Publications
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In the pipeline ...
Paris JR, King RA, Shaw S, Bourret V, Urbina MA, Hamilton PB, Moore, KA, Rowe D, Lange A, Usher J, Catchen JM, Wilson RW, Bury NR, Santos EM, Stevens JR. The relative roles of acclimation and adaptation in the evolution of metal-tolerance in brown trout (Salmo trutta L.).
Paris JR*, Jenkins TL*, McFarling R, Robinson PC, Ferrer Obiol J, Stevens JR, van Aerle R, Santos EM. The genome of the European lobster (Homarus gammarus).
Paris JR, Ficetola GF, Silva-Rocha I, Yang W, Carretero MA, Salvi D. Using genomics to resolve the question of hybridisation between the Critically Endangered Aeolian wall lizard (Podarcis raffonei) and the Italian wall lizard (Podarcis siculus)
Paris JR, Whiting JR, Daniel MJ, van der Zee M, Rodd FH, Hughes KA, Fraser BA. Ecological drivers of directional and balancing selection in wild guppy populations.
Bounas A, Ferrer Obiol J, Lombardo G, Secomandi S, Paris JR, …, Torroni A, Rubolini D. Population dynamics and adaptive evolution of a steppe-specialist raptor.
In Review
Sherpa S, Paris JR, Silva-Rocha I, Di Canio V, Carretero MA, Ficetola GF, Salvi D. Genetic depletion does not prevent rapid evolution in island-introduced lizards. In Review
Sherpa S, Salvi D, Silva-Rocha I, Capblancq T, Paris JR, Carretero MA, Ficetola GF. Reconstructing the complex colonization histories of lizards across Mediterranean archipelagos. In Review
Kardum Hjort C, Paris JR, Henrik G. Smith HG, Dudaniec RY. Selection despite low genetic diversity and high gene flow in a rapid island invasion of the bumblebee, Bombus terrestris. In Review
Trucchi E, Massa P, Giannelli F, Nitta Fernandes F, Ancona L, Stenseth NC, Ferrer Obiol J, Paris JR, Bertorelle G, Le Bohec C. Gene expression is the main driver of purifying selection in large penguin populations. In Review
Fully fledged
2023
Sozzoni M, Ferrer Obiol J, Formenti G, Tigano A, Paris JR, Balacco JR, Jain N, Tilley T, Collins J, Sims Y, Wood J, Benowitz-Fredericks M, Field KA, Seyoum E, Gatt MC, Léandri-Breton DJ, Nakajima C, Whelan S, Gianfranceschi L, Hatch SA, Elliott KH, Shoji A, Cecere JG, Jarvis ED, Pilastri A, Rubolini D. A chromosome-level reference genome for the black-legged kittiwake (Rissa tridactyla), a declining circumpolar seabird. Accepted in Genome Biology and Evolution
2023
Macleod KL, Paris JR, Jenkins TL, Stevens JR. The First Genome of the Cold-Water Octocoral, the Pink Sea Fan, Eunicella verrucosa. Genome Biology and Evolution, 15(6): evad083. https://doi.org/10.1093/gbe/evad083
2023
Nascimento-Schulze JC, Penaloza C, Paris JR, Whiting JR, Sanders MB, Bean TP, Houston RD, Fraser BA, Ellis R. Development of a medium density SNP-array for the blue mussel species-complex. Evolutionary Applications, 16(5): 1044 - 1060. https://doi.org/10.1111/eva.13552
2022
Ferrer Obiol J, Herranz JM, Paris JR, Whiting JR, Rozas J, Riutort M, González-Solís J (2022). Species delimitation using genomic data to resolve taxonomic uncertainties in a speciation continuum of pelagic seabirds. Molecular Phylogenetics and Evolution, 179: 107671 https://doi.org/10.1016/j.ympev.2022.107671
2022
Whiting JR, Paris JR, van der Zee MJ, Fraser BA. (2022). AF-vapeR: A multivariate genome scan for detecting parallel evolution using allele frequency change vectors. Methods in Ecology and Evolution, 13(10): 2167-2180. https://doi.org/10.1111/2041-210X.13952
2022
Paris JR, Whiting JR, Daniel MJ, Ferrer Obiol J, Parsons PJ, van der Zee MJ, Wheat CW, Hughes KA, Fraser BA. (2022). A large and diverse autosomal haplotype is associated with sex-linked colour polymorphism in the guppy. Nature Communications, 13: 1233. https://doi.org/10.1038/s41467-022-28895-4
2022
Whiting JR, Paris JR, Parsons PJ, Matthews S, Reynoso Y, Hughes KA, Reznick DN, Fraser BA (2022). On the genetic architecture of rapidly adapting and convergent life history traits in guppies. Heredity, 128(4): 250-260. https://doi.org/10.1038/s41437-022-00512-6
2022
Kardum Hjort C, Paris JR, Olsson P, Herbertsson L, de Miranda JR, Dudaniec RY, Smith HG. (2022). Genomic divergence and a lack of introgression between commercial and wild bumblebees (Bombus terrestris). Evolutionary Applications, 15(3): 365-382. https://doi.org/10.1111/eva.13346
2022
van der Zee MJ, Whiting JR, Paris JR, Bassar RD, Travis J, Weigel D, Reznick DN, Fraser BA (2022). Rapid genomic convergent evolution in experimental populations of Trinidadian guppies (Poecilia reticulata). Evolution Letters, 6(2): 149-161. https://doi.org/10.1002/evl3.272
2021
Whiting JR, Paris JR, van der Zee MJ, Parsons, PJ, Weigel D, Fraser BA. (2021). Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies. PLoS genetics 17 (5), e1009566. https://doi.org/10.1371/journal.pgen.1009566
2020
Hamilton PB, Lockyer A, Uren Webster T, Studholme DJ, Paris JR, Baynes A, Nicol E, Dawson D, Moore KA, Farbos A, Jobling S, Stevens JR, Tyler CR (2020). Populations of roach (Rutilus rutilus) in English rivers show local adaptation in genes responsive o endocrine disrupting chemicals. Environmental Science and Technology, 24(54):15935-15945. https://doi.org/10.1021/acs.est.0c00957.
2020
Fraser BA, Whiting JR, Paris JR, Weadick CJ, Parsons PJ, Charlesworth D, Bergero R, Bemm F, Hoffmann M, Kottler VA, Liu C, Dreyer C, Weigel D (2020). Improved reference genome uncovers novel sex-linked regions in the guppy (Poecilia reticulata). Genome Biology and Evolution, evaa187. https://doi.org/10.1093/gbe/evaa187
2020
Lange A, Paris JR, Gharbi K, Cézard T, Miyagawa S, Iguchi T, Studholme DJ, Tyler CR (2020). A newly developed genetic sex marker and its application to understanding chemically induced feminisation in roach (Rutilus rutilus). Molecular Ecology Resources, 20(4):1007-1022. https://doi.org/10.1111/1755-0998.13166
2020
Sherman KD, Paris JR, King RA, Moore KA, Dahlgren CP, Knowles LC, Stump K, Stevens JR, Tyler CR. (2020). RAD-Seq analysis and in situ monitoring of Nassau grouper reveal fine-scale population structure and origins of aggregating fish. Frontiers in Marine Science, 7 (157). https://doi.org/10.3389/fmars.2020.00157.
2019
Paris JR, Usher J (2019). Functional genomic characterization of metallothioneins in brown trout (Salmo trutta L.) using synthetic genetic analysis. Scientific Reports, 9, 11827 (2019). https://doi.org/10.1038/s41598-019-48303-0
2018
Ikediashi C*, Paris JR*, King RA, Beaumont WRC, Ibbotson A, Stevens JR (2018). Atlantic salmon Salmo salar L. in the chalk streams of England are genetically unique. Journal of Fish Biology, 92(3): 621-641. https://doi.org/10.1111/jfb.13538 * Joint First Co-authors
2018
Paris JR*, Sherman KD*, Bell E, Boulenger C, Delord C, El-Mahdi MBM, Fairfield EA, Griffiths AM, Gutmann Roberts C., Hedger RD, Holman LE, Hooper LH, Humphries NE, Katsiadaki I, King RA, Lemopoulos A, Payne CJ, Peirson G, Richter KK, Taylor MI, Trueman CN, Hayden B, Stevens JR (2018). Understanding and managing fish populations: keeping the toolbox fit for purpose. Journal of Fish Biology, 92(3): 727-751. https://doi.org/10.1111/jfb.13549 * Joint First Co-authors
2017
Dillon MJ, Paris JR, Bowkett AE, Bundard MJ, Harding L, Sayers G, Beckman KM, O’Brien MF, Cromie RL, Bates K, Fisher MC, Stevens JR, Thornton CR. (2017). Tracking amphibian pathogens using lateral-flow technology. Peer-reviewed conference proceeding presented at Zoo and Wildlife Health Conference, Berlin, Germany.
2017
Paris JR, Stevens JR, Catchen JM (2017) Lost in parameter space: A road map for Stacks. Methods in Ecology and Evolution, 8(10): 1360-1373. https://doi.org/10.1111/2041-210X.12775
2015
Paris JR, King RA, Stevens JR (2015) Human mining activity across the ages determines the genetic structure of modern brown trout (Salmo trutta L.) populations. Evolutionary Applications, 8(6):573-585. https://doi.org/10.1111/eva.12266