Researchers at UCD


Jens Carlsson

School of Biology & Environmental Science

Tel: +353-(0)1 716-2197


Employment History:
2012 - Now Lecturer, School of Biology and Environmental Science, University College Dublin, Ireland.
2015 - Now Adjunct Associate Professor, Duke University Marine Laboratory, Beaufort, North Carolina, USA.
2009 - 2015
Adjunct Assistant Professor, Duke University Marine Laboratory, Beaufort, North Carolina, USA.
2009 -  2012 Senior Researcher, School of Biological, Earth and Environmental Sciences, University College Cork, Ireland.
2007 - 2009 Visiting Assistant Professor, Duke University Marine Laboratory, Beaufort, North Carolina, USA.
2004 - 2007 Assistant Research Scientist, Virginia Institute of Marine Science, College of William and Mary, Gloucester Point, Virginia, USA.
2002 - 2004 Post-Doctoral Research Associate, Virginia Institute of Marine Science, College of William and Mary, Gloucester Point, Virginia, USA.
2001 - 2002 Marie Curie Post-Doctoral Fellow, Danish Institute for Fisheries Research, Department of Inland Fisheries, Silkeborg, Denmark.
2000 - 2001 Scientist, Department of Aquaculture, Swedish University of Agricultural Sciences

-PhD in Population Genetics, Swedish University of Agricultural Sciences, Sweden 2000.
-MSc in Biology, Swedish University of Agricultural Sciences, Sweden 1996.
-BSc in Biology, Swedish University of Agricultural Sciences, Sweden 1995.
-University Diploma in Fisheries Science, University of Gothenburg, Sweden 1994.

Link to lab web page: Area 52




Year 2000 Institution:
Qualification: PhD Subject: PhD in Population Genetics, Swedish University of Agricultural Sciences
Year 1996 Institution:
Qualification: MSc Subject: MSc in Biology, Swedish University of Agricultural Sciences
Year 1994 Institution: Goteborg University, Sweden
Qualification: Other Subject: University Diploma in Fisheries Science
Year 2005 Institution:
Qualification: BSc Subject: BSc in Biology, Swedish University of Agricultural Sciences



Sleeman DP, Carlsson J & Carlsson, JEL (2014) Mind the Gap II: new insights into the Irish postglacial. Belfast: Irish Naturalists' Journal. [Details]

Book Chapters

Sleeman DP and Carlsson J (2014) 'Introduction' In: Sleeman DP, Carlsson J & Carlsson, JEL (eds). Mind the Gap II: new insights into the Irish postglacial. Belfast: Irish Naturalists' Journal. [Details]
Carlsson J, Cross TF, McGinnity P, Prodöhl P, McDevitt A. (2014) 'The use of genetics to infer the origins of the terrestrial and freshwater elements of the Irish fauna' In: Sleeman DP, Carlsson J & Carlsson, JEL (eds). Mind the Gap II: new insights into the Irish postglacial. Belfast: Irish Naturalists' Journal. [Details]
Nordwall F & Carlsson J. (1999) 'Fiskar kan vandra, men varför och vart vandrar de?' In: Nordwall F & Carlsson J (eds). Fiske, skogsbruk och vattendrag, nyttjande i ett uthålligt perspektiv, Ammeråprojektet. Kälarne: Fiskeriverkets försökstation. [Details]
Carlsson J & Nilsson J. (1999) 'Genetisk variation hos öringpopulationer vem är släkt med vem?' In: Carlsson J & Nilsson J (eds). Fiske, skogsbruk och vattendrag, nyttjande i ett uthålligt perspektiv, Ammeråprojektet. Kälarne: Fiskeriverkets försökstation. [Details]

Peer Reviewed Journals

Boschen RE, Collins PCC, Tunnicliffe V, Carlsson J, Gardner JPA, Lowe J, McCrone A, Metaxas A, Sinniger F, Swaddling A (2016) 'A primer for use of genetic tools in selecting and testing the suitability of set-aside sites protected from deep-sea seafloor massive sulfide mining activities'. Ocean and Coastal Management, 122 :37-48. [DOI] [Details]
Collins PC, Carlsson J, Rowcroft P, Tibbles B (2016) 'Ecosystem status of the deep Black Sea, soft sediment, benthic community'. Marine Policy, 73 :216-223. [DOI] [Details]
Ferreira DG, Souza-Shibatta L, Shibatta, OA, Sofia SH, Carlsson J, Dias JHP, Makrakis S, Makrakis MC (2016) 'Genetic structure and diversity of migratory freshwater fish in a fragmented Neotropical river system'. Reviews in Fish Biology and Fisheries, 2 :1-23. [DOI] [Details]
Vartia, S; Villanueva-Cañas, JL; Finarelli, JA; Farrell, ED; Collins, PC; Hughes, GM; Carlsson, JEL; Gauthier, DT; McGinnity, P; Cross, TF; FitzGerald, RD; Mirimin, L; Crispie, F; Cotter, PD; Carlsson, J (2016) 'A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding'. Royal Society Open Science, 3 :150565. [DOI] [Details]
Vera M, Bello X, Alvarez-Dios J-A, Pardo BG, Sanchez L, Carlsson J, Carlsson JE, Bartolome C, Maside X & Martinez P (2015) 'Screening of repetitive motifs inside the genome of the flat oyster (Ostrea edulis): Transposable elements and short tandem repeats'. Marine Genomics, 3 :335-341. [DOI] [Details]
Galindo, B. A. and Ferreira, D. G. and Almeida, F. S. and Carlsson, J. and Sofia, S. H. (2015) 'Isolation and characterization of 13 polymorphic microsatellite loci in Hypostomus ancistroides (Teleostei, Loricariidae) and cross-amplification in related species'. JOURNAL OF FISH BIOLOGY, 86 (6):1860-1866. [DOI] [Details]
Gustavson MS, Collins PC, Finarelli JA, Egan D, Conchúir RÓ, Wightman GD, King JJ, Gauthier DT, Whelan K, Carlsson JEL & Carlsson J (2015) 'An eDNA assay for Irish Petromyzon marinus and Salmo trutta and field validation in running water'. Journal of Fish Biology, 87 :1254-1256. [DOI] [Details]
Nadolny R, Gaff H, Carlsson, J & Gauthier D (2015) 'omparative population genetics of two invading ticks: Evidence of the ecological mechanisms underlying tick range expansions'. Infection Genetics And Evolution, 35 :153-162. [Details]
Flannery G, Lynch SA, Carlsson J, Cross TF & Culloty SC (2014) 'Assessment of the impact of a pathogen, Bonamia ostreae, on Ostrea edulis oyster stocks with different histories of exposure to the parasite in Ireland'. Aquaculture, 432 :243-251. [Details]
Lynch SA, Morgan E, Carlsson J, Mackenzie C, Wooton E, Rowley A, Malham S & Culloty SC (2014) 'The health status of mussels, Mytilus spp., in Ireland and Wales with the molecular identification of a previously undescribed haplosporidian'. Journal Of Invertebrate Pathology, . [DOI] [Details]
O'Malley KG, Cross TF, Ballie D, Carlsson J, Coughlan JP, Dillane E, Prodöhl PA, McGinnity P (2014) 'Circadian clock gene (OtsClock1b) variation and time of ocean return in Atlantic salmon Salmo salar'. Fisheries Management and Ecology, 1 :82-87. [DOI] [Details]
Thaler AD, Plouviez S, Saleu W, Alei F, Jacobson A, Boyle EA, Schultz TF, Carlsson J, Van Dover CL (2014) 'Comparative population structure of two deep-sea hydrothermal-vent-associated decapods (Chorocaris sp. 2 and Munidopsis lauensis) from southwestern Pacific back-arc basins'. PLoS ONE, 9 e101345 . [DOI] [Details]
Vartia S, Collins PC, Cross TF, FitzGerald RD, Gauthier DT, McGinnity P, Mirimin L & Carlsson J (2014) 'Multiplexing with three-primer PCR for rapid and economical microsatellite validation'. Hereditas, . [Details]
Carlsson J, Gauthier D, Carlsson JEL, Coughlan JP, Dillane E, FitzGerald RD, Keating FU, McGinnity P, Mirimin L & Cross TF (2013) 'Rapid, economical SNP and microsatellite discovery based on de novo assembly of a reduced representation genome in a non-model organism: a case study of Atlantic cod Gadus morhua'. Journal of Fish Biology, 82 :944-958. [Details]
Collins PC, Croot P, Carlsson J, Colaço A, Grehan A, Hyeong K, Kennedy R, Mohn C, Smith S, Yamamoto H, Rowden A. (2013) 'A primer for the Environmental Impact Assessment of mining at seafloor massive sulfide deposits'. Marine Policy, 42 :198-209. [Details]
Collins PC, Kennedy R, Copley J, Boschen R, Forde J, Flemming N, Ju SJ, Lindsay D, Marsh L, Nye V, Patterson A, Watanabe H, Yamamoto H, Carlsson J, Thaler AD (2013) 'Ventbase: Developing a consensus among stakeholders in the deep-sea regarding environmental impact assessment for deep-sea mining'. Marine Policy, 42 :334-336. [Details]
Gauthier DT, Audemard CA., Carlsson, JEL, Darden TL, Denson M, Reece KS & Carlsson, J (2013) 'Genetic population structure of U.S. Atlantic coastal striped bass (Morone saxatilis)'. Heredity, 104 :510-520. [Details]
Lynch SA, Dillane E, Carlsson J & Culloty SC (2013) 'Development and assessment of a sensitive and cost effective cPCR to detect ostreid herpes virus 1 (OsHV-1) and variants'. Journal of Shellfish Research, 32 :657-664. [Details]
Wheeler AJ, Murton B, Copley J, Lim A, Carlsson J, Collins P, Dorschel B, Green D, Judge M, Nye V, Benzie J, Antoniacomi A, Coughlan M, Morris K (2013) 'Moytirra: Discovery of the first known deep-sea hydrothermal vent field on the slow-spreading Mid-Atlantic Ridge north of the Azores'. Geochemistry, Geophysics, Geosystems (G-cubed), 14 :4170-4184. [DOI] [Details]
Kochmann, J., Carlsson, J., Crowe, T. P. & Mariani, S. (2012) 'Genetic evidence for the uncoupling of local aquaculture activities and a population of an invasive species: a case study of Pacific oysters (Crassostrea gigas)'. Heredity, 103 :661-671. [Details]
Lynch, S.A., Carlsson, J., Reilly, A.O., Cotter, E. and Culloty, S.C. (2012) 'A previously undescribed ostreid herpes virus 1 (OsHV-1) genotype detected in the pacific oyster, Crassostrea gigas, in Ireland'. Parasitology, 139 (12):1526-1523. Available Online [DOI] [Details]
O'Farrell, B., Dennis, C., Benzie, J., McGinnity, P., Carlsson, J., de Eyto, E., Coughlan, J., Igoe, F., Meehan, R. and Cross, T. (2012) 'Balancing selection on MHC class I in wild brown trout (Salmo trutta)'. Journal of Fish Biology, 81 (4):1357-1374. [DOI] [Details]
Finn, J., Carlsson, J., Kelly, T. and Davenport, J. (2012) 'Avoidance of headwinds or exploitation of ground effect - why do birds fly low?'. Journal of Field Ornithology, 83 (2):192-202. Available Online [DOI] [Details]
O'Farrell, B., Benzie, J., McGinnity, P., Carlsson, J., de Eyto, E., Dillane, E., Graham, C., Coughlan, J. and Cross, T. (2012) 'MHC-mediated spatial distribution in brown trout (Salmo trutta) fry'. Heredity, 108:403-409 . Available Online [DOI] [Details]
O'Meara, D.B., Edwards, C.J., Sleeman, D.P., Cross, T.F., Statham, M.J., McDowell, J.R., Dillane, E., Coughlan, J.P., O'Leary, D., O'Reilly, C., Bradley, D.G. and Carlsson, J. (2012) 'Genetic relationships between Eurasian badgers Meles meles (Carnivora: Mustelidae) in Europe and implications for the colonisation history of Ireland'. Biological Journal of the Linnean Society, 106 (4):893-909. Available Online [DOI] [Details]
Carlsson J, Shephard S, Coughlan J, Trueman CN, Rogan E & Cross TF. (2011) 'Fine-scale population structure in a deep-sea teleost (Orange roughy, Hoplostethus atlanticus)'. Deep Sea Research Part I: Oceanographic Research Papers, 58 :627-636. [Details]
Schultz TF, Hsing P-Y, Eng A, Zelnio KA, Thaler AD, Carlsson J & Van Dover CL. (2011) 'Characterization of 18 polymorphic microsatellite loci from Bathymodiolus manusensis (Bivalvia, Mytilidae) from deep-sea hydrothermal vents'. Conservation Genetics Resources, 3 (1):25-27. [DOI] [Details]
Thaler AD, Zelnio K, Saleu W, Schultz TF, Carlsson J, Cunningham C, Vrijenhoek R & Van Dover CL (2011) 'The effects of spatial scale on the population dynamics of Ifremeria nautilei, a hydrothermal vent endemic gastropod from the southwest Pacific'. BMC Evolutionary Biology, 11 :372. [Details]
Thaler AD, Zelnio K, Jones R, Carlsson J, Van Dover C &, Schultz TF (2010) 'Characterization of 12 polymorphic microsatellite loci in Ifremeria nautilei, a chemoautotrophic gastropod from deep-sea hydrothermal vents'. Conservation Genetics Resources, 2 :222-226. [Details]
Zelnio KA, Thaler AD, Jones Re, Saleu W, Schultz TH, Van Dover CL & Carlsson J (2010) 'Characterization of nine polymorphic microsatellite loci in Chorocaris sp. (Crustacea, Caridea, Alvinocarididae) from deep-sea hydrothermal vents'. Conservation Genetics Resources, 2 :222-226. [Details]
Sagarin R, Carlsson J, Duval M, Freshwater W, Godfrey M, Litaker W, Munoz R, Noble R, Schultz T & Wynne B (2009) 'Bringing molecular tools into environmental resource management: Untangling the molecules to policy pathway'. Plos Biology, 7 :426-430. [Details]
Carlsson J (2008) 'Effects of microsatellite null alleles on assignment testing'. Heredity, 99 :616-623. [Details]
Carlsson J, Carnegie RB, Cordes JF, Hare MP, Leggett AT & Reece KS (2008) 'Evaluating recruitment contribution of a selectively bred Crassostrea virginica oyster aquaculture line used in restoration efforts'. Journal of Shellfish Research, 27 :1117-1124. [Details]
Carlsson J (2007) 'The effect of family structure on the likelihood for kin-biased distribution: an empirical study of brown trout populations'. Journal of Fish Biology, 71 :98-110. [Details]
Carlsson J & Reece KS (2007) 'Eight PCR primers to amplify EST-linked microsatellites in the Eastern oyster, Crassostrea virginica genome'. Molecular Ecology Notes, 7 :257-259. [Details]
Carlsson J, McDowell JR, Carlsson JEL & Graves JE (2007) 'Genetic identity of YOY bluefin tuna from the eastern and western Atlantic spawning areas'. Heredity, 98 :23-28. [Details]
Carlsson J, Morrison CL & Reece KS (2006) 'Wild and aquaculture populations of the eastern oyster compared using microsatellites'. Heredity, 97 :595-598. [Details]
Carlsson J, McDowell JR, Carlsson JEL, Ólafsdóttir D & Graves JE (2006) 'Genetic heterogeneity of Atlantic bluefin tuna caught in the eastern North Atlantic Ocean south of Iceland'. Ices Journal of Marine Science, 63 :1111-1117. [Details]
Jensen LF, Hansen MM, Carlsson J, Loeschcke V & Mensberg K-LD (2005) 'Spatial and temporal genetic differentiation and effective population size of brown trout (Salmo trutta, L.) in small Danish rivers'. Conservation Genetics, 6 :615-621. [Details]
Carlsson J, McDowell JR, Díaz-Jaimes P, Carlsson JEL, Boles SB, Gold JR & Graves JE (2004) 'Microsatellite and mitochondrial DNA analyses of Atlantic bluefin tuna (Thunnus thynnus thynnus) population structure in the Mediterranean Sea'. Molecular Ecology, 13 :3345-3356. [Details]
Carlsson J, Aarestrup K, Nordwall F, Näslund I, Eriksson T & Carlsson JEL. (2004) 'Migration of landlocked brown trout in two Scandinavian streams as revealed from trap data'. Ecology of Freshwater Fish, 13 :161-168. [Details]
Carlsson J, Carlsson JEL, Olsén KH, Hansen MM, Eriksson T & Nilsson J (2004) 'Kin-biased distribution in brown trout: an effect of redd location or kin recognition?'. Heredity, 94 :53-61. [Details]
Carlsson J & Carlsson JEL. (2002) 'Micro-scale distribution of brown trout: an opportunity for kin-selection?'. Ecology of Freshwater Fish, 11 :234-239. [Details]
Carlsson J & Nilsson J. (2001) 'Effects of geomorphological structures on genetic differentiation among brown trout populations in a northern Boreal river drainage'. Transactions of the American Fisheries Society, 130 :36-45. [Details]
Carlsson J & Nilsson J (2000) 'Population genetic structure of brown trout (Salmo trutta L.) within a northern boreal forest stream'. Hereditas, 132 :173-181. [Details]
Carlsson J, Olsén HK, Nilsson J, Øverli Ø & Stabell OB (1999) 'Microsatellites reveal fine-scale genetic structure in stream-living brown trout'. Journal of Fish Biology, 55 :1290-1303. [Details]


Research Interests

My research interests are in conservation, ecological and population genetics, as well as evolutionary biology. I employ genetic tools at population and individual levels to study genetic questions (gene flow, genetic drift, effective population size and selection) and to couple genetics with behaviors (kin-biased behaviours, reproductive success, mate choice, migratory behavior and life-history). I am also interested in conservation genetics, functional genomics and studies that combine population genetics, behaviour and ecology. In addition, I am interested in theoretical population genetics based on simulations and co-evolution of host-parasite systems. My research is primarily focused on aquatic organisms including fishes, shellfish and hydrothermal vent and methane seep fauna.

Research Projects

Sponsor : University College Dublin (UCD)
Title : Next Generation Sequencing and Environmental DNA
Start Date / End Date : 01-MAY-13 / 31-OCT-14
Sponsor : Science Foundation Ireland (SFI)
Title : Taxonomy and connectivity of animal species at the Moytirra hydrothermal vent field: developing methods for assessing ecological impacts of mineral extraction in the deep-sea
Start Date / End Date : 01-APR-13 / 30-JUN-15
Sponsor : Irish Research Council (IRC)
Title : Population structure, phlyogeography and stock expansion of the boarfish, Capros aper in Atlantic and Mediterranean waters
Start Date / End Date : 01-OCT-13 / 30-SEP-15