.org/10.1098/rspb.2024.2648

Niu J, Huss M, Garnier A, Vasemägi A, Gårdmark A (2024) Multi-decadal warming alters predator’s effect on prey community composition. Proceedings of the Royal Society B, 291:20240511 

Lichmann V, Ozerov M, López M-E, Noreikiene K, Kahar S, Pukk L, Burimski O, Gross R, Vasemägi A (2024) Whole-genome analysis reveals evolutionary and demographic history of Eurasian perch. Journal of Fish Biology, 1–15. https://doi.org/10.1111/jfb.15821

Noreikiene K, Aavik K-E, Kahar S, Lauringson M, Taube K, Diaz-Suarez A, Gross R, Vasemägi A (2024) Eggs on plate: Population-dependent effects of water rich in humic substances on egg size and hatching success in perch. Freshwater Biology, 69(9), 1307-132.

Layton K, Brieuc M, Castilho R, Díaz-Arce N, Estévez-Barcia D, Fonseca V, Fuentes-Pardo A, Jeffery N, Jiménez-Mena B, Junge C, Kaufmann J, T Leinonen, S Maes, P McGinnity, T Reed, C Reisser, Celine, G Silva, A Vasemägi, I Bradbury (2024) Predicting the future of our oceans – evaluating genomic forecasting approaches in marine species. Global Change Biology, 30(3):e17236.

Ozerov MY, Noreikiene K, Kahar S, Flajšhans M, Gross R, Vasemägi A (2024) Differential expression and alternative splicing analyses of multiple tissues reveal albinism-associated genes in the Wels catfish (Silurus glanis). Comparative Biochemistry and Physiology, Part B, 11:271:110941. 

Wibowo A, Haryono H, Kurniawan K, Prakoso VA, Dahruddin H, Surbani IL, Muslimin B, P. Jaya YY, Sudarsono S, Stuart IG, Ahnelt H, Funge-Smith S, Vasemägi A, Hubert N (2024) Genetic and morphological evidence of a single species of bronze featherback (Notopterus notopterus) in Sundaland. Global Ecology and Conservation. accepted. https://doi.org/10.1016/j.gecco.2023.e02786

Diaz-Suarez A, Noreikiene K,  Kahar S, Ozerov MY, Gross R, Kisand V, Vasemägi A (2024) DNA metabarcoding reveals spatial and temporal variation of fish eye fluke communities in lake ecosystems. International Journal for Parasitology, 54(1), 33-46. 

Burimski O, Vasemägi A, Gross R (2024) Changes in the spatio-temporal genetic structure of Baltic sea trout (Salmo trutta L.) over two decades: direct and indirect effects of stocking. Conservation Genetics, https://doi.org/10.1007/s10592-023-01582-7. 

Vasemägi A, Huss M, Gårdmark A, Ozerov MY (2023) On ability of perch to colonize new waterbodies - indirect evidence and sticky facts: a comment on Garcia et al. (2023). Biology Letters, 9: 20230533.

Torrealba D, Morales-Lange B, Mulero V, Vasemägi A, Mercado L, Gallardo-Matus J (2023) Heritability of immunity traits and resistance of Atlantic salmon against the sea louse Caligus rogercresseyi. Biology,12(8):1078. 

Taube K, Noreikiene K, Kahar S, Gross R, Ozerov M, Vasemägi A (2023) Subtle transcriptomic response of Eurasian perch (Perca fluviatilis) associated with Triaenophorus nodulosus plerocercoid infection. International Journal for Parasitology: Parasites and Wildlife, 22, 146-154.

Lauringson M, Kahar S, Veevo T, Silm M, Philpott D, Svirgsden R, Rohtla M, Päkk P, Gross R, Kaart T, Vasemägi A (2023) Spatial and intra-host distribution of myxozoan parasite Tetracapsuloides bryosalmonae among Baltic sea trout (Salmo trutta) Journal of Fish Diseases, 46(10):1073-1083.

Ogonowski, M., Karlsson, E., Vasemägi, A., Sundin, J., Bohman, P., Sundblad, G (2023) Temperature moderates eDNA-biomass relationships in northern pike. Environmental DNA, 5, 750-765.

Vasemägi A, Ozerov M, Noreikiene K, López M-L, Gårdmark A (2023) Unlocking the genome of Eurasian perch – from genes to ecology and back again. Ecology of Freshwater Fish. Ecology of Freshwater Fish. 00, 1-26.

Theissinger K, et al. (2023) How genomics can help biodiversity conservation. Trends in Genetics, 39(7):545-559.

Donadi S, Näslund J, Sandin L, Sers B, Vasemägi A, Degerman E (2023) 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. Ecography, e06522.

Niu J, Huss M, Vasemägi A, Gårdmark A (2023) Decades of warming alters maturation and reproductive investment in fish. Ecosphere, 14, 1, e4381.

Lopez M-E, Bergenius Nord M, Kaljuste O, Wennerström L, Hekim Z, Tiainen J, Vasemägi A (2022) Lack of panmixia of Bothnian Bay vendace -implications for fisheries management. Frontiers in Marine Science, section Marine Fisheries, Aquaculture and Living Resources, 9, https://doi.org/10.3389/fmars.2022.1028863.

Wibowo A, Kurniawan  K, Atminarso D, Prihadi TH, Baumgartner LJ, Rourke ML, Nagai S, Hubert N, Vasemagi A (2022) Assessing freshwater fish biodiversity of Kumbe River, Papua (Indonesia) through environmental DNA metabarcoding. Pacific Conservation Biology https://doi.org/10.1071/PC21078

M. Lauringson, M. Y. Ozerov, M-E. Lopez, V. Wennevik, E. Niemelä, T. Y. Vorontsova, A. Vasemägi (2022) Distribution and prevalence of the myxozoan parasite Tetracapsuloides bryosalmonae in northernmost Europe: analysis of three salmonid species. Diseases of Aquatic Organisms, 151:37-49. doi: 10.3354/dao03688.

Diaz-Suarez A, Noreikiene K,  Kisand V,  Burimski O, Svirgsden M D R, Rohtla M,  Ozerov M Y,  Gross R,  Vetemaa M,  Vasemägi A (2022) Temporal stability of small scale genetic structuring of Northern pike (Esox lucius) in the coastal Baltic Sea. Fisheries research, 254, 106402.

Karlsson E, Ogonowski M, Sundblad G, Sundin J, Svensson O, Nousiainen I, Vasemägi A (2022) Strong positive relationships between eDNA concentrations and biomass in juvenile and adult pike (Esox lucius) under controlled conditions: implications for monitoring. Environmental DNA, 4:881–893.

Ozerov O, Noreikiene K, Kahar K, Huss M, Huusko A, Kõiv T, Sepp M, López M, Gårdmark A, Gross R, Vasemägi A (2022) Whole-genome sequencing illuminates multifaceted targets of selection to humic substances in Eurasian perch. Molecular Ecology, 31(8):2367-2383. 

Mottola G, López ME, Vasemägi A, Nikinmaa M, Anttila K (2022) Are you ready for the heat? Phenotypic plasticity vs adaptation of heat tolerance in three-spined stickleback.  Ecosphere, 13 (4), e4015.

Formenti et al. (2022) The era of reference genomes in conservation genomics. Trends in Ecology and Evolution, 37(3):197-202. cited already 88 times (checked 25.10.2023)

Östergren  J, Palm S, Gilbey J, Spong G, Dannewitz J, Königsson H, Persson J, Vasemägi A (2021) A century of genetic homogenization in Baltic salmon – evidence from archival DNA. Proceedings of the Royal Society B, 288:20203147. 

Ahmad F, Debes V P, Pukk L, Kahar S, Hartikainen H, Gross R, Vasemägi A (2021) Know your enemy - transcriptome of myxozoan Tetracapsuloides bryosalmonae reveals potential drug targets against proliferative kidney disease in salmonids. Parasitology, 148(6), 726 – 739.

Lauringson M, Nousiainen I, Kahar S, Burimski O, Gross R, Kaart T, Vasemägi A (2021) Climate change-driven disease in sympatric hosts: temporal dynamics of parasite burden and proliferative kidney disease (PKD) in wild brown trout and Atlantic salmon. Journal of Fish Diseases, 44(6), 689-699.

Gilbey J, et al. (2021) Life in a drop: sampling environmental DNA for marine fishery management and ecosystem monitoring. Journal of Marine Policy, 124, 104331.

Ahmad F, Debes PV, Nousiainen I, Kahar S, Pukk L, Gross R, Ozerov M, Vasemägi A (2021) The strength and form of natural selection on transcript abundance in the wild. Molecular Ecology, 30(12), 2724-2737. From the Cover paper highlighted in commentary paper in Mol Ecol 

Ozerov M, Flajšhans M, Noreikiene K, Vasemägi A, Gross R (2020) Draft genome assembly of the freshwater apex predator wels catfish (Silurus glanis) using linked-read sequencing. G3: Genes, Genomes, Genetics, 10(11), 3897-3906.

Bradbury IR, Burgetz I, Coulson M, Verspoor E, Gilbey J, Lenhert S, Kess T, Cross T,  Vasemägi A, Solberg M, Fleming IA, McGinnity P (2020) Beyond hybridization: the genetic impacts of non-reproductive ecological interactions of salmon aquaculture on wild populations. Aquaculture Environment Interactions, 12, 429-445.

Noreikiene K, Ozerov M, Ahmad F, Kõiv T, Kahar S, Gross R, Sepp M, Pellizzone A, Vesterinen EJ,  Kisand V, Vasemägi A (2020) Humic-acid-driven escape from eye parasites revealed by RNA-seq and target-specific metabarcoding. Parasites & Vectors, 13, 433.

Lilley T, Sävilammi S, Ossa G, Blomberg A, Vasemägi A, Yung V, Johnson J (2020) Using genome-wide connectivity to predict disease vulnerability: Implications for the spread of white-nose syndrome in the southern-most bat species in the world. G3: Genes, Genomes, Genetics, 10(6), 2117-2126.

Wibowo A, Atminarso D, Baumgartner L, Vasemägi A (2020) High prevalence of non-native fish species in a remote region of the Mamberamo River, Indonesia. Pacific Conservation Biology, https://doi.org/10.1071/PC19004.

Lemopoulos A, Uusi-HeikkiläS, Hyvärinen P,  Alioravainen N, Prokkola JM, Elvidge CK, Vasemägi A, Vainikka A. (2019) Association mapping following a common-garden migration experiment reveals candidate genes for migration tendency in brown trout. G3: Genes, Genomes, Genetics, 9(9), 2887-2896.                       

Prokkola JM, Lemopoulos A, Uusi-Heikkilä S, Vasemägi A, Huusko A, Hyvärinen P, Koljonen M-L,  Koskiniemi J, Vainikka A (2019) Comparing RADseq and microsatellites for estimating genetic diversity and relatedness –implications for brown trout conservation. Ecology and Evolution, 9(4), 2106-2120.

Palomar G, Vasemägi A, Ahmad F, Nicieza AG, Cano JM (2019) Mapping of quantitative trait loci for life history traits segregating within common frog populations. Heredity, 122(6), 800-808.

Ozerov YM, Ahmad F, Gross R, Pukk L, Kahar S, Kisand V, Vasemägi A (2018) Highly continuous genome assembly of Eurasian perch (Perca fluviatilis) using linked-read sequencing. G3: Genes, Genomes, Genetics, 12, 3737-3743.

Sobociński B, Huusko A, Vasemägi A (2018) First record of Tetracapsuloides bryosalmonae (Myxozoa; Malacosporea) in European whitefish (Coregonus lavaretus). Bulletin of the European Association of Fish Pathologists, 38(4), 115-120.

Lemopoulos A, Uusi-Heikkilä S, Huusko A, Kokko H, Vasemägi A, Vainikka A (2018) Genome-wide divergence patterns support fine-scaled genetic structuring associated with migration tendency in brown trout. Canadian Journal of Fisheries and Aquatic Sciences, 75(10), 1680-1692. 

Ahmad F, Debes PV, Palomar G, Vasemägi A (2018) Association mapping reveals candidate loci for resistance and anemic response to an emerging temperature-driven parasitic disease in a wild salmonid fish. Molecular Ecology, 27(6), 1385-1401.

Atminarso D, Wibowo A, Kusuma WE, Prianto E, Ahnelt H, Vasemägi A, Kumazawa Y (2018) The complete mitochondrial DNA sequence of Pectenocypris sp. (Actinopterygii: Cyprinidae) from Serkap River, Sumatra, Indonesia. Mitochondrial DNA Part B: Resources, 3(1), 122–124.