Papers
METHOD DEVELOPMENT
Hintikka S, Carlsson JEL & Carlsson J. 2022. The bacterial hitchhiker’s guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind. Metabarcoding and Metagenomics 5: e80416. https://doi.org/10.3897/mbmg.6.80416.doi.org/10.3897/mbmg.6.80416
Zafeiropoulos H, Gargan L, Hintikka S, Pavloudi C & Carlsson J. 2021. The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data. Metabarcoding and Metagenomics 5: e69657. https://doi.org/10.3897/mbmg.5.69657.
Tighe AJ, Overby S, Thurman K, Gandola R, Fulanda B, Byrne J & Carlsson J. 2020. Investigating a simplified method for non-invasive genetic sampling in East African mammals using silica dried scat swabs. Ecology and Evolution. 2020;00:1–8. https://doi.org/10.1002/ece3.6115.
Atkinson S, Carlsson JEL, Ball B, Kelly-Quinn M & Carlsson J. 2019. Field application of an eDNA assay for the endangered white-clawed crayfish Austropotamobius pallipes. Freshwater Science. 38, no. 3 (September 2019): 503-509. https://doi.org/10.1086/704712.
Bennion M, Morrison L, Brophy D, Carlsson J, Abrahantes JC & Graham CT. 2019. Trace element fingerprinting of blue mussel (Mytilus edulis) shells and soft tissues successfully reveals harvesting locations. Science of the Total Environment. 685: 50-58. https://doi.org/10.1016/j.scitotenv.2019.05.233.
Williams M-A, O’Grady J, Ball B, Carlsson J, de Eytoe E, Regan F & Parle-McDermott A. 2019. The application of CRISPR-Cas for single species identification from environmental DNA. Molecular Ecology Resources. 2019, 1106-1114. https://doi.org/10.1111/1755-0998.13045.
Apolinári C, Ferreira DG, Cavenagh AF, Aprígio NGO, Galindo BA, Carlsson J & Sofia SH. 2018. Development and characterization of fifteen polymorphic microsatellite loci in Bryconamericus aff. iheringii (Teleostei: Characidae) and cross-amplification in related Characidae species. Neotropical Ichthyology, 16, e170135, 2018. https://doi.org/10.1590/1982-0224-20170135.
McClure MC, McCarthy J, Flynn P, McClure JC, Dair E, O'Connell DK & Kearney F. 2018. SNP Data Quality Control in a National Beef and Dairy Cattle System and Highly Accurate SNP Based Parentage Verification and Identification. Frontiers in Genetics, VOL 9, 84. https://doi.org/10.3389/fgene.2018.00084.
Whiston R, Finlay EK, McCabe M, Cormican S, Flynn P, Cromie A, Hansen PJ, Lyons A, Fair S, Lonergan P, O’ Farrelly C & Meade KG. 2017. A dual targeted β-defensin and exome sequencing approach to identify, validate and functionally characterise genes associated with bull fertility. Scientific Reports volume 7, Article number: 12287. https://doi.org/10.1038/s41598-017-12498-x.
Vartia S, Villanueva-Cañas JL, Finarelli J, 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 combintorial barcoding. Royal Society Open Science 2016, 3. https://doi.org/10.1098/rsos.150565.
Berry DP, O’Brien A, Wall E, McDermott K, Randles S, Flynn P, Park S, Grose J, Weld R & McHugh N. 2016. Inter- and intra-reproducibility of genotypes from sheep technical replicates on Illumina and Affymetrix platforms. Genetics Selection Evolution volume 48, Article number: 86. https://doi.org/10.1186/s12711-016-0267-0.
Vera M, Bello X, Alvarez-Dios J-A, Pardo BG, Sanchez L, Carlsson J, Carlsson JEL, 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. https://doi.org/10.1016/j.margen.2015.08.006.
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, 151: 43-54. https://doi.org/10.1111/hrd2.00044.
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. https://doi.org/10.1111/jfb.12034.
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. https://doi.org/10.1371/journal.pbio.1000069.
Carlsson J. 2008. Effects of microsatellite null alleles on assignment testing. Journal of Heredity, 99: 616-623. https://doi.org/10.1093/jhered/esn048.
MARINE
Curnick DJ, Deaville R, Bortoluzzi RB, Cameron L, Carlsson JEL, Carlsson J, Dolton HR, Gordon CA, Hosegood P, Nilsson A, Perkins MW, Purves KJ, Spiro S, Vecchiato M, Williams RS & Payne NL. 2023. Northerly range expansion and first confirmed records of the smalltooth sand tiger shark, Odontaspis ferox, in the United Kingdom and Ireland. Journal of Fish Biology. https://doi.org/10.1111/jfb.15529.
Farrel ED, Andersson L, Bekkevold D, Campbell N, Carlsson J, Clarke MW, Egan A, Folkvord A., Gras M, Lusseau SM, Mackinson S, Nolan C, O’Connell S, O’Malley M, Pastoors M, Petters ME & White E. 2022. A baseline for the genetic stock identification of Atlantic herring, Clupea harengus, in ICES Divisions 6.a, 7.b–c. Royal Society Open Science. https://doi.org/10.1098/rsos.220453.
Gallagher J, Lordan C, Hughes GM, Jonasson JP & Carlsson J. 2022. Microsatellites obtained using high throughput sequencing and a novel microsatellite genotyping method reveals population genetic structure in Norway Lobster, Nephrops norvegicus. Journal of Sea Research, 179, 2022, 102139. https://doi.org/10.1016/j.seares.2021.102139.
Tighe AJ, Ruane NM & Carlsson J. 2022. Potential origins of fish toti-like viruses in invertebrates. Journal of General Virology. 2022;103:001775. https://doi.org/10.1099/jgv.0.001775.doi.org/10.1099/jgv.0.001775
Gargan LM, Brooks PR, Vye SR, Ironside JE, Jenkins SR, Crowe TP & Carlsson J. 2021. The use of environmental DNA metabarcoding and quantitative PCR for molecular detection of marine invasive non-native species associated with artificial structures. Biological Invasions (2021). https://doi.org/10.1007/s10530-021-02672-8.
Talbot AT, Gargan L, Moran G, Prudent L, O’Connor I, Mirimin L, Carlsson J, MacCarthy E. 2021. Investigation of the transcriptomic response in Atlantic salmon (Salmo salar) gill exposed to Paramoeba perurans during early onset of disease. Scientific Reports. 11, 20682 (2021). https://doi.org/10.1038/s41598-021-99996-1.
Cusa M, Falcão L, De Jesus J, Biolatti C, Blondeel, Bracken FSA, Devriese L, Garcés‑Pastor S, Minoudi S, Gubili C, Acutis PL & Mariani S. 2021. Fish out of water: consumers’ unfamiliarity with the appearance of commercial fish species. Sustainability Science. https://doi.org/10.1007/s11625-021-00932-z.
Rotter A, Barbier M, Bertoni F, Bones AM., Cancela ML, Carlsson J, Carvalho MF, Cegłowska M, Chirivella-Martorell J, Conk Dalay M, Cueto M, Dailianis T, Deniz I, Díaz-Marrero AR., Drakulovic D, Dubnika A, Edwards C, Einarsson H, Erdoǧan A, Eroldoǧan Orhan T, Ezra D, Fazi S, FitzGerald RJ., Gargan LM, Gaudêncio SP, Gligora U Marija, Ivošević DeNardis N, Jónsdóttir R, Kataržytė M, Klun K, Kotta J, Ktari L, Ljubešić Z, Lukić Bilela L, Mandalakis M, Massa-Gallucci A, Matijošytė I, Mazur-Marzec H, Mehiri M, Nielsen Søren L, Novoveská L, Overlingė D, Perale G, Ramasamy P, Rebours C, Reinsch T, Reyes F, Rinkevich B, Robbens J, Röttinger E, Rudovica V, Sabotič J, Safarik I, Talve S, Tasdemir D, Theodotou Schneider X, Thomas OP, Toruńska-Sitarz A, Varese Giovanna C, Vasquez MI, 2021. The essentials of marine biotechnology. Frontiers in Marine Science. 8: 158. https://doi.org/10.3389/fmars.2021.629629.
Lynch SA, Lepée-Rivero S, Kelly R, Quinn E, Coghlan A, Bookelaar B, Morgan E, Finarelli JA, Carlsson J & Culloty SC. 2020. Detection of novel haplosporidian protistan parasites supports an increase to their known diversity, geographic range, and host specificity. Parasitology. 1–9. https://doi.org/10.1017/S0031182019001628.
Rincón-Tomás B, González FJ, Somoza L, Sauter K, Madureira P, Medialdea T, Carlsson J, Reitner J, Hoppert M. 2020. Siboglinidae tubes as an additional niche for microbial communities in the Gulf of Cádiz — a microscopical appraisal. Microorganisms. 8, 367. https://doi.org/10.3390/microorganisms8030367.
Rotter A, Bacu A, Barbier M, Bertoni F, Bones AM, Cancela ML, Carlsson J, Carvalho MF, Cegłowska M, Dalay MC, Dailianis T, Deniz I, Drakulovic D, Dubnika A, Einarsson H, Erdoğan A, Eroldoğan OT, Ezra D, Fazi S, FitzGerald RJ, Gargan LM, Gaudêncio SP, Ivošević DeNardis N, Joksimovic D, Kataržytė M, Kotta J, Mandalakis M, Matijošytė I, Mazur-Marzec H, Massa-Gallucci A, Mehiri M, Nielsen SL, Novoveská L, Overlingė D, Portman ME, Pyrc K, Rebours C, Reinsch T, Reyes F, Rinkevich B, Robbens J, Rudovica V, Sabotič J, Safarik I, Talve S, Tasdemir D, Theodotou Schneider X, Thomas OP, Toruńska-Sitarz A, Varese GC & Vasquez MI. 2020. A new network for the advancement of marine biotechnology in Europe and beyond. Frontiers in Marine Science, 12 May 2020. https://doi.org/10.3389/fmars.2020.00278.
Tighe AJ, Gallagher MD, Carlsson J, Matejusova I, Swords F, Macqueen D & Ruane N. 2020. Nanopore whole genome sequencing and partitioned phylogenetic analysis supports a new salmonid alphavirus subtype (SAV7). Diseases of Aquatic Organisms. 142:203-211. https://doi.org/10.3354/dao03546.
Gallagher J, Finarelli JA, Jonasson JP, & Carlsson J. 2019. Mitochondria D-loop DNA analyses of Norway lobster (Nephrops norvegicus) reveals genetic isolation between Atlantic and East Mediterranean populations. Journal of the Marine Biological Association of the United Kingdom. 1–8. https://doi.org/10.1017/S0025315418000929.
Tighe AJ, Carlsson, J, Morrissey T & Ruane N. 2019. Genetic diversity of piscine myocarditis virus in Atlantic salmon Salmo salar L. in Ireland. Journal of Fish Diseases. Aug;42(8):1161-1168. https://doi.org/10.1111/jfd.13018.
Gargan LM, Morato T, Pham CK, Finarelli JA, Carlsson JEL & Carlsson J. 2017. Development of a sensitive detection method to survey pelagic biodiversity using eDNA and quantitative PCR: a case study of devil ray at seamounts. Marine Biology. 164:112. https://doi.org/10.1007/s00227-017-3141-x.
Farrell ED, Carlsson JEL & Carlsson J. 2016. Next Gen Pop Gen: implementing a high-throughput approach to population genetics in boarfish (Capros aper). Royal Society Open Science, 3:160651. https://doi.org/10.1098/rsos.160651.
Vera M, Carlsson J, Carlsson JEL, Cross T, Lynch S, Kamermans P, Villalba A, Culloty A & Martinez P. 2016. Current genetic status, temporal stability and structure of the remnant wild European flat oyster populations: conservation and restoring implications. Marine Biology. 163:239. https://doi/10.1007/s00227-016-3012-x.
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. https://doi.org/10.1016/j.aquaculture.2014.04.038.
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. 18: 59-65. https://doi.org/10.1016/j.jip.2014.02.012.
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. https://doi.org/10.1093/jhered/est031.
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. https://doi.org/10.2983/035.032.0305.
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. https://doi.org/10.1093/jhered/ess042.
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. https://doi.org/10.1017/S0031182012000881.
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. https://doi.org/10.1016/j.dsr.2011.03.009.
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. https://doi.org/10.2983/0730-8000-27.5.1117.
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. https://doi.org/10.1111/j.1471-8286.2006.01573.x.
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. https://doi.org/10.1093/jhered/esl046.
McDowell JR, Carlsson JEL & Graves JE. 2007. Genetic analysis of blue marlin (Makaira nigricans) stock structure in the Atlantic Ocean. Gulf and Caribbean Research, 19: 75-82. https://doi.org/10.18785/gcr.1902.09.
Carlsson J, Morrison CL & Reece KS. 2006. Wild and aquaculture populations of the eastern oyster compared using microsatellites. Journal of Heredity, 97: 595-598. https://doi.org/10.1093/jhered/esl034.
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. https://doi.org/10.1016/j.icesjms.2006.04.009.
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. https://doi.org/10.1111/j.1365-294X.2004.02336.x.
DEEP SEA
Lennon E, Philips ND, Garbett A, Carlsson J, Carlsson JEL, Crowley D, Judge M, Yeo I & Collins PC. 2021. Going deeper, darker and further: Observations charting an egg nursery, a range and depth extension for the deep-sea spiny tailed skate Bathyraja spinicauda, first records from the Mid Atlantic Ridge. Deep-Sea Research Part I. 175: 103584. https://doi.org/10.1016/j.dsr.2021.103584.
Collins PC, Hunter WR, Carlsson JEL, Carlsson J. 2020. Fortuitous insights into the ecology of a recently charted deep-sea hydrothermal vent, using snails’ feet. Deep Sea Research Part I: Oceanographic Research Papers. 716: 103358. https://doi.org/10.1016/j.dsr.2020.103358.
Van Dover CL, Colaço A, Collins PC, Croot P, Metaxas A, Murton BJ, Swaddling A, Boschen-Rose RE, Carlsson J, Cuyvers L, Fukushima T, Gartman A, Kennedy R, Kriete C, Mestre NC, Molodtsova T, Myhrvold A, Pelleter E, Popoola SO, Qian P-Y, Sarrazin J, Sharma R, Suh YJ, Sylvan JB, Tao C, Tomczak M & Vermilye J. 2020. Research is needed to inform environmental management of hydrothermally inactive and extinct polymetallic sulfide (PMS) deposits. Marine Policy. 104183. https://doi.org/10.1016/j.marpol.2020.104183.
Yearsley JM, Salmanidou DM, Carlsson J, Burns D & Van Dover CL. 2020. Biophysical models of persistent connectivity and barriers on the northern Mid-Atlantic Ridge. Deep Sea Research Part II: Topical Studies in Oceanography: 180: 104819. https://doi.org/10.1016/j.dsr2.2020.104819.
Boschen RE, Collins PC, 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 & Coastal Management. 122: 37-48. https://doi.org/10.1016/j.ocecoaman.2016.01.007.
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. https://doi.org/10.1016/j.marpol.2016.07.016.
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. https://doi.org/10.1016/j.marpol.2013.01.020.
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. https://doi.org/10.1016/j.marpol.2013.03.002.
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. https://doi.org/10.1002/ggge.20243.
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. https://doi.org/10.1007/s12686-010-9272-8.
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. https://doi.org/10.1186/1471-2148-11-372.
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. https://doi.org/10.1007/s12686-010-9174-9.
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. https://doi.org/10.1007/s12686-010-9243-0.
FRESHWATER
Tighe AJ, Grayson S, Byrne J, Hintikka S, Jessen L, Dempsey J, Browne L, Kelly-Quinn M, Fulanda B, Ruane NM & Carlsson J. 2022. Nanopore metatranscriptomics reveals cryptic catfish species as potential Shigella flexneri vectors in Kenya. Scientific Reports. 12:13875. https://doi.org/10.1038/s41598-022-17036-y.
Ferreira DG, Carlsson J, Galindo BA, Frantine-Silva W, Apolinário-Silva C, Meschini JS, Zanatta AS, Almeida FS & Sofia SH. 2022. The role of free-flowing tributary rivers in the maintenance of genetic diversity of a migratory fish species living in a river fragmented by dams. Hydrobiologia 2022). https://doi.org/10.1007/s10750-021-04782-9.
Gargan LM, Mo TA, Carlsson JEL, Ball B, Fossøy F & Carlsson J. 2021. Development of an environmental DNA assay and field validation for the detection of invasive pink salmon Oncorhynchus gorbuscha. Environmental DNA. https://doi.org/10.1002/edn3.250.
Atkinson S, Bruen M, O' Sullivan JJ, Turner JN, Ball B, Carlsson J, Bullock C, Casserly C & Kelly-Quinn M. 2020. An inspection-based assessment of obstacles to salmon, trout, eel and lamprey migration and river channel connectivity in Ireland. Science of the Total Environment. 719: 137215. https://doi.org/10.1016/j.scitotenv.2020.137215.
Hume JB, Bracken FSA, Mateus CS & Brant CO. 2020. Synergizing basic and applied scientific approaches to help understand lamprey biology and support management actions. Journal of Great Lakes Research. https://doi.org/10.1016/j.jglr.2020.07.002.
Allain SJR, Gandola R, Tighe A &Wilkinson JW. 2019. An investigation into the provenance of Bedford’s midwife toads. Bedfordshire Naturalist. 74 (Part 1). http://stevenallain.co.uk/publications/pub57.pdf.
Atkinson S, Carlsson JEL, Ball B, Kelly-Quinn M & Carlsson J. 2019. Field application of an eDNA assay for the endangered white-clawed crayfish Austropotamobius pallipes. Freshwater Science. 38, no. 3 (September 2019): 503-509. https://doi.org/10.1086/704712.
Bracken FSA, Rooney SM, Kelly-Quinn M, King JJ & Carlsson J. 2018. Identifying spawning sites and other critical habitat in lotic systems using eDNA “snapshots”: A case study using the sea lamprey Petromyzon marinus L. Ecology and Evolution. 2018;00: 1–15. https://doi.org/10.1002/ece3.4777.
Atkinson S, Carlsson JEL, Ball B, Egan D, Kelly-Quinn M, Whelan K & Carlsson J. 2018. A quantitative PCR based environmental DNA assay for detecting Atlantic salmon (Salmo salar L.). Aquatic Conservation: Marine and Freshwater Ecosystems. https://doi.org//10.1002/aqc.2931.
Carlsson JEL, Egan D, Collins PC, Farrell ED, Igoe F & Carlsson J. 2017. A qPCR MGB probe based eDNA assay for European freshwater pearl mussel (Margaritifera margaritifera L.). Aquatic Conservation: Marine and Freshwater Ecosystems. 2017: 1-4. https://doi.org/10.1002/aqc.2788.
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. Review and Fish Biology and Fisheries. 2: 1-23. https://doi.org/10.1007/s11160-016-9441-2.
Galindo BA, Ferreira DG, Almeida FS, Carlsson J & Sofia SH. 2015. Isolation and characterization of thirteen polymorphic microsatellite loci in Hypostomus ancistroides (Teleostei, Loricariidae) and cross-amplification in related species. Journal of Fish Biology, 86: 1860-1866. https://doi.org/10.1111/jfb.12675.
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: 1254-1262. https://doi.org/10.1111/jfb.12781.
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. https://doi.org/10.1111/fme.12058.
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. https://doi.org/10.1111/j.1095-8649.2012.03421.x.
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. https://doi.org/10.1038/hdy.2011.87.
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. https://doi.org/10.1111/j.1095-8649.2007.01546.x.
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. https://doi.org/10.1007/s10592-005-9014-8.
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. https://doi.org/10.1111/j.1600-0633.2004.00058.x.
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. https://doi.org/10.1038/sj.hdy.6800376.
Carlsson J & Carlsson JEL. 2002. Micro-scale distribution of brown trout: an opportunity for kin-selection? Ecology of Freshwater Fish, 11: 234-239. https://doi.org/10.1034/j.1600-0633.2002.00017.x.
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. https://doi.org/10.1577/1548-8659(2001)130%3C0036:EOGSOG%3E2.0.CO;2.
Carlsson J & Nilsson J. 2000. Population genetic structure of brown trout (Salmo trutta L.) within a northern boreal forest stream. Hereditas, 132: 173-181. https://doi.org/10.1111/j.1601-5223.2000.00173.x.
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. https://doi.org/10.1111/j.1095-8649.1999.tb02076.x.
TERRESTRIAL
Fernandes DM, Mittnik A, Olalde I, Lazaridis I, Cheronet O, Rohland N, Mallick S, Bernardos R, Broomandkhoshbacht N, Carlsson J, Culleton BJ, Ferry M, Gamarra B, Lari M, Mah M, Michel M, Modi A, Novak M, Oppenheimer J, Sirak KA, Stewardson K, Mandl K, Schattke C, Özdoğan KT, Lucci M, Gasperetti G, Candilio F, Salis G, Vai S, Camarós E, Calò C, Catalano G, Cueto M, Forgia V, Lozano M, Marini E, Micheletti M, Miccichè RM, Palombo MR, Ramis D, Schimmenti V, Sureda P, Teira L, Teschler-Nicola M, Kennett DJ, Lalueza-Fox C, Patterson N, Sineo L, Coppa A, Caramelli D, Pinhasi R & Reich D. 2020. The Spread of Steppe and Iranian Related Ancestry in the Islands of the Western Mediterranean. Nature Ecology & Evolution. 1-12. https://doi.org/10.1038/s41559-020-1102-0.
Sleeman DP, Carlsson J & Carlsson JEL. 2019. Remains of a Spiny Mouse (Acomys cahirinus) in Dublin. Irish Naturalists’ Journal Vol. 36 Part 2. 172-173.
Tighe AJ, Gandola R, Fulanda B, Thurman K, Overby S, Byrne J & Carlsson J. 2018. Testing PCR amplification from elephant dung using silica-dried swabs. Pachyderm. No. 59 July 2017 – June 2018: 56-65.
McClure M, Mullen M, Waters S, Kearney JF, McClure J, Flynn, P & Weld, R. (2016). P6001 Effectively managing bovine genetic disease risk via genotyping the Irish national herd. Journal of Animal Science. 94. 148. https://doi.org/10.2527/jas2016.94supplement4148x.
Nadolny R, Gaff H, Carlsson, J & Gauthier D. 2015. Comparative population genetics of two invading ticks: Evidence of the ecological mechanisms underlying tick range expansions. Infection, Genetics and Evolution, 35: 153-162. https://doi.org/10.1016/j.meegid.2015.08.009.
Toolan DP, Sheehan M, McElroy MC, Flynn P, Weld R & McClure M. (2014) Congenital paunch calf syndrome in Ireland. Veterinary Record 175, 124. https://doi.org/10.1136/vr.g4882
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. https://doi.org/10.1111/j.1557-9263.2012.00369.x.
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. https://doi.org/10.1111/j.1095-8312.2012.01927.x.