• Aucun résultat trouvé

Le présent mémoire influencera la gestion du Flétan du Groenland dans les régions du Saguenay, de l’estuaire, ainsi que du golfe du Saint-Laurent. La définition des stocks dans ces zones restait floue jusqu’à ce jour, en raison de la disparité des conclusions entre les études réalisées sur cette question. La grande puissance des marqueurs SNPs permet donc d’apporter une meilleure résolution des unités de gestion à prévaloir dans un plan de

conservation, basé sur les forces évolutives affectant la dynamique des populations du turbot, dans un contexte de changements climatiques, où l’environnement est en mutation. Ces résultats ont été combinés à des analyses de la connectivité de cette espèce entre l’est et l’ouest de l’Atlantique, des patrons de migrations et de l’effet de la température sur la croissance des juvéniles, puis présentées à divers gestionnaires du ministère Pêches et Océans Canada afin d’appliquer les principes de la gestion intégrée. Plus globalement, ce projet présente un exemple éloquent de l’importance des marqueurs liés au sexe dans les études employant le séquençage de haut débit. De plus, ce projet n’appuie pas l’utilisation des micro-haplotypes comme une solution potentielle au manque de puissance d’assignation lors d’étude de génomique des populations d’espèces halieutiques ou, plus largement, d’espèces ayant une faible différenciation génétique entre les populations.

Bibliographie

Albert, O. T., and Vollen, T. (2014). A major nursery area around the Svalbard archipelago provides recruits for the stocks in both Greenland halibut management areas in the Northeast Atlantic. ICES Journal of Marine Science: Journal du Conseil, fsu191.

Alexander, D. H., Novembre, J. and Lange, K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome research, 19(9), 1655-1664.

Aljanabi, S. M. and I. Martinez (1997). Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Research 25(22): 4692-4693. Allendorf, F. W., Hohenlohe, P. A., and Luikart, G. (2010). Genomics and the future of conservation genetics. Nature reviews genetics, 11(10), 697-709.

Anderson, E. C., and Thompson, E. A. (2002). A model-based method for identifying species hybrids using multilocus genetic data. Genetics, 160(3), 1217-1229.

Anderson, E. C., Waples, R. S., and Kalinowski, S. T. (2008). An improved method for predicting the accuracy of genetic stock identification. Canadian Journal of Fisheries and Aquatic Sciences, 65(7), 1475-1486.

Andrews, K. R., Good, J. M., Miller, M. R., Luikart, G. and Hohenlohe, P. A. (2016). Harnessing the power of RADseq for ecological and evolutionary genomics. Nature Reviews Genetics, 17(2), 81.

Arthur, J. R. and E. Albert (1993). Use of parasites for separating stocks of Greenland halibut (Reinhardtius hippoglossoides) in the canadian northwest Atlantic. Canadian Journal of Fisheries and Aquatic Sciences 50(10): 2175-2181.

Bailey, K. M. (1997). Structural dynamics and ecology of flatfish populations. Journal of Sea Research, 37(3), 269-280.

Baetscher, D. S., Anderson, E. C., Gilbert‐Horvath, E. A., Malone, D. P., Saarman, E. T., Carr, M. H., and Garza, J. C. (2019). Dispersal of a nearshore marine fish connects marine reserves and adjacent fished areas along an open coast. Molecular ecology, 28(7), 1611- 1623.

Baetscher, D. S., Clemento, A. J., Ng, T. C., Anderson, E. C., and Garza, J. C. (2018). Microhaplotypes provide increased power from short‐read DNA sequences for relationship inference. Molecular ecology resources, 18(2), 296-305.

Barth, J. M., Berg, P. R., Jonsson, P. R., Bonanomi, S., Corell, H., Hemmer‐Hansen, J., Moksnes, P. O., Johannesson, K., Jorde, P. E., Knutsen, H., Moksnes, P.-O., Star, B., Stenseth, N. C., Svedang, H., Jentoft, S. and André, C. (2017). Genome architecture enables local adaptation of Atlantic cod despite high connectivity. Molecular ecology, 26(17), 4452-4466.

Beacham, T. D., Wallace, C., MacConnachie, C., Jonsen, K., McIntosh, B., Candy, J. R., Devlin, R. H. and Withler, R. E. (2017). Population and individual identification of coho salmon in British Columbia through parentage-based tagging and genetic stock identification: an alternative to coded-wire tags. Canadian journal of fisheries and aquatic sciences, 74(9), 1391-1410.

Beck, M. W., Heck Jr, K. L., Able, K. W., Childers, D. L., Eggleston, D. B., Gillanders, B. M., Halpern, B., Hays, C. G., Hoshino, K., Minello, T. J., Orth, R. J., Sheridan, P. F. and M. R. Weinstein. (2001). The identification, conservation, and management of estuarine and marine nurseries for fish and invertebrates. Bioscience 51(8): 633-641.

Begg, G. A., K. D. Friedland and J. B. Pearce. (1999). Stock identification and its role in stock assessment and fisheries management: an overview. Fisheries Research 43(1-3): 1- 8.

Bell, H. L. (1982). Sexual differences in the foraging behaviour of the frill‐necked flycatcher Arses telescopthalmus in New Guinea. Australian Journal of Ecology, 7(2), 137-147. Benestan, L., Gosselin, T., Perrier, C., Sainte‐Marie, B., Rochette, R., and Bernatchez, L. (2015). RAD genotyping reveals fine‐scale genetic structuring and provides powerful population assignment in a widely distributed marine species, the A merican lobster (H

omarus americanus). Molecular ecology, 24(13), 3299-3315.

Benestan, L., Moore, J. S., Sutherland, B. J., Le Luyer, J., Maaroufi, H., Rougeux, C., Normandeau, E., Rycroft, N., Attema, J., Harris, L. N., Tallman, R. F., Greenwood S. J., Clark F. K. and L. Bernatchez. (2017). Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems. Molecular ecology, 26(24), 6767-6783.

Berg, P. R., Star, B., Pampoulie, C., Bradbury, I. R., Bentzen, P., Hutchings, J. A., and Jakobsen, K. S. (2017). Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions. Heredity, 119(6), 418.

Bohonak, A. J., & Jenkins, D. G. (2003). Ecological and evolutionary significance of dispersal by freshwater invertebrates. Ecology letters, 6(8), 783-796.

Boje, J. (2002). Intermingling and seasonal migrations of Greenland halibut (Reinhardtius

hippoglossoides) populations determined from tagging studies. Fishery Bulletin, 100(3),

414-422.

Bowering, W. R., and W. B. Brodie (1995). Greenland halibut (Reinhardtius

hippoglossoides). A review of the dynamics of its distribution and fisheries off eastern

Canada and Greenland. Deep-water fisheries of the North Atlantic Oceanic slope (pp. 113- 160). Springer Netherlands.

Bowering, W. R. (1988). An analysis of morphometric characters of Greenland halibut (Reinhardtius hippoglossoides) in the northwest Atlantic using a multivariate-analysis of covariance. Canadian Journal of Fisheries and Aquatic Sciences 45(4): 580-585.

Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A., and Cresko, W. A. (2013). Stacks: an analysis tool set for population genomics. Molecular ecology, 22(11), 3124- 3140.

Chen, K. Y., Marschall, E. A., Sovic, M. G., Fries, A. C., Gibbs, H. L., and Ludsin, S. A. (2018). assign POP: An r package for population assignment using genetic, non‐genetic, or integrated data in a machine‐learning framework. Methods in Ecology and Evolution, 9(2), 439-446.

Christie, M. R. (2010). Parentage in natural populations: novel methods to detect parent‐ offspring pairs in large data sets. Molecular Ecology Resources, 10(1), 115-128.

Collins, F. S., Guyer, M. S., & Chakravarti, A. (1997). Variations on a theme: cataloging human DNA sequence variation. Science, 278(5343), 1580-1581.

Cornuet, J. M., Piry, S., Luikart, G., Estoup, A., and Solignac, M. (1999). New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics, 153(4), 1989-2000.

Cote, J., Clobert, J., Brodin, T., Fogarty, S., & Sih, A. (2010). Personality-dependent dispersal: characterization, ontogeny and consequences for spatially structured populations. Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1560), 4065-4076.

Cooper, D. W., Maslenikov, K. R., and Gunderson, D. R. (2007). Natural mortality rate, annual fecundity, and maturity at length for Greenland halibut (Reinhardtius

hippoglossoides) from the northeastern Pacific Ocean. Fishery Bulletin, 105(2), 296-304.

Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G., Marth, G. T., Sherry, S. T., McVean, G. and Durbin R. (2011). The variant call format and VCFtools. Bioinformatics, 27(15), 2156-2158.

Dann, T. H., Habicht, C., Baker, T. T., and Seeb, J. E. (2013). Exploiting genetic diversity to balance conservation and harvest of migratory salmon. Canadian Journal of Fisheries and Aquatic Sciences, 70(5), 785-793.

Dahlgren, C., Kellison, G., Adams, A., Gillanders, B., Kendall, M., Layman, C., Ley, J. A., Nagelkerken, I. and Serafy, J. (2006). Marine nurseries and effective juvenile habitats: concepts and applications. Marine Ecology Progress Series 312: 291-295.

Davey, J. W., P. A. Hohenlohe, P. D. Etter, J. Q. Boone, J. M. Catchen and L. M. Blaxter (2011). Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics 12(7): 499-510.

Devloo‐Delva, F., Maes, G. E., Hernández, S. I., Mcallister, J. D., Gunasekera, R. M., Grewe, P. M., Thomson, R. B. and Feutry, P. (2019). Accounting for kin sampling reveals genetic connectivity in Tasmanian and New Zealand school sharks, Galeorhinus

De Wit, P., M. H. Pespeni and S. R. Palumbi. (2015). SNP genotyping and population genomics from expressed sequences - current advances and future possibilities. Molecular Ecology 24(10): 2310-2323.

DFO, 2003. Updated estimates of exploitation from tagging of Atlantic cod (Gadus morhua) in NAFO Subdiv. 3Ps during 1997-2003. Canadian Scientific Advisory Secretariat Science Advisory Report, vol. 2003/091. Canadian Scientific Advisory Secretariat, p. 31. DFO, 2012. Assessment of Greenland Halibut (Reinhardtius hippoglossoides) stock status in the Gulf of St. Lawrence (4RST) in 2010 and diet description for this population. Canadian Scientific Advisory Secretariat Science Advisory Report, vol. 2012/140. Canadian Scientific Advisory Secretariat, p. 86.

DFO, 2013. Oceanographic Conditions in the Atlantic Zone in 2012. Canadian Scientific Advisory Secretariat Science Advisory Report, vol. 2013/057. Canadian Scientific Advisory Secretariat, p. 18.

DFO, 2015. Assessment of Greenland Halibut in the Gulf of St. Lawrence (4RST) in 2014. DFO Canadian Scientific Advisory Secretariat Science Report, 2015/056. Canadian Scientific Advisory Secretariat, p. 16.

DFO, 2019. Assessment of the Gulf of St. Lawrence (4RST) Greenland Halibut stock in 2018. DFO Canadian Scientific Advisory Secretariat Science Report, 2019/023. Canadian Scientific Advisory Secretariat, p. 23.

Dingle, H., & Drake, V. A. (2007). What is migration?. Bioscience, 57(2), 113-121.

Duong, T. Y., Scribner, K. T., Forsythe, P. S., Crossman, J. A., and Baker, E. A. (2013). Interannual variation in effective number of breeders and estimation of effective population size in long‐lived iteroparous lake sturgeon (Acipenser fulvescens). Molecular Ecology, 22(5), 1282-1294.

Dupont-Prinet, A., Vagner, M., Chabot, D., and Audet, C. (2013). Impact of hypoxia on the metabolism of Greenland halibut (Reinhardtius hippoglossoides). Canadian Journal of Fisheries and Aquatic Sciences, 70(3), 461-469.

Ekblom, R. and Galindo, J. (2011). Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity, 107(1), 1.

Elliott, N. G., Haskard, K. and Koslow, J. A. (1995). Morphometric analysis of orange roughy (Hoplostethus atlanticus) off the continental slope of southern Australia. Journal of Fish Biology, 46(2), 202-220.

Elshire, R. J., Glaubitz, J. C., Sun, Q., Poland, J. A., Kawamoto, K., Buckler, E. S., and Mitchell, S. E. (2011). A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PloS one, 6(5), e19379.

Ensing, D., Crozier, W. W., Boylan, P., O'Maoiléidigh, N., and McGinnity, P. (2013). An analysis of genetic stock identification on a small geographical scale using microsatellite markers, and its application in the management of a mixed‐stock fishery for Atlantic salmon Salmo salar in Ireland. Journal of fish biology, 82(6), 2080-2094.

Fairbairn, D. J. (1981). Biochemical genetic analysis of population differentiation in Greenland halibut (Reinhardtius hippoglossoides) from the Northwest Atlantic, Gulf of St. Lawrence, and Bering Sea. Canadian Journal of Fisheries and Aquatic Sciences, 38(6), 669-677.

FAO. 2016. Climate Change Implications for fisheries and aquaculture: Summary of the

findings of the Intergovernmental Panel on Climate Change Fifth Assessment Report, by Seggel, A., DeYoung, C. & Soto, D. FAO Fisheries and Aquaculture Circular No. 1122. Italy.

FAO. 2018. The State of World Fisheries and Aquaculture - 2018 (SOFIA). Rome, Italy Foll, M., and Gaggiotti, O. (2008). A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics, 180(2), 977-993.

Ford, M., Pearsons, T. N., and Murdoch, A. (2015). The spawning success of early maturing resident hatchery Chinook salmon in a natural river system. Transactions of the American Fisheries Society, 144(3), 539-548.

Fraser, D. J., Debes, P. V., Bernatchez, L., and Hutchings, J. A. (2014). Population size, habitat fragmentation, and the nature of adaptive variation in a stream fish. Proceedings of the Royal Society B: Biological Sciences, 281(1790), 20140370.

Gagnaire, P. A., Broquet, T., Aurelle, D., Viard, F., Souissi, A., Bonhomme, F., Arnaud- Haond, S. and Bierne, N. (2015). Using neutral, selected, and hitchhiker loci to assess connectivity of marine populations in the genomic era. Evolutionary applications, 8(8), 769- 786.

Galbraith, P. S., Chassé, J., Gilbert, D., Larouche, P., Caverhill, C., Brickman, D., Lefaivre, D., Pettigrew, B., Denive, L., and Lafleur, C. (2017). Physical oceanographic conditions in the Gulf of St. Lawrence in 2016 (pp. v+-91). Canadian Science Advisory Secretariat. Gamble, T. and Zarkower, D. (2014). Identification of sex‐specific molecular markers using restriction site‐associated DNA sequencing. Molecular Ecology Resources, 14(5), 902- 913.

Ghinter, L., Lambert, Y., and Audet, C. (2019). Influence of sex on growth of juvenile Greenland halibut (Reinhardtius hippoglossoides) in the Estuary and Gulf of St. Lawrence. Fisheries Research, 219, 105332.

Gilbert D., Sundby B., Gobeil C., Mucci A. and Tremblay G.-H. (2005). A seventy-two-year record of diminishing deep-water oxygen in the St. Lawrence estuary: the northwest Atlantic connection. Limnol. Oceanogr. 50: 1654-1666

Gomaa, N. H., MONTESINOS‐NAVARRO, A. L. I. C. I. A., ALONSO‐BLANCO, C. A. R. L. O. S., and Pico, F. X. (2011). Temporal variation in genetic diversity and effective population size of Mediterranean and subalpine Arabidopsis thaliana

González-Astorga, J., and Núñez-Farfán, J. (2001). Effect of habitat fragmentation on the genetic structure of the narrow endemic Brongniar tia vazquezii. Evolutionary Ecology Research, 3(7), 861-872.

Goudet, J. (2005). Hierfstat, a package for R to compute and test hierarchical F‐statistics. Molecular Ecology Resources, 5(1), 184-186.

Griffiths, A. M., Machado-Schiaffino, G., Dillane, E., Coughlan, J., Horreo, J. L., Bowkett, A. E., Minting, P., Toms, S., Roche, W., Gragan, P., McGinnity, P., Cross, T., Bright, D., Garcia-Vazquez, E. and Stevens (2010). Genetic stock identification of Atlantic salmon (Salmo salar) populations in the southern part of the European range. BMC genetics, 11(1), 31.

Hall, M. A. (1996). On bycatches. Reviews in fish biology and fisheries, 6(3), 319-352. Han, G., Loder, J. W. and Smith, P. C. (1999). Seasonal-mean hydrography and circulation in the Gulf of St. Lawrence and on the eastern Scotian and southern Newfoundland shelves. Journal of Physical Oceanography, 29(6), 1279-1301.

Hilborn, R., & Walters, C. J. (Eds.). (2013). Quantitative fisheries stock assessment: choice, dynamics and uncertainty. Springer Science & Business Media.

Hellberg, M. E., Burton, R. S., Neigel, J. E., & Palumbi, S. R. (2002). Genetic assessment of connectivity among marine populations. Bulletin of marine science, 70(1), 273-290. Hoarau, G., Rijnsdorp, A. D., Van der Veer, H. W., Stam, W. T., and Olsen, J. L. (2002). Population structure of plaice (Pleuronectes platessa L.) in northern Europe: microsatellites revealed large‐scale spatial and temporal homogeneity. Molecular Ecology, 11(7), 1165-1176.

Israel, J. A., Cordes, J. F., Blumberg, M. A., and May, B. (2004). Geographic patterns of genetic differentiation among collections of green sturgeon. North American Journal of Fisheries Management, 24(3), 922-931.

Jackson, T. M., Roegner, G. C., and O'Malley, K. G. (2018). Evidence for interannual variation in genetic structure of Dungeness crab (Cancer magister) along the California Current System. Molecular ecology, 27(2), 352-368.

Jombart, T. (2008). adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics, 24(11), 1403-1405.

Jørgensen, O. A., & Arboe, N. H. (2013). Distribution of the commercial fishery for Greenland halibut and Northern shrimp in Baffin Bay.

Junquera, S., Roman, E., Morgan, J., Sainza, M. and Ramilo, G. (2003). Time scale of ovarian maturation in Greenland halibut (Reinhardtius hippoglossoides, Walbaum). ICES Journal of Marine Science, 60(4), 767-773.

Khan, R. A., M. Dawe, R. Bowering and R. K. Misra (1982). Blood protozoa as an aid for seperating stocks of Greenland halibut, Reinhardtius hippoglossoides, in the northwest Atlantic. Canadian Journal of Fisheries and Aquatic Sciences 39(9): 1317-1322.

Kidd, K. K., and Speed, W. C. (2015). Criteria for selecting microhaplotypes: mixture detection and deconvolution. Investigative genetics, 6(1), 1.

Kidd, K. K., Pakstis, A. J., Speed, W. C., Lagace, R., Chang, J., Wootton, S., and Ihuegbu, N. (2013). Microhaplotype loci are a powerful new type of forensic marker. Forensic Science International: Genetics Supplement Series, 4(1), e123-e124.

Kidd, K. K., Pakstis, A. J., Speed, W. C., Lagacé, R., Chang, J., Wootton, S., Haigh, E. and Kidd, J. R. (2014). Current sequencing technology makes microhaplotypes a powerful new type of genetic marker for forensics. Forensic Science International: Genetics, 12, 215-224.

Kirtman, B., Power, S. B., Adedoyin, A. J., Boer, G. J., Bojariu, R., Camilloni, I., Doblas- Reyes, F., Fiore A. M. & Prather, M. (2013). Near-term climate change: projections and predictability.

Larson, W. A., Utter, F. M., Myers, K. W., Templin, W. D., Seeb, J. E., Guthrie III, C. M., and Seeb, L. W. (2012). Single-nucleotide polymorphisms reveal distribution and migration of Chinook salmon (Oncorhynchus tshawytscha) in the Bering Sea and North Pacific Ocean. Canadian Journal of Fisheries and Aquatic Sciences, 70(1), 128-141.

Lemopoulos, A., Prokkola, J. M., Uusi‐Heikkilä, S., Vasemägi, A., Huusko, A., Hyvärinen, P., Koljonen, M-L, Koskiniemi, J. and Vainikka, A. (2019). Comparing RADseq and microsatellites for estimating genetic diversity and relatedness—Implications for brown trout conservation. Ecology and Evolution, 9(4), 2106-2120.

Lewison, R. L., Soykan, C. U., Cox, T., Peckham, H., Pilcher, N., LeBoeuf, N., MacDonald, S., Moore, J., Safina, C. and Crowder, L. B. (2011). Ingredients for addressing the challenges of fisheries bycatch. Bulletin of Marine Science, 87(2), 235-250.

Li, H., and Durbin, R. (2009). Fast and accurate short read alignment with Burrows– Wheeler transform. bioinformatics, 25(14), 1754-1760.

Liebgold, E. B., Gerlach, N. M., and Ketterson, E. D. (2019). Density‐dependent fitness, not dispersal movements, drives temporal variation in spatial genetic structure in dark‐ eyed juncos (Junco hyemalis). Molecular ecology, 28(5), 968-979.

Lischer, H. E., and Excoffier, L. (2011). PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics, 28(2), 298-299. Lotterhos, K. E., and Whitlock, M. C. (2015). The relative power of genome scans to detect local adaptation depends on sampling design and statistical method. Molecular ecology, 24(5), 1031-1046.

Lowe, W. H., & Allendorf, F. W. (2010). What can genetics tell us about population connectivity?. Molecular ecology, 19(15), 3038-3051.

Luikart, G., P. R. England, D. Tallmon, S. Jordan and P. Taberlet (2003). The power and promise of population genomics: From genotyping to genome typing. Nature Reviews Genetics 4(12): 981-994.

Manel, S., O. E. Gaggiotti and R. S. Waples (2005). Assignment methods: matching biological questions techniques with appropriate. Trends in Ecology & Evolution 20(3): 136-142.

Marchini, J., Howie, B., Myers, S., McVean, G. and Donnelly, P. (2007). A new multipoint method for genome-wide association studies by imputation of genotypes. Nature genetics, 39(7), 906-913.

Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. journal, 17(1), 10-12.

Mascher, M., Muehlbauer, G. J., Rokhsar, D. S., Chapman, J., Schmutz, J., Barry, K., ... and Himmelbach, A. (2013). Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). The Plant Journal, 76(4), 718-727.

McCormack, J. E., Hird, S. M., Zellmer, A. J., Carstens, B. C. and Brumfield, R. T. (2013). Applications of next-generation sequencing to phylogeography and phylogenetics. Molecular phylogenetics and evolution, 66(2), 526-538.

McKinney, G. J., Seeb, J. E., and Seeb, L. W. (2017). Managing mixed-stock fisheries: genotyping multi-SNP haplotypes increases power for genetic stock identification. Canadian Journal of Fisheries and Aquatic Sciences, 74(4), 429-434.

Meirmans, P. G., and Van Tienderen, P. H. (2004). GENOTYPE and GENODIVE: two programs for the analysis of genetic diversity of asexual organisms. Molecular Ecology Notes, 4(4), 792-794.

Metzker, M. L. (2010). Sequencing technologies—the next generation. Nature reviews genetics, 11(1), 31-46.

Messmer, A. M., Leong, J. S., Rondeau, E. B., Mueller, A., Despins, C. A., Minkley, D. R., Kent, M. P., Lien, S., Boyce, B., Morrison, B., Fast, M. D., Norman J. D., Danzmann, J. D. and Koop, B. F. (2018). A 200K SNP chip reveals a novel Pacific salmon louse genotype linked to differential efficacy of emamectin benzoate. Marine genomics, 40, 45-57.

Meyer, C. L., Vitalis, R., Saumitou‐Laprade, P. and Castric, V. (2009). Genomic pattern of adaptive divergence in Arabidopsis halleri, a model species for tolerance to heavy metal. Molecular Ecology, 18(9), 2050-2062.

Ministère de l’Agriculture des Pêcheries et de l’Alimentation. Monographie de l’industrie du flétan du Groenland au Québec. 2014

Moore, J. S., and Benestan, L. (2018). Let's talk about sex: A rigorous statistical framework to assign the sex of individuals from reduced‐representation sequencing data. Molecular ecology resources, 18(2), 191-193.

Morgan, M. J. and W. R. Bowering (1997). Temporal and geographic variation in maturity at length and age of Greenland halibut (Reinhardtius hippoglossoides) from the Canadian north-west Atlantic with implications for fisheries management. Ices Journal of Marine Science 54(5): 875-885.

Morgan, M. J., Bowering, W. R., Gundersen, A. C., Hoines, A., Morin, B., Smirnov, O., and Hjorleifsson, E. (2003). A comparison of the maturation of Greenland halibut (Reinhardtius hippoglossoides) from populations throughout the North Atlantic. Journal of Northwest Atlantic Fishery Science, 31, 99.

NAFO. MS 1994. Report of Scientific Council, 8–22 June 1994 meeting. NAFO SCS Doc., No. 19, Serial No. N2435, 88 p.

Narum, S. R., Buerkle, C. A., Davey, J. W., Miller, M. R., and Hohenlohe, P. A. (2013). Genotyping‐by‐sequencing in ecological and conservation genomics. Molecular ecology, 22(11), 2841-2847.

Northridge, S. P. (1991). Driftnet fisheries and their impacts on non-target species: a worldwide review. FAO Fisheries Technical Paper, No.320. Rome, FAO. 1991. 115p. Ogata, M., Lambert, M., Ezaz, T., and Miura, I. (2018). Reconstruction of female heterogamety from admixture of XX‐XY and ZZ‐ZW sex‐chromosome systems within a frog species. Molecular ecology, 27(20), 4078-4089.

Oksanen, J., Kindt, R., Legendre, P., O’Hara, B., Stevens, M. H. H., Oksanen, M. J., & Suggests, M. A. S. S. (2007). The vegan package. Community ecology package, 10, 631- 637.

O'Malley, K. G., Camara, M. D., and Banks, M. A. (2007). Candidate loci reveal genetic differentiation between temporally divergent migratory runs of Chinook salmon (Oncorhynchus tshawytscha). Molecular ecology, 16(23), 4930-4941.

Paetkau, D., Calvert, W., Stirling, I., & Strobeck, C. (1995). Microsatellite analysis of population structure in Canadian polar bears. Molecular ecology, 4(3), 347-354.

Paetkau, D., Slade, R., Burden, M. and Estoup, A. (2004). Genetic assignment methods for the direct, real‐time estimation of migration rate: a simulation‐based exploration of accuracy and power. Molecular ecology, 13(1), 55-65.

Palumbi, S. R. (2004). Marine reserves and ocean neighborhoods: the spatial scale of marine populations and their management. Annu. Rev. Environ. Resour., 29, 31-68.

Pêche et Océans Canada. Évaluation du flétan du Groenland du golfe du Saint-Laurent (4RST) en 2014. 2015

Peklova, I., Hussey, N. E., Hedges, K. J., Treble, M. A. and A. T. Fisk, (2012). Depth and temperature preferences of the deepwater flatfish Greenland halibut Reinhardtius

hippoglossoides in an Arctic marine ecosystem. Marine Ecology Progress Series, 467,

193-205.

Palumbi, S. R. (2004). Marine reserves and ocean neighborhoods: the spatial scale of marine populations and their management. Annu. Rev. Environ. Resour., 29, 31-68.

Pritchard, J. K., Stephens, M. and P. Donnelly. (2000). Inference of population structure using multilocus genotype data. Genetics, 155(2), 945-959.

Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., ... & Sham, P. C. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. The American journal of human genetics, 81(3), 559-575.

Rannala, B. and J. L. Mountain. (1997). Detecting immigration by using multilocus genotypes. Proceedings of the National Academy of Sciences, 94(17), 9197-9201.

Riginos, C., Crandall, E. D., Liggins, L., Bongaerts, P., & Treml, E. A. (2016). Navigating the currents of seascape genomics: how spatial analyses can augment population genomic studies. Current zoology, 62(6), 581-601.

Roy, D., D. C. Hardie, MA. Treble, J. D. Reist and D. E. Ruzzante. (2014). Evidence supporting panmixia in Greenland halibut (Reinhardtius hippoglossoides) in the Northwest Atlantic. Canadian Journal of Fisheries and Aquatic Sciences 71(5): 763-774.

Reid, D. P., Smith, C. A., Rommens, M., Blanchard, B., Martin-Robichaud, D., & Reith, M. (2007). A genetic linkage map of Atlantic halibut (Hippoglossus hippoglossus L.). Genetics, 177(2), 1193-1205.

Riget, F. and Boje, J. (1989). Fishery and some biological aspects of Greenland halibut (Reinhardtius hippoglossoides) in West Greenland waters. Northwest Atlantic Fisheries Organization Scientific Council Studies, (13), 41-52.

Sampson, J. N., Kidd, K. K., Kidd, J. R., & Zhao, H. (2011). Selecting SNPs to identify ancestry. Annals of human genetics, 75(4), 539-553.

Saucier, F. J., Roy, F., Gilbert, D., Pellerin, P., and Ritchie, H. (2003). Modeling the formation and circulation processes of water masses and sea ice in the Gulf of St. Lawrence, Canada. Journal of Geophysical Research: Oceans, 108(C8).

Satterthwaite, W. H., Ciancio, J., Crandall, E., Palmer-Zwahlen, M. L., Grover, A. M., O’Farrell, M. R., Anderson, E. C., Mohr, M. S., and Garza, J. C. (2015). Stock composition and ocean spatial distribution inference from California recreational Chinook salmon fisheries using genetic stock identification. Fisheries research, 170, 166-178.

Smedbol, R. K., & Wroblewski, J. S. (2002). Metapopulation theory and northern cod population structure: interdependency of subpopulations in recovery of a groundfish population. Fisheries Research, 55(1-3), 161-174.

Sohn, D., Ciannelli, L., & Duffy‐Anderson, J. T. (2010). Distribution and drift pathways of Greenland halibut (Reinhardtius hippoglossoides) during early life stages in the eastern Bering Sea and Aleutian Islands. Fisheries Oceanography, 19(5), 339-353.

Tian, C., Kosoy, R., Lee, A., Ransom, M., Belmont, J. W., Gregersen, P. K., and Seldin, M. F. (2008). Analysis of East Asia genetic substructure using genome-wide SNP arrays. PLoS One, 3(12), e3862.

Van Dyck, H., & Baguette, M. (2005). Dispersal behaviour in fragmented landscapes: routine or special movements?. Basic and Applied Ecology, 6(6), 535-545.

Vrana R. K. and W. Wheeler. (1992) Individual organisms as terminal entities: laying the species problem to rest. Cladistics 8: 67–72.

Li, Y. H., & Wang, H. P. (2017). Advances of genotyping-by-sequencing in fisheries and aquaculture. Reviews in fish biology and fisheries, 27(3), 535-559.

Waples, R. S. and Gaggiotti, O. (2006). What is a population? An empirical evaluation of

Documents relatifs