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Anti Vasemägi

Anti Vasemägi
My research covers a broad spectrum of topics in evolutionary biology, genomics, population genetics and ecology focusing on understanding the drivers of genetic and phenotypic variation in aquatic organisms. Specifically, I am interested in understanding the relationships between genotype and phenotype and how contemporary natural selection works on ecological time-scales.

Research

My ongoing research projects fall into four areas:

1)    Population genomics –analysis of biodiversity, demography and footprints of selection

Related publications:

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, accepted.

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

Related publications:

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

Related publications:

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, early online.

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, in press.

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.

Ongoing projects:

Atlantic salmon fisheries and conservation in the context of growing threats and a changing environment

Genomics of Coinfection of Pathogens in Salmonid Fish

Related publications:

Ahmad F, (2021) Know your enemy - transcriptome of myxozoan Tetracapsuloides bryosalmonae reveals potential drug targets against proliferative kidney disease in salmonids. Parasitology, early online

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, early online.

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.

Supervision

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

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’.

Selected publications

>80 peer-reviewed scientific articles, 3 book chapters. Check Researchgate & Google Scholar for more information.

2021

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, accepted. 

Ahmad F, (2021) Know your enemy - transcriptome of myxozoan Tetracapsuloides bryosalmonae reveals potential drug targets against proliferative kidney disease in salmonids. Parasitology, 

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, accepted.

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.

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, early online.

2020

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, in press.

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, accepted.

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.

2019

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.

2018

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.

2017

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.

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, 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.

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 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.

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.

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: Genes, Genomes, Genetics, 7(2), 637-645.

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.

Wibowo A, Wahlberg N, Vasemägi A (2017) Barcoding of fish larvae reveals uncharacterized biodiversity in tropical peat swamps of Southern Papua, Indonesia. Marine and Freshwater Research, 68(6), 1079-1087.

2016

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.

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.

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.

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.

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.

Kahar S, Debes VP,  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, 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(4), 399-407 .

Li S-L, Vasemägi A, Ramula S (2016) Genetic variation facilitates seedling establishment but not population growth rate of a perennial invader. Annuals of Botany, 1, 187-194.

2015

Ozerov M, 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, 28(5), 1170-1183.

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.

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.

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.

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.

Links

 

 


Contact
Professor at the Institutionen för akvatiska resurser
Telephone: +46104784277
Postal address:
Sötvattenslaboratoriet, Stångholmsvägen 2
17893 DROTTNINGHOLM
Visiting address: Stångholmsvägen 2, Drottningholm