Genomic signatures of parasite-driven natural selection in north European Atlantic salmon (Salmo salar)
Tài liệu tham khảo
Abdelkhalek, 2014, Identification of immune relevant genes using Expressed Sequence Tags (ESTs) in Common carp (Caprinus caprio) gills, J. Fac. Agric. Kyushu Univ., 59, 109, 10.5109/1434399
Abraham, 2000, Raf-1-associated protein phosphatase 2A as a positive regulator of kinase activation, J. Biol. Chem., 275, 22300, 10.1074/jbc.M003259200
Acevedo-Whitehouse, 2006, Is MHC enough for understanding wildlife immunogenetics?, Trends Ecol. Evol., 21, 433, 10.1016/j.tree.2006.05.010
Adlard, 2015, The butterfly effect: parasite diversity, environment, and emerging disease in aquatic wildlife, Trends Parasitol., 31, 160, 10.1016/j.pt.2014.11.001
Alexa, 2016
Aljanabi, 1997, Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques, Nucleic Acids Res., 25, 4692, 10.1093/nar/25.22.4692
Artamonova, 2008, Evolutionary consequences of parasite invasion: a case study of Atlantic salmon Salmo salar L, Dokl. Biol. Sci., 423, 412, 10.1134/S0012496608060136
Ashburner, 2000, Gene ontology: tool for the unification of biology, Nat. Genet., 25, 25, 10.1038/75556
Asplund, 2004, Geographical structure and postglacial history of mtDNA haplotype variation in Atlantic salmon (Salmo salar L.) among rivers of the White and Barents Sea basins, Ann. Zool. Fenn., 41, 465
Aykanat, 2015, Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population, Mol. Ecol., 24, 5158, 10.1111/mec.13383
Bakke, 1990, Differences in the host resistance of Atlantic salmon. Salmo salar L., stocks to the monogenean Gyrodactylus salaris Malmberg, 1957, J. Fish Biol., 37, 577, 10.1111/j.1095-8649.1990.tb05890.x
Bakke, T. a, Harris, P.D., Hansen, H., Cable, J., Hansen, L.P., 2004. Susceptibility of Baltic and East Atlantic salmon Salmo salar stocks to Gyrodactylus salaris (Monogenea). Dis. Aquat. Org. 58, 171–7. doi:https://doi.org/10.3354/dao058171.
Bansal, 2017, Development of a potent wound healing agent based on the liver fluke Granulin structural fold, J. Med. Chem., 60, 4258, 10.1021/acs.jmedchem.7b00047
Barson, 2015, Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon, Nature, 528, 405, 10.1038/nature16062
Bierne, 2011, The coupling hypothesis: why genome scans may fail to map local adaptation genes, Mol. Ecol., 20, 2044, 10.1111/j.1365-294X.2011.05080.x
Björck, 1995, A review of the history of the Baltic Sea, 13.0–8.0ka BP, Quat. Int., 27, 19, 10.1016/1040-6182(94)00057-C
Blank, 2009, Inhibitory ITAMs as novel regulators of immunity, Immunol. Rev., 232, 59, 10.1111/j.1600-065X.2009.00832.x
Boehm, 2012, Evolution of lymphoid tissues, Trends Immunol., 33, 315, 10.1016/j.it.2012.02.005
Boilard, 2010, A novel anti-inflammatory role for secretory phospholipase A2 in immune complex-mediated arthritis, EMBO Mol. Med., 2, 172, 10.1002/emmm.201000072
Bourret, 2013, SNP-array reveals genome-wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar), Mol. Ecol., 22, 532, 10.1111/mec.12003
Bowden, 2008, Modulation of the immune system of fish by their environment, Fish Shellfish Immunol., 25, 373, 10.1016/j.fsi.2008.03.017
Brohede, 2005, PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays, Nucleic Acids Res., 33, 1, 10.1093/nar/gni142
Brown, 2004, Toward a metabolic theory of ecology, Ecology, 85, 1771, 10.1890/03-9000
Calder, 2001, Polyunsaturated fatty acids, inflammation, and immunity, Lipids, 36, 1007, 10.1007/s11745-001-0812-7
Caraux, 2017, Phospholipase C-y2 is essential for NK cell cytotoxicity and innate immunity to malignant and virally infected cells, Blood, 107, 994, 10.1182/blood-2005-06-2428
Carballeira, 2008, New advances in fatty acids as antimalarial, antimycobacterial and antifungal agents, Prog. Lipid Res., 47, 50, 10.1016/j.plipres.2007.10.002
Carval, 2010, A unified model for the coevolution of resistance, tolerance, and virulence, Evolution, 64, 2988
Castro, 2013, Disease resistance is related to inherent swimming performance in Atlantic salmon, BMC Physiol., 13, 1, 10.1186/1472-6793-13-1
Cepeda, 2011, Identification of genes involved in immune response of Atlantic salmon (Salmo salar) to IPN virus infection, using expressed sequence tag (EST) analysis, Aquaculture, 318, 54, 10.1016/j.aquaculture.2011.04.045
Chi, 2016, Th17 master transcription factors RORα and RORγ regulate the expression of IL-17C, IL-17D and IL-17F in Cynoglossus semilaevis, Dev. Comp. Immunol., 55, 169, 10.1016/j.dci.2015.11.001
Chuang, 2000, The CD28 and CTLA-4 receptors associate with the serine/threonine phosphatase PP2A, Immunity, 13, 313, 10.1016/S1074-7613(00)00031-5
Conesa, 2005, Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics, 21, 3674, 10.1093/bioinformatics/bti610
Costa, 2013, IL-22 is a key player in the regulation of inflammation in fish and involves innate immune cells and PI3K signaling, Dev. Comp. Immunol., 41, 746, 10.1016/j.dci.2013.08.021
Dionne, 2007, Clinal variation in MHC diversity with temperature: evidence for the role of host-pathogen interaction on local adaptation in Atlantic salmon, Evolution, 61, 2154, 10.1111/j.1558-5646.2007.00178.x
Elphinstone, 2003, An inexpensive and high-throughput procedure to extract and purify total genomic DNA for population studies, Mol. Ecol. Notes, 3, 317, 10.1046/j.1471-8286.2003.00397.x
Fabian Grammes, 2017
Faure, 2013, Pathogen-induced autophagy signaling in innate immunity, J. Innate Immun., 5, 456, 10.1159/000350918
Flatman, 2002, Regulation of Na-K-2Cl cotransport by phosphorylation and protein-protein interactions, Biochim. Biophys. Acta, 1566, 140, 10.1016/S0005-2736(02)00586-2
Foll, 2008, A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective, Genetics, 180, 977, 10.1534/genetics.108.092221
Freeman, 2014, Phagocytosis: receptors, signal integration, and the cytoskeleton, Immunol. Rev., 262, 193, 10.1111/imr.12212
Fumagalli, 2011, Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution, PLoS Genet., 7, 1, 10.1371/annotation/ca428083-dbcb-476a-956c-d7bb6e317cf7
Funder, 2002, Hydrography and mollusc faunas of the Baltic and the White Sea-North Sea seaway in the Eemian, Palaeogeogr. Palaeoclimatol. Palaeoecol., 184, 275, 10.1016/S0031-0182(02)00256-0
Gilbey, 2006, Identification of genetic markers associated with Gyrodactylus salaris resistance in Atlantic salmon Salmo salar, Dis. Aquat. Org., 71, 119, 10.3354/dao071119
Gillooly, 2001, Effects of size and temperature on metabolic rate, Science (80-), 293, 2248, 10.1126/science.1061967
Goetzl, 2004, Sphingosine 1-phosphate and its G protein-coupled receptors constitute a multifunctional immunoregulatory system, J. Cell. Biochem., 92, 1104, 10.1002/jcb.20053
Günther, 2013, Robust identification of local adaptation from allele frequencies, Genetics, 195, 205, 10.1534/genetics.113.152462
Guo, 2016, Population genomic evidence for adaptive differentiation in the Baltic Sea herring, Mol. Ecol., 25, 2833, 10.1111/mec.13657
Haarder, 2013, Expression of immune relevant genes in rainbow trout following exposure to live Anisakis simplex larvae, Exp. Parasitol., 135, 564, 10.1016/j.exppara.2013.09.011
Haasl, 2016, Fifteen years of genomewide scans for selection: trends, lessons and unaddressed genetic sources of complication, Mol. Ecol., 25, 5, 10.1111/mec.13339
Hanington, 2009, Development of macrophages of cyprinid fish, Dev. Comp. Immunol., 33, 411, 10.1016/j.dci.2008.11.004
Harbige, 2003, Fatty acids, the immune response, and autoimmunity: a question of n-6 essentiality and the balance between n-6 and n-3, Lipids, 38, 323, 10.1007/s11745-003-1067-z
Hedrick, 2013, Lymphatic regulation in nonmammalian vertebrates, J. Appl. Physiol., 115, 297, 10.1152/japplphysiol.00201.2013
Heinz, 2015, The lipid-modifying enzyme SMPDL3B negatively regulates innate immunity, Cell Rep., 11, 1919, 10.1016/j.celrep.2015.05.006
Hiroi, 2008, Evidence for an apical Na–Cl cotransporter involved in ion uptake in a teleost fish, J. Exp. Biol., 211, 2584, 10.1242/jeb.018663
Hoban, 2016, Finding the genomic basis of local adaptation: pitfalls, practical solutions, and future directions, Am. Nat., 188, 379, 10.1086/688018
Hoffmann, 2002, Control of Cl- transport in the operculum epithelium of Fundulus heteroclitus: long- and short-term salinity adaptation, Biochim. Biophys. Acta, 1566, 129, 10.1016/S0005-2736(02)00587-4
Holm, 2017, Contrasting expression of immune genes in scaled and scaleless skin of Atlantic salmon infected with young stages of Lepeophtheirus salmonis, Dev. Comp. Immunol., 67, 153, 10.1016/j.dci.2016.10.008
Johnsen, 1991, The Gyrodactylus story in Norway, Aquaculture, 98, 289, 10.1016/0044-8486(91)90393-L
Kadiri, 2015, The nuclear retinoid-related orphan receptor-alpha regulates adipose tissue glyceroneogenesis in addition to hepatic gluconeogenesis, Am. J. Physiol. Endocrinol. Metab., 309, 105, 10.1152/ajpendo.00518.2014
Kaltz, 1998, Local adaptation in host-parasite systems, Heredity (Edinb)., 81, 361, 10.1046/j.1365-2540.1998.00435.x
Kang, 2010, Salinity-dependent expression of a Na+, K+, 2Cl− cotransporter in gills of the brackish medaka Oryzias dancena: a molecular correlate for hyposmoregulatory endurance, Comp. Biochem. Physiol. A, 157, 7, 10.1016/j.cbpa.2010.05.013
Kania, 2010, Molecular and immunohistochemical studies on epidermal responses in Atlantic salmon Salmo salar L. induced by Gyrodactylus salaris Malmberg, 1957, J. Helminthol., 84, 166, 10.1017/S0022149X09990460
Kiiskinen, 2003, Effects of daylength and winter fasting on growth and smolting of one-year-old Saimaa landlocked salmon (Salmo salar m. sebago Girard) under fish farm conditions, Ann. Zool. Fenn., 40, 441
Kjærner-Semb, 2016, Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection, BMC Genomics, 17, 1, 10.1186/s12864-016-2867-z
Krasnov, 2011, Genomic survey of early responses to viruses in Atlantic salmon, Salmo salar L, Mol. Immunol., 49, 163, 10.1016/j.molimm.2011.08.007
Krasnov, 2012, Gene expression in Atlantic salmon skin in response to infection with the parasitic copepod Lepeophtheirus salmonis, cortisol implant, and their combination, BMC Genomics, 13, 1, 10.1186/1471-2164-13-130
Kudersky, 2003, Distribution and Range Formation History of the Monogenean Gyrodactylus salaris Malmberg, 1957 — A Parasite of Juvenile Atlantic salmon Salmo salar Linnaeus, 77
Kumari, 2009, Interleukin-17D in Atlantic salmon (Salmo salar): molecular characterization, 3D modelling and promoter analysis, Fish Shellfish Immunol., 27, 647, 10.1016/j.fsi.2009.08.009
Kusakabe, 2017, Genetic basis for variation in salinity tolerance between stickleback ecotypes, Mol. Ecol., 26, 304, 10.1111/mec.13875
Kuusela, 2007, Hybrid origin of Baltic salmon-specific parasite Gyrodactylus salaris: a model for speciation by host switch for hemiclonal organisms, Mol. Ecol., 16, 5234, 10.1111/j.1365-294X.2007.03562.x
Kuusela, 2009, Clonal structure of salmon parasite Gyrodactylus salaris on a coevolutionary gradient on Fennoscandian salmon (Salmo salar), Ann. Zool. Fenn., 46, 21, 10.5735/086.046.0103
Lachance, 2013, SNP ascertainment bias in population genetic analyses: why it is important, and how to correct it, BioEssays, 35, 780, 10.1002/bies.201300014
Langefors, 2001, Allelic polymorphism in MHC class II B in four populations of Atlantic salmon (Salmo salar), Immunogenetics, 53, 329, 10.1007/s002510100329
Li, 2014, Polycomb chromobox (Cbx) 7 modulates activation-induced CD4+ T cell apoptosis, Arch. Biochem. Biophys., 564, 184, 10.1016/j.abb.2014.10.004
Li, 2017, Transcriptome profiling of developing spleen tissue and discovery of immune-related genes in grass carp (Ctenopharyngodon idella), Fish Shellfish Immunol., 60, 400, 10.1016/j.fsi.2016.12.012
Lien, 2016, The Atlantic salmon genome provides insights into rediploidization, Nature, 533, 200, 10.1038/nature17164
Lillico, 2017, Teleost leukocyte immune-type receptors activate distinct phagocytic modes for target acquisition and engulfment, J. Leukoc. Biol., 98, 235, 10.1189/jlb.2A0215-039RR
Lim, 2007, An essential role for Talin during aMB2-mediated phagocytosis, Mol. Biol. Cell, 18, 976, 10.1091/mbc.e06-09-0813
Limborg, 2012, Signatures of natural selection among lineages and habitats in Oncorhynchus mykiss, Ecol. Evol., 2, 1, 10.1002/ece3.59
Limborg, 2012, Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus), Mol. Ecol., 21, 3686, 10.1111/j.1365-294X.2012.05639.x
Lindenstrom, 2006, Skin expression of IL-1b in East Atlantic salmon, Salmo salar L., highly susceptible to Gyrodactylus salaris infection is enhanced compared to a low susceptibility Baltic stock, J. Fish Dis., 29, 123, 10.1111/j.1365-2761.2006.00696.x
Lionetto, 2006, The Na+ K+ 2Cl- cotransporter and the osmotic stress response in a model salt transport epithelium, Acta Physiol., 187, 115, 10.1111/j.1748-1716.2006.01536.x
Lumme, 2015, The formation of landlocked populations of Atlantic salmon, 26
Mace, 2009, A dual role for Talin in NK cell cytotoxicity: activation of LFA-1-mediated cell adhesion and polarization of NK cells, J. Immunol., 182, 948, 10.4049/jimmunol.182.2.948
Makrinos, 2016, Natural environmental impacts on teleost immune function, Fish Shellfish Immunol., 53, 50, 10.1016/j.fsi.2016.03.008
Matejusová, 2006, Gene expression profiles of some immune relevant genes from skin of susceptible and responding Atlantic salmon (Salmo salar L.) infected with Gyrodactylus salaris (Monogenea) revealed by suppressive subtractive hybridisation, Int. J. Parasitol., 36, 1175, 10.1016/j.ijpara.2006.04.009
Medzhitov, 2007, Recognition of microorganisms and activation of the immune response, Nature, 449, 819, 10.1038/nature06246
Mikrou, 2009, CR3 complement receptor: cloning and characterization in rainbow trout, Fish Shellfish Immunol., 26, 19, 10.1016/j.fsi.2008.10.005
Mitchell, 2013, An evolutionary perspective on the broad antiviral specificity of MxA, Curr. Opin. Microbiol., 16, 493, 10.1016/j.mib.2013.04.005
Moen, 2007, Mapping of a quantitative trait locus for resistance against infectious salmon anaemia in Atlantic salmon (Salmo salar): comparing survival analysis with analysis on affected/resistant data, BMC Genet., 8, 1, 10.1186/1471-2156-8-53
Moen, 2015, Epithelial cadherin determines resistance to infectious pancreatic necrosis virus in Atlantic salmon, Genetics, 200, 1313, 10.1534/genetics.115.175406
Nakamura, 1993, Protein phosphatase type 2B (calcineurin)-mediated, FK506-sensitive regulation of intracellular ions in yeast is an important determinant for adaptation to high salt stress conditions, EMBO J., 12, 4063, 10.1002/j.1460-2075.1993.tb06090.x
Nakanishi, 2015, T cells in fish, Biology (Basel), 4, 640
Narum, 2011, Candidate genetic markers associated with anadromy in Oncorhynchus mykiss of the Klickitat River, Trans. Am. Fish. Soc., 140, 843, 10.1080/00028487.2011.588131
Naumenko, 1996, Main features of the thermal regime of Lake Ladoga during the ice-free period, Hydrobiologia, 322, 10.1007/BF00031807
Nielsen, 2005, Genomic scans for selective sweeps using SNP data, Genome Res., 15, 1566, 10.1101/gr.4252305
Nielsen, 2009, Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua), BMC Evol. Biol., 9, 1, 10.1186/1471-2148-9-276
Nilsen, 2003, Smolting in anadromous and landlocked strains of Atlantic salmon (Salmo salar), Aquaculture, 222, 71, 10.1016/S0044-8486(03)00103-0
Nilsen, 2008, Endocrine systems in juvenile anadromous and landlocked Atlantic salmon (Salmo salar): seasonal development and seawater acclimation, Gen. Comp. Endocrinol., 155, 762, 10.1016/j.ygcen.2007.08.006
Nilsson, 2001, Matrilinear phylogeography of Atlantic salmon (Salmo salar L.) in Europe and postglacial colonization of the Baltic Sea area, Mol. Ecol., 10, 89, 10.1046/j.1365-294X.2001.01168.x
Oleksyk, 2008, Identifying selected regions from heterozygosity and divergence using a light-coverage genomic dataset from two human populations, PLoS One, 3, 1, 10.1371/journal.pone.0001712
Oleksyk, 2010, Genome-wide scans for footprints of natural selection, Philos. Trans. R. Soc. B Biol. Sci., 365, 185, 10.1098/rstb.2009.0219
Orr, 2000, Adaptation and the cost of complexity, Evolution, 54, 13, 10.1111/j.0014-3820.2000.tb00002.x
Oshiumi, 2010, DEAD/H BOX 3 (DDX3) helicase binds the RIG-I adaptor IPS-1 to up-regulate IFN-B-inducing potential, Eur. J. Immunol., 40, 940, 10.1002/eji.200940203
Ozerov, 2010, Genetic structure of freshwater Atlantic salmon (Salmo salar L.) populations from the lakes Onega and Ladoga of northwest Russia and implications for conservation, Conserv. Genet., 11, 1711, 10.1007/s10592-010-0064-1
Ozerov, 2012, “Riverscape” genetics: river characteristics influence the genetic structure and diversity of anadromous and freshwater Atlantic salmon (Salmo salar) populations in northwest Russia, Can. J. Fish. Aquat. Sci., 69, 1, 10.1139/f2012-114
Ozerov, 2013, Temporal variation of genetic composition in Atlantic salmon populations from the Western White Sea Basin: influence of anthropogenic factors?, BMC Genet., 14, 1, 10.1186/1471-2156-14-88
Pankratz, 2010, Associations between SNPs in candidate immune-relevant genes and rubella antibody levels: a multigenic assessment, BMC Immunol., 11, 1, 10.1186/1471-2172-11-48
Papakostas, 2014, Gene pleiotropy constrains gene expression changes in fish adapted to different thermal conditions, Nat. Commun., 5, 1, 10.1038/ncomms5071
Park, 2011, Granulin is a soluble cofactor for toll-like receptor 9 signaling, Immunity, 34, 505, 10.1016/j.immuni.2011.01.018
Peng, 2003, Polyunsaturated fatty acid profiles of whole body phospholipids and triacylglycerols in anadromous and landlocked Atlantic salmon (Salmo salar L.) fry, Comp. Biochem. Physiol., 134, 335, 10.1016/S1096-4959(02)00263-4
Pritchard, 2016, Single nucleotide polymorphisms to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees, Evol. Appl., 9, 1017, 10.1111/eva.12407
Przeworski, 2005, The signature of positive selectionon standing genetic variation, Evolution, 59, 2312, 10.1554/05-273.1
Purcell, 2007, PLINK: a tool set for whole-genome association and population-based linkage analyses, Am. J. Hum. Genet., 81, 559, 10.1086/519795
Quinlan, 2010, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, 26, 841, 10.1093/bioinformatics/btq033
R Core Team, 2016
Råberg, 2007, Disentangling genetic variation for resistance and tolerance to infectious diseases in animals, Science (80-), 318, 812, 10.1126/science.1148526
Rebl, 2010, Toll-like receptor signaling in bony fish, Vet. Immunol. Immunopathol., 134, 139, 10.1016/j.vetimm.2009.09.021
Reyes-Lopez, 2015, Differential immune gene expression profiles in susceptible and resistant full-sibling families of Atlantic salmon (Salmo salar) challenged with infectious pancreatic necrosis virus (IPNV), Dev. Comp. Immunol., 53, 210, 10.1016/j.dci.2015.06.017
Saarnisto, 2001, Deglaciation chronology of the Scandinavian Ice Sheet from the Lake Onega Basin to the Salpausselkä End Moraines, Glob. Planet. Change, 31, 387, 10.1016/S0921-8181(01)00131-X
Sadeghi, 2015, The retinoid-related orphan receptor alpha is essential for the end-stage effector phase of experimental epidermolysis bullosa acquisita, J. Pathol., 237, 111, 10.1002/path.4556
Sancho, 2002, Regulation of microtubule- organizing center orientation and actomyosin cytoskeleton rearrangement during immune interactions, Immunol. Rev., 189, 84, 10.1034/j.1600-065X.2002.18908.x
Schiöth, 2005, The GRAFS classification system of G-protein coupled receptors in comparative perspective, Gen. Comp. Endocrinol., 142, 94, 10.1016/j.ygcen.2004.12.018
Schlötterer, 2003, Hitchhiking mapping - functional genomics from the population genetics perspective, Trends Genet., 19, 32, 10.1016/S0168-9525(02)00012-4
Schröder, 2011, Viruses and the human DEAD-box helicase DDX3: inhibition or exploitation?, Biochem. Soc. Trans., 39, 679, 10.1042/BST0390679
Shiozaki, 1995, Counteractive roles of protein phosphatase 2C (PP2C) and a MAP kinase kinase homolog in the osmoregulation of fission yeast, EMBO J., 14, 492, 10.1002/j.1460-2075.1995.tb07025.x
Smit, 2007, Pharmacogenomic and structural analysis of constitutive G protein-coupled receptor activity, Annu. Rev. Pharmacol. Toxicol., 47, 53, 10.1146/annurev.pharmtox.47.120505.105126
Smout, 2009, A granulin-like growth factor secreted by the carcinogenic liver fluke, Opisthorchis viverrini, promotes proliferation of host cells, PLoS Pathog., 5, 1, 10.1371/journal.ppat.1000611
Sommer, 2005, The importance of immune gene variability (MHC) in evolutionary ecology and conservation, Front. Zool., 2, 1, 10.1186/1742-9994-2-1
Stanton, 2014, HCMV pUL135 remodels the actin cytoskeleton to impair immune recognition of infected cells, Cell Host Microbe, 16, 201, 10.1016/j.chom.2014.07.005
Sun, 2015, Nuclear receptor RORα regulates pathologic retinal angiogenesis by modulating SOCS3-dependent inflammation, PNAS, 112, 10401, 10.1073/pnas.1504387112
Sunyer, 2013, Fishing for mammalian paradigms in the teleost immune system, Nat. Immunol., 14, 1, 10.1038/ni.2549
Tadiso, 2011, Gene expression analyses of immune responses in Atlantic salmon during early stages of infection by salmon louse (Lepeophtheirus salmonis) revealed bi-phasic responses coinciding with the copepod-chalimus transition, BMC Genomics, 12, 1, 10.1186/1471-2164-12-141
Tolstikov, 2006, Mean multiannual temperature regime of the surface water layer in the near-shore regions of the White Sea, Oceanology, 46, 318, 10.1134/S0001437006030039
Tonteri, 2005, Phylogeography of anadromous and non-anadromous Atlantic salmon (Salmo salar) from northern Europe, Ann. Zool. Fenn., 41, 1
Tonteri, 2007, The effect of migratory behaviour on genetic diversity and population divergence: a comparison of anadromous and freshwater Atlantic salmon Salmo salar, J. Fish Biol., 70, 381, 10.1111/j.1095-8649.2007.01519.x
Tonteri, 2008, Use of differential expression data for identification of novel immune relevant expressed sequence tag-linked microsatellite markers in Atlantic salmon (Salmo salar L.), Mol. Ecol. Resour., 8, 1486, 10.1111/j.1755-0998.2008.02317.x
Tonteri, 2009, Microsatellites reveal clear genetic boundaries among Atlantic salmon (Salmo salar) populations from the Barents and White seas, northwest Russia, Can. J. Fish. Aquat. Sci., 66, 717, 10.1139/F09-010
Tonteri, 2010, Beyond MHC: signals of elevated selection pressure on Atlantic salmon (Salmo salar) immune-relevant loci, Mol. Ecol., 19, 1273, 10.1111/j.1365-294X.2010.04573.x
Trombetta, 2003, Activation of Lysosomal function during dendritic cell maturation, Science, 299, 1400, 10.1126/science.1080106
Vasemägi, 2005, Expressed sequence tag-linked microsatellites as a source of gene-associated polymorphisms for detecting signatures of divergent selection in Atlantic salmon (Salmo salar L.), Mol. Biol. Evol., 22, 1067, 10.1093/molbev/msi093
Vilas, 2015, A genome scan for candidate genes involved in the adaptation of turbot (Scophthalmus maximus), Mar. Genomics, 23, 77, 10.1016/j.margen.2015.04.011
Wagner, 2011, The pleiotropic structure of the genotype–phenotype map: the evolvability of complex organisms, Nat. Rev. Genet., 12, 204, 10.1038/nrg2949
Wang, 2011, Functional characterization of a nonmammalian IL-21: rainbow trout Oncorhynchus mykiss IL-21 upregulates the expression of the Th cell signature cytokines IFN-γ, IL-10, and IL-22, J. Immunol., 186, 708, 10.4049/jimmunol.1001203
Watkins, 2012, Monoubiquitination promotes calpain cleavage of the protein phosphatase 2A (PP2A) regulatory subunit a4, altering PP2A stability and microtubule-associated protein phosphorylation, J. Biol. Chem., 287, 24207, 10.1074/jbc.M112.368613
Whitlock, 2015, Reliable detection of loci responsible for local adaptation: inference of a null model through trimming the distribution of Fst, Am. Nat., 186, 26, 10.1086/682949
Winder, 2004, Climate change uncouples trophic interactions in an aquatic ecosystem, Ecology, 85, 2100, 10.1890/04-0151
Yamamoto, 1995, Two forms of Hox11, a T cell leukemia oncogene, are expressed in fetal spleen but not in primary lymphocytes, Mol. Immunol., 32, 1177, 10.1016/0161-5890(95)00100-X
Yang, 2006, Nuclear receptor expression links the circadian clock to metabolism, Cell, 126, 801, 10.1016/j.cell.2006.06.050
Yang, 2008, T helper 17 lineage differentiation is programmed by orphan nuclear receptors RORa and RORy, Immunity, 28, 29, 10.1016/j.immuni.2007.11.016
Zapata, 2006, Ontogeny of the immune system of fish, Fish Shellfish Immunol., 20, 126, 10.1016/j.fsi.2004.09.005
Zhu, 2013, Advances in research of fish immune-relevant genes: a comparative overview of innate and adaptive immunity in teleosts, Dev. Comp. Immunol., 39, 39, 10.1016/j.dci.2012.04.001
Zueva, 2014, Footprints of directional selection in wild Atlantic salmon populations: evidence for parasite-driven evolution?, PLoS One, 9, 1, 10.1371/journal.pone.0091672
