Anti Vasemägi (PhD, docent)

Present address:
Dept. of Biology
Natura-building, office 121
20014 University of Turku

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Curriculum Vitae

Publications & data

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Refereed journals


Relationships among the gut microbiome, PKD status and measured environmental variables (Vasemägi et al. 2017mSphere).

Circos plot showing the strong synteny between X. tropicalis and R. temporaria (Palomar et al. 2017).

Normal and swollen kidney of brown trout suffering proliferative kidney disease (PKD) Bruneaux et al. (2017).

Box plots showing significant marker-trait associations for fork length in wild (white boxes) and hatchery (grey boxes) environment. Solid and dashed lines represent significant and non-significant marker-trait associations, respectively (Vasemägi et al. 2016 FE)

Relationship between observed and simulated neutral Fst distribution and divergence on gill-raker number (Pst) in European whitefish (Ozerov et al. 2015 JEB).

Relationship between juvenile density and effective number of breeders in brown trout (Ozerov et al. 2015 ConsBiol).

Distribution and prevalence of PKD agent in Estonian brown trout populations (Dash & Vasemägi 2014).

Temporal change in genetic structure of perch (Pukk et al. 2013).

Non-random distribution of SNPs across the genome of nine-spined stickleback (Bruneaux et al. 2012)

LD patters along MHCI region in brown trout (Dash & Vasemägi 2012, MER).

Got milk? Read why high lactose tolerance in North Europeans cannot be explained by selection from in-situ milk consumption (Vuorisalo et al. 2012).

Protein-protein interaction model in the brackishwater whitefish (Papakostas et al. 2012).

Live G. salaris on Atlantic salmon. Click to the video or here to enlarge (Ozerov et al. 2010).

Studied salmon populations and temperature gradient in Northern Europe (Tonteri et al. 2010).

Population prioritization of wild Finnish grayling populations along the genetic diversity and differentiation axes (Frontiers in Zoology, 6:6).

The relationship between isolation by distance (IBD) and the proportion of loci exhibiting clinal variation (Genetics, 173).


Electroporegram of the developed EST-microsatellite. Click appendix of Mol.Ecol.Notes 5, to view the rest of the loci.


Fin-damaged Atlantic salmon strayer of hatchery origin caught from the R. Umeälven, Sweden. Click supplementary appendix of Heredity 95, to see more photos.


First book to review genetic data on Atlantic salmon. International team of contributing authors. Blackwells, Oxford.

Present and potential production of salmon in Estonian rivers. Estonian Academy publishers,Tallinn.

  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, accepted.
  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.
  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), doi: 10.1128/mSphere.00418-17.2(6).
  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, in press.
  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.
  Forsström T, Ahmad F, Vasemägi A (2017) Invasion genomics: genotyping-by-sequencing approach reveals regional genetic structure and signatures of temporal selection in an introduced mud crab. Marine Biology, 164, 186.
  Niinemets Ü, Kahru A, Mander Ü, Nõges P, Nõges T, Tuvikene A, Vasemägi A (2017) Interacting environmental and chemical pollutant stresses under global change in aquatic ecosystems: stress responses, adaptation and scaling. Regional Environmental Change, 7, 2061-2077.
  Niinemets Ü, Kahru A, Nõges P, Tuvikene A, Vasemägi A, Mander Ü, Nõges T (2017) Environmental feedbacks in aqueousaquatic ecosystems under global change: why do we need to consider also chemical stressors? Regional Environmental Change, 7, 2079-2096.
  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.
  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.

c Supplementary appendix

a Ozerov M, Vähä JP, Wennevik V, Niemelä E, Svenning MA, Prusov S, Fernandez RD, Unneland L, Vasemägi A, Falkegård M, Kalske T, Christiansen B (2017) Comprehensive microsatellite baseline for genetic stock identification of Atlantic salmon (Salmo salar L.) in northernmost Europe. ICES Journal of Marine Science, 8, 2159-2169.
a Hägerstrand H, Himberg M, Jokikokko E, von Numers M, Mrówczyńska L, Vasemägi A, Wiklund T, Lill J-O (2017) Otolith elemental characteristics of whitefish (Coregonus lavaretus) from brackish waters of the Gulf of Bothnia, Baltic Sea. Ecology of Freshwater Fish, 26, 66–74.
  Palomar G, Ahmad F, Vasemägi A, Matsuba C, Nicieza AG, Cano JM (2017) Comparative high-density linkage mapping reveals conserved genome structure but variation in levels of heterochiasmy and location of recombination cold spots in the common frog G3, 7(2), 637–645.
c 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.
  Wibowo A, Wahlberg N, Vasemägi A (2017) Barcoding of fish larvae reveals uncharacterised biodiversity in tropical peat swamps of Southern Papua, Indonesia. Marine and Freshwater Research, early online.
  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.
  Ozerov MY, Himberg M, Debes PV, Hägerstrand H, Vasemägi A (2016) Combining genetic markers with an adaptive meristic trait improves performance of mixed-stock analysis in Baltic whitefish. ICES Journal of Marine Science, 73 (10), 2529-2538.
a Pukk L, Gross R, Vetemaa M, Vasemägi A (2016) Genetic discrimination of brackish and freshwater populations of Eurasian perch (Perca fluviatilis L.) in the Baltic Sea drainage: implications for fish forensics. Fisheries Research, 183, 155–164.
c 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.
a Li S-L, Vasemägi A, Ramula S. Genetic variation facilitates seedling establishment but not population growth rate of a perennial invader (2016). Annuals of Botany, 117, 1, 187-194.
c 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, 1687–1695.
a 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.
a Kahar S, Debes PV, Vuori KAM, Vähä J-P, Vasemägi A (2016) Heritability, environmental effects, and genetic and phenotypic correlations of oxidative stress-resistance-related enzyme activities during early-life stages in Atlantic salmon. Evolutionary Biology, 1-12.
  Li S-L, Vasemägi A, Ramula S (2016) Genetic variation and population structure of the garden escaper Lupinus polyphyllus in Finland. Plant Systematics and Evolution, 302, 399.
a Himberg M, von Numers M, Vasemägi A, Heselius S-J, Wiklund T, Lill J-O, Hägerstrand H (2015) Gill raker counting for approximating the ratio of river and sea-spawning whitefish (Coregonus lavaretus L.) in the Gulf of Bothnia (Baltic Sea). Acta Ichthyologica et Piscatoria, 45 (2), 125–131.
Ozerov MYu, Himberg M, Aykanat T, Sendek DS, Hägerstrand H, Verliin A, Krause T, Olsson J , Primmer CR & Vasemägi A (2015) 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. Journal of Evolutionary Biology, 5, 1170–1183.

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.


Ozerov M, Jürgenstein T, Aykanat T, Vasemägi A (2015) Use of sibling relationship reconstruction to complement traditional monitoring in fisheries management and conservation of brown trout. Conservation Biology, 29(4), 1164-1175.


a Hartikainen H, Filippenko D, Okamura B, Vasemägi A (2015) First microsatellite loci of the myxozoan parasite Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease (PKD). Diseases of Aquatic Organisms, 113, 85-88.
a Mäkinen H, Vasemägi A, McGinnity P, Cross T, Primmer C. Population genomic analysis of early phases of the Atlantic salmon (Salmo salar) domestication/captive breeding (2015) Evolutionary Applications, 1, 93–107.
c Bruneaux M, Nikinmaa M, Laine VN, Lindström K, Primmer CR, Vasemägi A (2014) Differences in the metabolic response to temperature acclimation in nine-spined stickleback (Pungitius pungitius) populations from contrasting thermal environments. Journal of Experimental Zoology Part A, 10, 550–565.
c Dash M, Vasemägi A (2014) Characterization of the proliferative kidney disease (PKD) agent Tetracapsuloides bryosalmonae in brown trout populations in Estonia. Diseases of Aquatic Organisms, 109 139–148.
Pukk L, Kisand V, Ahmad F, Gross R, Vasemägi A. Double-restriction-site-associated DNA (dRAD) approach for fast microsatellite marker development in Eurasian perch (Perca fluviatilis L.) (2014) Conservation Genetics Resources, 6, 183–184.
Vesterlund S-R, Kakko M, Vasemägi A, Sorvari J (2014) The buff-tailed bumblebee Bombus terrestris in Southern Finland: status and monitoring. Entomologica Fennica 25, 49–57.
Papakostas S, Vasemägi A, Himberg M, Primmer CR (2014) Proteome variance differences within populations of European whitefish (Coregonus lavaretus) originating from contrasting salinity environments. Journal of Proteomics, 105, 144-150.
Filippenko D, Hartikainen H, Okamura B, Vasemägi A (2014) Characterisation of polymorphic microsatellite loci for the bryozoan Fredericella sultana, the primary host of the causative agent of salmonid proliferative kidney disease. Conservation Genetics Resources, 2, 481-482.
Vesterlund S-R, Sorvari J, Vasemägi A. Molecular identification of cryptic bumblebee species from degraded samples using PCR-RFLP approach (2014) Molecular Ecology Resources, 14, 122-126.
Ozerov M, Vasemägi A, Wennevik V, Diaz-Fernandez R, Kent M, Gilbey J, Prusov S, Niemelä E, Vähä J-P (2013) Finding markers that make a difference: DNA pooling and SNP-arrays identify population informative markers for genetic stock identification. PLOS One, 8(12), DOI: 10.1371/journal.pone.0082434.
Wennerström L, Laikre L, Ryman N, Utter FM, Ab Ghani NI, André C, DeFaveri J, Johansson D, Kautsky L, Merilä J, Mikhailova N, Pereyra R, Sandström A, Teacher AGF, Wenne R, Vasemägi A, Zbawicka M, Johannesson K, Primmer CR (2013) Genetic biodiversity in the Baltic Sea: species-specific patterns challenge management. Biodiversity and Conservation, 22, 3045-3065.
Johnston SE, Lindqvist M, Niemelä E, Orell P, Erkinaro J, Kent MP, Lien S, Vähä J-P, Vasemägi A, Primmer CR (2013) Fish scales and SNP chips: SNP genotyping and allele frequency estimation in individual and pooled DNA from historical samples of Atlantic salmon (Salmo salar). BMC Genomics, 14, 439.
Swatdipong A, Vasemägi A, Niva T, Koljonen M-L, Primmer CR. Genetic mixed-stock analysis of lake-run brown trout fisheries catch in the Inari basin, northern Finland: implications for conservation and management (2013) Journal of Fish Biology, 83, 598-617.

Shou-Li L, Vasemägi A, Matos-Maraví P, Ramula S (2013) Development and testing of microsatellite loci for the invasive herb Lupinus polyphyllus through 454 pyrosequencing. Molecular Ecology Resources, 13, 4, 760–762.

Molecular Ecology Resources Primer Development Consortium* Permanent Genetic Resources added to Molecular Ecology Resources Database 1 February 2013–31 March 2013. Molecular Ecology Resources, 13: 760–762. doi: 10.1111/1755-0998.12121

Pukk P, Kuparinen A, Järv L, Gross R, Vasemägi V (2013) Genetic and life-history changes associated with fisheries-induced population collapse. Evolutionary Applications, 1-12, DOI: 10.1111/eva.12060.

Bourret V, Kent MP, Primmer CR, Vasemägi A, Karlsson S, Hindar K, McGinnity P, Verspoor E, Bernatchez L, Lien S (2013) SNP-array reveals genome wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar). Molecular Ecology, 22, 532-551.

Bruneaux M, Johnston SE, Herczeg G, Merilä J, Primmer CR, Vasemägi A (2013) Molecular evolutionary and population genetic analysis of ninespine stickleback using a modified RAD tag approach. Molecular Ecology, 22, 565-582.
Ozerov MY, Vasemägi A, Wennevik V, Niemelä E, Prusov SV, Kent M-P and Vähä J-P (2013) Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.) BMC Genomics, 14(1):12.

Vasemägi A, Nilsson J, McGinnity P, Cross T, O’Reilly P, Glebe B, Peng B, Berg PR, Primmer CR (2012) Screen for footprints of selection during domestication/captive breeding of Atlantic salmon. Comparative and Functional Genomics, doi:10.1155/2012/628204.


Dash M, Vasemägi A (2012) Development of highly polymorphic major histocompatibility-associated microsatellite markers in Atlantic salmon (Salmo salar) and brown trout (Salmo trutta). Molecular Ecology Resources, 12, 779-781.

Molecular Ecology Resources Primer Development Consortium* Permanent Genetic Resources added to Molecular Ecology Resources Database 1 February 2012 – 31 March 2012. Molecular Ecology Resources, 12: 779–781. doi: 10.1111/j.1755-0998.2012.03155.



Vuorisalo T, Arjamaa O, Vasemägi A, Taavitsainen J_P, Tourunen A, Saloniemi I (2012) Historical evidence suggests that high lactose tolerance in North Europeans cannot be explained by selection from in-situ milk consumption. Perspectives in Biology and Medicine, 55, 163-174.

See also commentary-article in ‘Humanities in the Societal Challenges: 12 compelling cases for policymakers’.


Papakostas S, Vasemägi A, Vähä J-P, Himberg M, Peil L, Primmer C (2012) A proteomics approach reveals divergent molecular responses to salinity in populations of European whitefish (Coregonus lavaretus). Molecular Ecology, 21, 3516-3530.

See also commentary-article by Dalziel & Schulte (2012) Ecological proteomics: Finding molecular markers that matter, Molecular Ecology , 21, 3382–3384.

Swatdipong A, Vasemägi A, Niva T, Koljonen M-L, Primmer CR (2010) High level of population genetic structuring in lake-run brown trout, Salmo trutta, of the Inari basin, northern Finland. Journal of Fish Biology 9, 2048-2071.
Ozerov MY, Lumme J, Päkk P, Rintamäki P, Ziętara MS, Barskaya Y, Lebedeva D, Saadre E, Gross R, Primmer CR, Vasemägi A (2010) High Gyrodactylus salaris infection rate in triploid Atlantic salmon Salmo salar. Diseases of Aquatic Organisms, 91, 129-136.
Vasemägi A, Gross R, Palm D, Paaver T & Primmer CR (2010). Discovery and application of insertion-deletion (INDEL) polymorphisms for QTL mapping of early life-history traits in Atlantic salmon. BMC Genomics 11, 156.

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Tonteri A, Vasemägi A, Lumme J & Primmer CR (2010). Beyond MHC: signals of elevated selection pressure in Atlantic salmon (Salmo salar) immune relevant loci. Molecular Ecology 7, 1273-1282.

Swatdipong A, Primmer CR, Vasemägi A (2010) Historical and recent genetic bottlenecks in European grayling, Thymallus thymallus. Conservation Genetics 11, 279–292.
Vasemägi A (2009) Eel mystery: time makes a difference. Heredity, 103, 3–4.
Swatdipong A, Vasemägi A, Koskinen MT, Piironen P and Primmer CR (2009) Unanticipated population structure of European grayling in its northern distribution: implications for conservation prioritization. Frontiers in Zoology, 6:6.

Tonteri A, Vasemägi A, LummeJ, Primmer CR (2008) Use of differential expression data for identification of novel immune relevant expressed sequence tag-linked microsatellite markers in Atlantic salmon (Salmo salar L.) Molecular Ecology Resources 6, 1486-1490.

Ryynänen H, Tonteri A, Vasemägi A, Primmer CR (2007) A comparison of the efficiency of single nucleotide polymorphisms (SNPs) and microsatellites for the estimation of population and conservation genetic parameters in north European Atlantic salmon (Salmo salar) populations. Journal of Heredity 98, 692-704.


Vasemägi A (2006) The adaptive hypothesis of clinal variation revisited: single-locus clines as a result of spatially restricted geneflow. Genetics 173, 2411-2414.

Vasemägi A and Primmer CR (2005) Challenges for identifying functional genetic variation: the promise of combining complementary research strategies. Molecular Ecology 14, 3623-3642.
Vasemägi A, Nilsson J, Primmer CR (2005) Expressed sequence tag (EST) linked microsatellites as a source of gene associated polymorphisms for detecting signatures of divergent selection in Atlantic salmon (Salmo salar L.). Molecular Biology and Evolution 22, 1067-1076.


Vasemägi A, Nilsson J and Primmer CR (2005) Seventy five EST-linked Atlantic salmon (Salmo salar L.) microsatellite markers and their cross-species amplification in salmonids. Molecular Ecology Notes 5, 282-288.



























Supplementary appendix with primer sequences and electropherograms
Supplementary appendix with cross-species amplification information unctionally important
Vasemägi A, Gross R, Paaver T, Koljonen ML, Säisä M, Nilsson J (2005) Analysis of gene associated tandem repeat markers in Atlantic salmon (Salmo salar L.) populations: implications for restoration and conservation in the Baltic Sea. Conservation Genetics 6, 385-397.
Säisä M, Koljonen ML, Gross R, Nilsson J, Tahtinen J, Koskiniemi J, Vasemägi A (2005) Population genetic structure and postglacial colonization of Atlantic salmon (Salmo salar) in the Baltic Sea area based on microsatellite DNA variation. Canadian Journal of Fisheries and Aquatic Sciences 62, 1887-1904.
Vasemägi A, Gross R, Paaver T, Koljonen ML, Nilsson J (2005) Extensive immigration from compensatory hatchery releases into wild Atlantic salmon population in the Baltic sea: spatio-temporal analysis over 18 years. Heredity 95, 76-83.
Supplementary appendix
Vasemägi A, Gross R, Paaver T, Kangur M, Nilsson J, Eriksson L-O (2001) Identification of the origin of Atlantic salmon (Salmo salar L.) population in a recently recolonized river in the Baltic Sea. Molecular Ecology 10, 2877-2882.
Nilsson J, Gross R, Dove O, Jansson H, Kohlmann K, Löytynoja A, Nielsen EE, Paaver T, Penttilä H, Primmer CR, Vasemägi A, Veselov A, Öst T, Lumme J. (2001) Matrilinear phylogeography of Atlantic salmon (Salmo salar L.) in Europe and postglacial colonization of the Baltic Sea area. Molecular Ecology 10, 89-102.


Book chapters & non-refereed publications

Vasemägi A (2014) Ühest ohtlikust lõhilaste parasiithaigusest Eestis. Eesti Loodus, in press.
Pukk L, Vasemägi A (2013) Miks kalad muutuvad väiksemaks? Kalastaja, 68.

Vuorisalo T, Arjamaa O, Vasemägi A, Taavitsainen J_P, Tourunen A, Saloniemi I (2012) Suomalaisten laktoosinsiedon alkuperä. DUODeCIM, 128, 1321-1322.

Vasemägi A (2011) Fishing for genes that matter in wild. (Kummipükstes geene püüdmas – lõhe molekulaar-ökoloogilistest uuringutest Eestis). Estonian Science Foundation yearbook.
ICES WGAGFM Report (2008) Report of the Working Group on the Application of Genetics in Fisheries and Mariculture (WGAGFM). Dahle G, Johansen T, Vasemägi A, Carvalho G, Florin A-B, Was A, Prödohl P, Khrustaleva AM. Review the potential for application of SNP´s (single nucleotide polymorphisms) in fisheries genetics and aquaculture. Pitlochry, UK.
ICES WGAGFM Report (2008) Report of the Working Group on the Application of Genetics in Fisheries and Mariculture (WGAGFM). Boudry P, Gilbey J, Vasemägi A , Lallias D & Gosling E. Review current and future prospects of QTL based studies in fisheries and aquaculture. Pitlochry, UK.
Cross TF, McGinnity P, Coughlan J, Dillane E, Ferguson A, Koljonen M-L, O’Reilly P, Vasemägi A, Wilkins NP (2006) Genetic considerations for Stocking and Ranching of Atlantic salmon. In The Atlantic Salmon: Genetics, Conservation and Management, (eds.) Verspoor, E., L. Stradmeyer and J. Nielsen. Blackwells, Oxford.

Paaver T, Gross R,Vasemägi A (2001) Genetic characterization of Estonian salmon populations. In Present and potential production of salmon in Estonian rivers (eds. M. Kangur, B. Wahlberg) pp.77-84. Estonian Academy publishers, Tallinn.

Paaver T, Tohvert T, Gross R,Vasemägi A (1998) Changes of quality indices of common carp during overwintering in a storage basin. Estonian Agricultural University Proceedings, Tartu, 69, 65-71. Reports
Aho T, et al. incl.Vasemägi A (2004) Genetic Diversity in Commercially Exploited Fish Species. Nordic Council of Ministers Report, Iceland. 17 pp.



Page updated January 12, 2018