My ongoing research projects fall into four areas:
1) Population genomics –analysis of biodiversity, demography and footprints of selection
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, https://doi.org/10.3389/fmars.2022.1028863.
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.
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.
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.
Ozerov My, 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.
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.
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.
Vasemägi A, Sulku J, Bruneaux M, Thalmann O, Mäkinen H, Ozerov M (2017) Prediction of deleterious mitochondrial mutations in a euryhaline fish: test of demographic and habitat-dependent effects. Ecology and Evolution, 7, 3826–3835.
Ozerov MY, Gross R, Bruneaux M, Vähä J-P, Burimski O, Pukk L, Vasemägi A (2016) Genome-wide introgressive hybridization patterns in wild Atlantic salmon influenced by inadvertent gene flow from hatchery releases Molecular Ecology, 25(6), 1275-1293.
Pukk L, Ahmad F, Hasan S, Kisand V, Gross R, Vasemägi A (2015) Less is more: extreme genome complexity reduction with ddRAD using Ion Torrent semiconductor technology Molecular Ecology Resources, 15, 1145-1152.
Mäkinen H, Vasemägi A, McGinnity P, Cross T, Primmer C. (2015) Population genomic analysis of early phases of the Atlantic salmon (Salmo salar) domestication/captive breeding. Evolutionary Applications, 1, 93-107.
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.
Ongoing project: Developing environmental DNA (eDNA) approaches for fish monitoring
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.
Forsström T, Vasemägi A (2016) Can environmental DNA (eDNA) be used for detection and monitoring of introduced crab species in the Baltic Sea? Marine Pollution Bulletin, 109(1), 350-355.
3) Ecological genomics – linking genes and traits to populations, environment and ecosystems
Ongoing project: Molecular mechanisms of darkwater adaptation
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.
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.
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.
Debes PV, Visse M, Panda B, Ilmonen P, Vasemägi A (2016) Is telomere length a molecular marker for past thermal stress in wild fish? Molecular Ecology, 25(21), 5412-5424.
Vasemägi A, Kahar S, Ozerov MY (2016) Genes that affect Atlantic salmon growth in hatchery do not have the same effect in the wild. Functional Ecology, 30(10), 1687-1695.
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.
Atlantic salmon fisheries and conservation in the context of growing threats and a changing environment
Genomics of Coinfection of Pathogens in Salmonid Fish
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.
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.
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.
Vasemägi A, Visse M, Kisand V (2017) The effect of environmental factors and an emerging parasitic disease on gut microbiome of wild salmonid fish. mSpere, 2(6) e00418-17.
Stauffer J, Bruneaux M, Panda B, Visse M, Vasemägi A, Ilmonen P (2017) Telomere length and antioxidant defense associate with parasite-induced retarded growth in wild brown trout. Oecologia, 185(3), 365-374.
Vasemägi A, Nousiainen I, Saura A, Vähä J-P, Valjus J, Huusko A (2017) First record of proliferative kidney disease agent Tetracapsuloides bryosalmonae in wild brown trout and European grayling in Finland. Diseases of Aquatic Organisms, 125(1), 73-78.
Debes PV, Gross R, Vasemägi A (2017) Quantitative genetic variation in, and environmental effects on, pathogen resistance and temperature-dependent disease severity in a wild trout. American Naturalist, 190(2), 244-265.
Bruneaux M, Visse M. Pukk L, Gross R, Saks L, Vasemägi A (2017) Parasite infection and decreased thermal tolerance: impact of proliferative kidney disease (PKD) on a wild salmonid fish in the context of climate change. Functional Ecology, 31, 216-226.
M. E. López (2019-2022)
K. Noreikiene (2018-2020)
P. Debes (2014-2016)
M. Ozerov (2013-2018)
A. Wibowo (2014)
D. Philippenko (2013-2014)
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).
2018- Main supervisor of PhD student Magnus Lauringson (Estonian University of Life Sciences, co-supervisor P. Päkk).
2015- Main supervisor of PhD student Freed Ahmad (University of Turku, co-supervisor P. Debes).
Finished PhD thesis
2013-2017 Co-supervisor of PhD student Tiia Forsström funded by University of Turku graduate school (main supervisor V. Jormalainen). PhD thesis ‘Introduced marine crab species in the northern Baltic Sea: from detection to impacts‘`.
2010-2016 Main supervisor of PhD student Lilian Pukk (Co-supervisors R. Gross, T. Paaver, Estonian University of Life Sciences). PhD thesis ‘Analysis of molecular genetic and life-history traits in Eurasian perch (Perca fluviatilis L.)’.
2009-2015 Co-supervisor (main supervisor J. Sorvari) of PhD student Salla-Riikka Vesterlund (University of Turku) funded by Maj ja Tor Nessling Foundation. PhD thesis ‘Bumblebees in a Changing Climate: Evaluating the Effects of Temperature on Queen Performance’.
2006-2009 Co-supervisor of PhD student Akarapong Swaditpong (University of Turku, Finland). Main supervisor Prof. C. Primmer. PhD thesis ‘Conservation genetics of exploited Finnish Salmonid fishes’.
>93 peer-reviewed scientific articles, 3 book chapters. Check Researchgate & Google Scholar for more information.