DR Jens Carlsson

Principal Investigator
jens.carlsson(at)ucd.ie
My research interests include working with population genetic questions focused on population connectivity, estimation of migration rates and migratory behaviour, population sizes and family structure on a range of animals including fish, oysters, terrestrial mammals, hydrothermal vent and methane seep fauna. In addition to organismal biology, I have a strong interest in bioinformatics and developing new molecular approaches for marker development, genotyping and using next generation sequencing techniques (454 Roche, Illumina and Ion Torrent.

My research efforts have led to many opportunities to work internationally and I have enjoyed successful collaboration with scientists from a range of countries and disciplines. My work has included advisory services for Swedish, British, Irish, Danish and American governmental agencies. I am actively involved in several scientific disciplines as evident from the publication and review record. I often review manuscripts and grant applications focused on several scientific fields including, ecology, evolutionary, population and conservation genetics and behaviour. I also act as an editor for Journal of Fish Biology. In addition to research, I am interest in the development of sub-sea mineral extraction and its impact on deep-sea biology. This interest is mirrored in my role as member of the steering committee of VentBase (a multinational, multidisciplinary forum with industry and NGO participation).

Publications
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, Accepted.

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. 03/2014; DOI:10.1016/j.jip.2014.02.012

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.

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.

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.

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.

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). Journal of Heredity, 104: 510-520.

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.

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. 14: 4170-4184.

Kochmann J, Carlsson J, Crowe TP & 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). Journal of Heredity. 103: 661-671.

Lynch SA, Carlsson J, Reilly AO, Cotter E & Culloty SC. 2012. A previously undescribed ostreid herpes virus 1 (OsHV-1) genotype detected in the pacific oyster, Crassostrea gigas, in Ireland. Parasitology 139: 1-7.

O’Farrell B, Dennis C, Benzie J, McGinnity P, Carlsson J, de Eyto E, Coughlan J, Igoe F, Meehan R & Cross T. 2012. Balancing selection on MHC class I in wild brown trout (Salmo trutta). Journal of Fish Biology. 81: 1357-1374.

Finn J, Carlsson J, Kelly T & Davenport J. 2012. Avoidance of headwinds or exploitation of ground effect – why do birds fly low? Journal of Field Ornithology. 89: 192-202.

O’Farrell B, Benzie J, McGinnity P, Carlsson J, de Eyto E, Dillane E, Graham C, Coughlan J & Cross T. 2012. MHC-mediated spatial distribution in brown trout (Salmo trutta) fry. Heredity 108: 403-409.

O’Meara DB, Edwards CJ, Sleeman DP, Cross TF, Statham MJ, McDowell JR, Dillane E, Coughlan JP, O’Leary D, O’Reilly C, Bradley DG & 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: 893-909.

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. 58: 627-636.

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: 25-27.

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.

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: 101-103.

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.

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.

Carlsson J. 2008. Effects of microsatellite null alleles on assignment testing. Journal of Heredity. 99: 616-623.

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.

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 (Supplement A): 98–110.

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.

Carlsson J, McDowell JR, Carlsson JEL & Graves JE. 2007. Genetic identity of YOY bluefin tuna from the eastern and western Atlantic spawning areas. Journal of Heredity. 98: 23–28.

Carlsson J, Morrison CL & Reece KS. 2006. Wild and aquaculture populations of the eastern oyster compared using microsatellites. Journal of Heredity. 97: 595-598.

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.

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.

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.

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.

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. Featured paper in Heredity.

Carlsson J & Carlsson JEL*. 2002. Micro-scale distribution of brown trout: an opportunity for kin-selection? Ecology of Freshwater Fish. 11: 234-239.

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.

Carlsson J & Nilsson J. 2000. Population genetic structure of brown trout (Salmo trutta L.) within a northern boreal forest stream. Hereditas. 132: 173-181.

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.

Book chapters (peer reviewed)

Carlsson J & Nilsson J. 1999. Genetisk variation hos öringpopulationer – vem är släkt med vem? (In: Fiske, skogsbruk och vattendrag – nyttjande i ett uthålligt perspektiv, Ammeråprojektet, ed. I. Näslund). Fiskeriverkets försökstation, 840 64 Kälarne.

Nordwall F & Carlsson J. 1999. Fiskar kan vandra, men varför och vart vandrar de? (In: Fiske, skogsbruk och vattendrag – nyttjande i ett uthålligt perspektiv, Ammeråprojektet, ed. I Näslund). Fiskeriverkets försökstation, 840 64 Kälarne.

*Student author