My ongoing research projects fall into four areas:
1) Population genomics –analysis of biodiversity, demography and footprints of selection
Selected recent publications:
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, in press.
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.
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. et al. (2023) How genomics can help biodiversity conservation. Trends in Genetics, 39(7):545-559.
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 to be considered for publication in Frontiers in Marine Science, section Marine Fisheries, Aquaculture and Living Resources,
Formenti et al. (2022) The era of reference genomes in conservation genomics. TREE, https://doi.org/10.1016/j.tree.2021.11.008
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, https://doi.org/10.1002/ecs2.4015
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.
2) Environmental DNA – moving from detection towards quantification
Environmental DNA (eDNA) is a promising tool for science-based management of aquatic environments. The ability to detect single species as well as biodiversity from a water sample has wide applicability and the potential of eDNA is reflected in its rapid development. However, methodological issues remain before quantitative eDNA can be used practically; robust molecular techniques need to be developed, and eDNA-biomass relationships need to be described. Development of eDNA techniques for fish monitoring is particularly interesting for species currently lacking suitable monitoring techniques.
Related publications:
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.
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
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. https://doi.org/10.1002/edn3.298
Gilbey J, Carvalho G, Castilho R, Coscia I, Coulson MW, Dahle G, Derycke S, Francisco SM, Helyar SJ, Johansen T, Junge C, Layton KKS, Martinsohn J, Matejusova I, Robalo JI, Rodríguez-Ezpeleta N, Silva G, Strammerj I, Vasemägi A, Volckaert FAM (2021) Life in a drop: sampling environmental DNA for marine fishery management and ecosystem monitoring. Journal of Marine Policy, 124, 104331.
3) Ecological genomics – linking genes and traits to populations, environment and ecosystems
Ongoing project: Molecular mechanisms of darkwater adaptation
Selected recent publications:
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.
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. https://doi.org/10.1111/mec.16409
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 https://doi.org/10.1002/ecs2.4015
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.
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.
4) Host-parasite genomics & interactions
We focus on various model systems including myxozoan parasite Tetracapsuloides bryosalmonae, trematode eye flukes belonging to the Diplostomidae family, sea lice Caligus elongates and microbial pathogens.
Selected recent publications:
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, S0020-7519(23)00173-X.
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.
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.
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.
Lauringson M, Ozerov MY, Lopez M-E, Wennevik V, Niemelä E, Vorontsova TY, Vasemägi A (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.
Ahmad F, Debes PV, 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.
Postdocs
M. E. López (2019-2022)
K. Noreikiene (2018-2020)
P. Debes (2014-2016)
M. Ozerov (2013-2018)
A. Wibowo (2014)
D. Philippenko (2013-2014)
PhD Students
2021- Co-supervisor of PhD student Konrad Taube (Estonian University of Life Sciences, main supervisor R. Gross).
2020- Main supervisor of PhD student Vitaly Lichman (Estonian University of Life Sciences, co-supervisors R. Gross, M. Ozerov).
2020- Co-supervisor of PhD student Jingyao Niu (Swedish University of Agricultural Sciences, main supervisor A. Gårdmark, co-supervisor M. Huss).
2019- Main supervisor of PhD student Alfonso Diaz Suarez (Estonian University of Life Sciences, co-supervisor V. Kisand).
2019- Main supervisor of PhD student Erik Karlsson (Swedish University of Agricultural Sciences, co-supervisor M. Ogonowski, G. Sundblad, J. Sundin).
Finished PhD thesis
2018-2024 Main supervisor of PhD student Magnus Lauringson (Estonian University of Life Sciences, co-supervisor P. Päkk).
2015-2023 Main supervisor of PhD student Freed Ahmad (University of Turku, co-supervisor P. Debes).
2013-2017 Co-supervisor of PhD student Tiia Forsström funded by University of Turku graduate school (main supervisor V. Jormalainen).
2010-2016 Main supervisor of PhD student Lilian Pukk (Co-supervisors R. Gross, T. Paaver, Estonian University of Life Sciences).
2009-2015 Co-supervisor (main supervisor J. Sorvari) of PhD student Salla-Riikka Vesterlund (University of Turku).
2006-2009 Co-supervisor of PhD student Akarapong Swaditpong (University of Turku, Finland). Main supervisor Prof. C. Primmer.
>108 peer-reviewed scientific articles, 3 book chapters. Check Researchgate & Google Scholar for more information.