pseudotetraploid salmonids. BMC Genomics, 8(1), 422. https://doi.org/10.1186/1471-2164-8-422

De Coster, W., D'Hert, S., Schultz, D. T., Cruts, M., & Van Broeckhoven, C. (2018). NanoPack: Visualizing and processing long-read sequencing data. *Bioinformatics*, 34(15), 2666-2669. https://doi.org/10.1093/bioinformatics/bty149

De Coster, W., Weissensteiner, M. H., & Sedlazeck, F. J. (2021). Towards population-scale long-read sequencing. *Nature Reviews Genetics*, 22(9), 572-587. https://doi.org/10.1038/s41576-021-00367-3

Debes, P. V., Piavchenko, N., Ruokolainen, A., Ovaskainen, O., Moustakas-Verho, J. E., Parre, N., Aykanat, T., Erkinaro, J., & Primmer, C. R. (2021). Polygenic and major-locus contributions to sexual maturation timing in Atlantic salmon. *Molecular Ecology*, 30(18), 4505-4519. https://doi.org/10.1111/mec.16062

Delahaye, C., & Nicolas, J. (2021). Sequencing DNA with nanopores: Troubles and biases. *PLoS One*, 16(10), e0257521. https://doi.org/10.1371/journal.pone.0257521

Dionne, M., Caron, F., Dodson, J. J., & Bernatchez, L. (2008). Landscape genetics and hierarchical genetic structure in Atlantic salmon: The interaction of gene flow and local adaptation. *Molecular Ecology*, 17(10), 2382-2396. https://doi.org/10.1111/j.1365-294X.2008.03771.x

Dorant, Y., Cayuela, H., Wellband, K., Laporte, M., Rougemont, Q., Mérot, C., Normandeau, E., Rochette, R., & Bernatchez, L. (2020). Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species. *Molecular Ecology*, 18, 4765-4782. https://doi.org/10.1111/mec.15565

Ebbesson, L. O. E., Ekström, P., Ebbesson, S. O. E., Stefansson, S. O., & Holmqvist, B. (2003). Neural circuits and their structural and chemical reorganization in the light-brain-pituitary axis during parr-smolt transformation in salmon. *Aquaculture*, 222(1), 59-70. https://doi.org/10.1016/S0044-8486(03)00102-9

Eisbrenner, W. D., Botwright, N., Cook, M., Davidson, E. A., Dominik, S., Elliott, N. G., Henshall, J., Jones, S. L., Kube, P. D., Lubieniecki, K. P., Peng, S., & Davidson, W. S. (2014). Evidence for multiple sex-determining loci in Tasmanian Atlantic salmon (*Salmo salar*). *Heredity*, 113(1), 86-92. https://doi.org/10.1038/hdy.2013.55

Feuk, L., Carson, A. R., & Scherer, S. W. (2006). Structural variation in the human genome. *Nature Reviews Genetics*, 7(2), 85-97. https://doi.org/10.1038/nrg1767

Feuk, L., Marshall, C. R., Wintle, R. F., & Scherer, S. W. (2006). Structural variants: Changing the landscape of chromosomes and design of disease studies. *Human Molecular Genetics*, 15, R57-R66. https://doi.org/10.1093/hmg/ddl057

Fontaine, P.-M., Levesque, F., Proulx, M., & Heppell, M. (2000). *Étude du saumon de la rivière Romaine en 1999 - Rapport présenté à la direction Expertise et support technique de production*. Hydro-Québec par le Groupe conseil GENIVAR.

Forester, B. R., Laporte, M., & Manel, S. (2018). Detecting multilocus adaptation using redundancy analysis (RDA). https://popgen.nescent.org/2018-03-27_RDA_GEA.html

Forester, B. R., Lasky, J. R., Wagner, H. H., & Urban, D. L. (2018). Comparing methods for detecting multilocus adaptation with multivariate genotype-environment associations. *Molecular Ecology*, 27(9), 2215-2233. https://doi.org/10.1111/mec.14584

Fraser, D. J., & Bernatchez, L. (2005). Adaptive migratory divergence among sympatric brook charr populations. *Evolution*, 59(3), 611-624. https://doi.org/10.1111/j.0014-3820.2005.tb01020.x

Gamazon, E. R., & Stranger, B. E. (2015). The impact of human copy number variation on gene expression. *Briefings in Functional Genomics*, 14(5), 352-357. https://doi.org/10.1093/bfgp/elv017

GENIVAR. (2002). *Aménagement hydroélectrique de la Romaine-1 – Étude de la population de saumon atlantique de la rivière Romaine en 2001*. GENIVAR.

Gjedrem, T., & Rye, M. (2018). Selection response in fish and shellfish: A review. *Reviews in Aquaculture*, 10(1), 168-179. https://doi.org/10.1111/raq.12154

Hämälä, T., Wafula, E. K., Guiltinan, M. J., Ralph, P. E., dePamphilis, C. W., & Tiffin, P. (2021). Genomic structural variants constrain and facilitate adaptation in natural populations of *Theobroma cacao*, the chocolate tree. *Proceedings of the National Academy of Sciences*, 118(35), e2102914118. https://doi.org/10.1073/pnas.2102914118

Harris, R. S. (2007). *Improved pairwise alignment of genomic DNA. (Philosophiae Doctor (PhD)).* The Pennsylvania State University.

Heller, D., & Vingron, M. (2019). SVIM: Structural variant identification using mapped long reads. *Bioinformatics*, 35(17), 2907-2915. https://doi.org/10.1093/bioinformatics/btz041

Hickey, G., Heller, D., Monlong, J., Sibbesen, J. A., Sirén, J., Eizenga, J., Dawson, E. T., Garrison, E., Novak, A. M., & Paten, B. (2020). Genotyping structural variants in pangenome graphs using the vg toolkit. *Genome Biology*, 21(1), 35. https://doi.org/10.1186/s13059-020-1941-7

Ho, S. V. S., Urban, A. E., & Mills, R. E. (2020). Structural variation in the sequencing era. *Nature Reviews Genetics*, 21(3), 171-189. https://doi.org/10.1038/s41576-019-0180-9

Hoar, W. S. (1988). The physiology of smolting salmonids. In W. S. Hoar & D. J. Randall (Eds.), *Fish physiology* (Vol. 11, pp. 275-343). Academic Press.

Houston, R. D., & Macqueen, D. J. (2019). Atlantic salmon (*Salmo salar* L.) genetics in the 21st century: Taking leaps forward in aquaculture and biological understanding. *Animal Genetics*, 50(1), 3-14. https://doi.org/10.1111/age.12748

Hübner, S. (2022). Are we there yet? Driving the road to evolutionary graph-pangenomics. *Current Opinion in Plant Biology*, 66, 102195. https://doi.org/10.1016/j.pbi.2022.102195

Huddleston, J., Chaisson, M. J. P., Steinberg, K. M., Warren, W., Hoekzema, K., Gordon, D., Graves-Lindsay, T. A., Munson, K. M., Kronenberg, Z. N., Vives, L., Peluso, P., Boitano, M., Chin, C. S., Korlach, J., Wilson, R. K., & Eichler, E. E. (2017). Discovery and genotyping of structural variation from long-read haploid genome sequence data. *Genome Research*, 27(5), 677-685. https://doi.org/10.1101/gr.214007.116

Jain, C., Rhie, A., Hansen, N. F., Koren, S., & Phillippy, A. M. (2022). Long-read mapping to repetitive reference sequences using Winnowmap2. *Nature Methods*, 19(6), 705-710. https://doi.org/10.1038/s41592-022-01457-8

Jain, C., Rhie, A., Zhang, H., Chu, C., Walenz, B. P., Koren, S., & Phillippy, A. M. (2020). Weighted minimizer sampling improves long read mapping. *Bioinformatics*, 36(Supplement_1), i111-i118. https://doi.org/10.1093/bioinformatics/btaa435

Jones, F. C., Grabherr, M. G., Chan, Y. F., Russell, P., Mauceli, E., Johnson, J., Swofford, R., Pirun, M., Zody, M. C., White, S., Birney, E., Searle, S., Schmutz, J., Grimwood, J., Dickson, M. C., Myers, R. M., Miller, C. T., Summers, B. R., Knecht, A. K., ... Kingsley, D. M. (2012). The genomic basis of adaptive evolution in threespine sticklebacks. *Nature*, 484(7392), 55-61. https://doi.org/10.1038/nature10944

Joron, M., Frezal, L., Jones, R. T., Chamberlain, N. L., Lee, S. F., Haag, C. R., Whibley, A., Becuwe, M., Baxter, S. W., Ferguson, L., Wilkinson, P. A., Salazar, C., Davidson, C., Clark, R., Quail, M. A., Beasley, H., Glithero, R., Lloyd, C., Sims, S., ... french-Constant, R. (2011). Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry. *Nature*, 477(7363), 203-206. https://doi.org/10.1038/nature10341

Jun, G., Wing, M. K., Abecasis, G. R., & Kang, H. M. (2015). An efficient and scalable analysis framework for variant extraction and refinement from population scale DNA sequence data. *Genome Research*, 25, 918-925. https://doi.org/10.1101/gr.176552.114
Kawlecki, T. J., & Ebert, D. (2004). Conceptual issues in local adaptation. *Ecology Letters*, 7(12), 1225-1241. https://doi.org/10.1111/j.1461-0248.2004.00684.x

Kenchington, E. L., Harding, G. C., Jones, M. W., & Prodöhl, P. A. (2009). Pleistocene glaciation events shape genetic structure across the range of the American lobster, Homarus americanus. *Molecular Ecology*, 18(8), 1654-1667. https://doi.org/10.1111/j.1365-294X.2009.04118.x

Kirkpatrick, M., & Barton, N. (2006). Chromosome inversions, local adaptation and speciation. *Genetics*, 173(1), 419-434. https://doi.org/10.1534/genetics.105.047985

Kirsche, M., Prabhu, G., Sherman, R., Ni, B., Battle, A., Aganezov, S., & Schatz, M. C. (2023). Jasmine and iris: Population-scale structural variant comparison and analysis. *Nature Methods*, 20, 408-417. https://doi.org/10.1038/s41592-022-01753-3

Kirubakaran, T. G., Grove, H., Kent, M. P., Sandve, S. R., Baranski, M., Nome, T., de Rosa, M. C., Righino, B., Johansen, T., Otterå, H., Sonesson, A., Lien, S., & Andersen, Ø. (2016). Two adjacent inversions maintain genomic differentiation between migratory and stationary ecotypes of Atlantic cod. *Molecular Ecology*, 25(10), 2130-2143. https://doi.org/10.1111/mec.13592

Klemetsen, A., Amundsen, P.-A., Dempson, J. B., Jonsson, B., Jonsson, N., O'Connell, M. F., & Mortensen, E. (2003). Atlantic salmon *Salmo salar* L., brown trout *Salmo trutta* L. and Arctic charr *Salvelinus alpinus* (L.): A review of aspects of their life histories. *Ecology of Freshwater Fish*, 12(1), 1-59. https://doi.org/10.1034/j.1600-0633.2003.00010.x

Klopfenstein, D. V., Zhang, L., Pedersen, B. S., Ramírez, F., Warwick Vesztyrocy, A., Naldi, A., Mungall, C. J., Yunes, J. M., Botvinnik, O., Weigel, M., Dampier, W., Dessimoz, C., Flick, P., & Tang, H. (2018). GOATOOLS: A python library for gene ontology analyses. *Scientific Reports*, 8(1), 10872. https://doi.org/10.1038/s41598-018-28948-z

Kong, A., Thorleifsson, G., Gudbjartsson, D. F., Masson, G., Sigurdsson, A., Jonasdottir, A., Walters, G. B., Jonasdottir, A., Gylfason, A., Kristinsson, K. T., Gudjonsson, S. A., Frigge, M. L., Helgason, A., Thorsteinsdottir, U., & Stefansson, K. (2010). Fine-scale recombination rate differences between sexes, populations and individuals. *Nature*, 467(7319), 1099-1103. https://doi.org/10.1038/nature09525

Korneliussen, T. S., Albrechtsen, A., & Nielsen, R. (2014). ANGSD: Analysis of next generation sequencing data. BMC Bioinformatics, 15(1), 356. https://doi.org/10.1186/s12859-014-0356-4

Kosugi, S., Momozawa, Y., Liu, X. X., Terao, C., Kubo, M., & Kamatani, Y. (2019). Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing. *Genome Biology*, 20, 18. https://doi.org/10.1186/s13059-019-1720-5

Küpper, C., Stocks, M., Risse, J. E., dos Remedios, N., Farrell, L. L., McRae, S. B., Morgan, T. C., Karlionova, N., Pinchuk, P., Verkuil, Y. I., Kitaysky, A. S., Wingfield, J. C., Piersma, T., Zeng, K., Slate, J., Blaxter, M., Lank, D. B., & Burke, T. (2016). A supergene determines highly divergent male reproductive morphs in the ruff. *Nature Genetics*, 48(1), 79-83. https://doi.org/10.1038/ng.3443

Kusche, H., Cote, G., Hernandez, C., Normandeau, E., Boivin-Delisle, D., & Bernatchez, L. (2017). Characterization of natural variation in north American Atlantic Salmon populations (Salmonidae: *Salmo salar*) at a locus with a major effect on sea age. *Ecology and Evolution*, 7(15), 5797-5807. https://doi.org/10.1002/ece3.3132

Langlois-Parisé, I., T. Dion, M.-C., & Therrien, J.-C. (2018). Rapport d'activité 2016 au LARSA, Bilan récapitulatif des opérations, Programme de restauration des populations de saumons de la rivière Romaine. LARSA. Université Laval. Québec.

Layer, R. M., Chiang, C., Quinlan, A. R., & Hall, I. M. (2014). LUMPY: A probabilistic framework for structural variant discovery. *Genome Biology*, 15(6), R84. https://doi.org/10.1186/gb-2014-15-6-r84

Lehnert, S. J., Bentzen, P., Kess, T., Lien, S., Horne, J. B., Clément, M., & Bradbury, I. R. (2019). Chromosome polymorphisms track trans-Atlantic divergence and secondary contact in Atlantic salmon.

*Molecular Ecology*, 28(8), 2074-2087. https://doi.org/10.1111/mec.15065

Lemay, M.-A., Sibbesen, J. A., Torkamaneh, D., Hamel, J., Levesque, R. C., & Belzile, F. (2022). Combined use of Oxford Nanopore and Illumina sequencing yields insights into soybean structural variation biology. *BMC Biology*, 20(1), 53. https://doi.org/10.1186/s12915-022-01255-w

Levy-Sakin, M., Pastor, S., Mostovoy, Y., Li, L., Leung, A. K. Y., McCaffrey, J., Young, E., Lam, E. T., Hastie, A. R., Wong, K. H. Y., Chung, C. Y. L., Ma, W., Sibert, J., Rajagopalan, R., Jin, N., Chow, E. Y. C., Chu, C., Poon, A., Lin, C., ... Kwok, P. Y. (2019). Genome maps across 26 human populations reveal population-specific patterns of structural variation. *Nature Communications*, 10(1), 1025. https://doi.org/10.1038/s41467-019-08992-7

Li, H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. *ArXiv*, 1303.

Lien, S., Koop, B. F., Sandve, S. R., Miller, J. R., Kent, M. P., Nome, T., Hvidsten, T. R., Leong, J. S., Minkley, D. R., Zimin, A., Grammes, F., Grove, H., Gjuvsland, A., Walenz, B., Hermansen, R. A., von Schalburg, K., Rondeau, E. B., di Genova, A., Samy, J. K., ... Davidson, W. S. (2016). The Atlantic salmon genome provides insights into rediploidization. *Nature*, 533(7602), 200-205. https://doi.org/10.1038/nature17164

Lin, K., Smit, S., Bonnema, G., Sanchez-Perez, G., & de Ridder, D. (2015). Making the difference: Integrating structural variation detection tools. *Briefings in Bioinformatics*, 16(5), 852-864. https://doi.org/10.1093/bib/bbu047

Liu, S., Gao, G., Layer, R. M., Thorgaard, G. H., Wiens, G. D., Leeds, T. D., Martin, K. E., & Palti, Y. (2021). Identification of high-confidence structural variants in domesticated rainbow trout using whole-genome sequencing. *Frontiers in Genetics*, 12, 639355. https://doi.org/10.1038/fgene.2021.639355

Liu, Y., Huang, Y., Wang, G., & Wang, Y. (2020). A deep learning approach for filtering structural variants in short read sequencing data. *Briefings in Bioinformatics*, 22(4), bbaa370. https://doi.org/10.1093/bib/bbaa370

Lu, G., & Bernatchez, L. (1999). Correlated trophic specialization and genetic divergence in sympatric lake whitefish ecotypes (*Coregonus clupeaformis*): Support for the ecological speciation hypothesis. *Evolution*, 53(5), 1491-1505. https://doi.org/10.1111/j.1558-5646.1999.tb05413.x

Mahmoud, M., Gobet, N., Cruz-Davalos, D. I., Mounier, N., Dessimoz, C., & Sedlazeck, F. J. (2019). Structural variant calling: The long and the short of it. *Genome Biology*, 20(1), 14. https://doi.org/10.1186/s13059-019-1828-7

Marçais, G., Delcher, A. L., Phillippy, A. M., Coston, R., Salzberg, S. L., & Zimin, A. (2018). MUMmer4: A fast and versatile genome alignment system. *PLoS Computational Biology*, 14(1), e1005944. https://doi.org/10.1371/journal.pcbi.1005944

McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., & DePristo, M. (2010). The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. *Genome Research*, 20(9), 1297-1303. https://doi.org/10.1101/gr-107524.110

Meisner, J., & Albrechtsen, A. (2018). Inferring population structure and admixture proportions in low-depth NGS data. *Genetics*, 210(2), 719-731. https://doi.org/10.1534/genetics.118.301336

Mérot, C., Berdan, E. L., Babin, C., Normandeau, E., Wellenreuther, M., & Bernatchez, L. (2018). Intercontinental karyotype - environment parallelism supports a role for a chromosomal inversion in local adaptation in a seaweed fly. *Proceedings of the Royal Society B: Biological Sciences*, 285(1881), 10. https://doi.org/10.1098/rspb.2018.0519

Mérot, C., Oomen, R. A., Tigano, A., & Wellenreuther, M. (2020). A roadmap for understanding the evolutionary significance of structural
Kawlecki, T. J., & Ebert, D. (2004). Conceptual issues in local adaptation. *Ecology Letters*, 7(12), 1225-1241. https://doi.org/10.1111/j.1461-0248.2004.00684.x

Kenchington, E. L., Harding, G. C., Jones, M. W., & Prodöhl, P. A. (2009). Pleistocene glaciation events shape genetic structure across the range of the American lobster, Homarus americanus. *Molecular Ecology*, 18(8), 1654-1667. https://doi.org/10.1111/j.1365-294X.2009.04118.x

Kirkpatrick, M., & Barton, N. (2006). Chromosome inversions, local adaptation and speciation. *Genetics*, 173(1), 419-434. https://doi.org/10.1534/genetics.105.047985

Kirsche, M., Prabhu, G., Sherman, R., Ni, B., Battle, A., Aganezov, S., & Schatz, M. C. (2023). Jasmine and iris: Population-scale structural variant comparison and analysis. *Nature Methods*, 20, 408-417. https://doi.org/10.1038/s41592-022-01753-3

Kirubakaran, T. G., Grove, H., Kent, M. P., Sandve, S. R., Baranski, M., Nome, T., de Rosa, M. C., Righino, B., Johansen, T., Otterå, H., Sonesson, A., Lien, S., & Andersen, Ø. (2016). Two adjacent inversions maintain genomic differentiation between migratory and stationary ecotypes of Atlantic cod. *Molecular Ecology*, 25(10), 2130-2143. https://doi.org/10.1111/mec.13592

Klemetsen, A., Amundsen, P.-A., Dempson, J. B., Jonsson, B., Jonsson, N., O'Connell, M. F., & Mortensen, E. (2003). Atlantic salmon *Salmo salar* L., brown trout *Salmo trutta* L. and Arctic charr *Salvelinus alpinus* (L.): A review of aspects of their life histories. *Ecology of Freshwater Fish*, 12(1), 1-59. https://doi.org/10.1034/j.1600-0633.2003.00010.x

Klopfenstein, D. V., Zhang, L., Pedersen, B. S., Ramírez, F., Warwick Vesztyrocy, A., Naldi, A., Mungall, C. J., Yunes, J. M., Botvinnik, O., Weigel, M., Dampier, W., Dessimoz, C., Flick, P., & Tang, H. (2018). GOATOOLS: A python library for gene ontology analyses. *Scientific Reports*, 8(1), 10872. https://doi.org/10.1038/s41598-018-28948-z

Kong, A., Thorleifsson, G., Gudbjartsson, D. F., Masson, G., Sigurdsson, A., Jonasdottir, A., Walters, G. B., Jonasdottir, A., Gylfason, A., Kristinsson, K. T., Gudjonsson, S. A., Frigge, M. L., Helgason, A., Thorsteinsdottir, U., & Stefansson, K. (2010). Fine-scale recombination rate differences between sexes, populations and individuals. *Nature*, 467(7319), 1099-1103. https://doi.org/10.1038/nature09525

Korneliussen, T. S., Albrechtsen, A., & Nielsen, R. (2014). ANGSD: Analysis of next generation sequencing data. *BMC Bioinformatics*, 15(1), 356. https://doi.org/10.1186/s12859-014-0356-4

Kosugi, S., Momozawa, Y., Liu, X. X., Terao, C., Kubo, M., & Kamatani, Y. (2019). Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing. *Genome Biology*, 20, 18. https://doi.org/10.1186/s13059-019-1720-5

Küpper, C., Stocks, M., Risse, J. E., dos Remedios, N., Farrell, L. L., McRae, S. B., Morgan, T. C., Karlionova, N., Pinchuk, P., Verkuil, Y. I., Kitaysky, A. S., Wingfield, J. C., Piersma, T., Zeng, K., Slate, J., Blaxter, M., Lank, D. B., & Burke, T. (2016). A supergene determines highly divergent male reproductive morphs in the ruff. *Nature Genetics*, 48(1), 79-83. https://doi.org/10.1038/ng.3443

Kusche, H., Cote, G., Hernandez, C., Normandeau, E., Boivin-Delisle, D., & Bernatchez, L. (2017). Characterization of natural variation in north American Atlantic Salmon populations (Salmonidae: *Salmo salar*) at a locus with a major effect on sea age. *Ecology and Evolution*, 7(15), 5797-5807. https://doi.org/10.1002/ece3.3132

Langlois-Parisé, I., T. Dion, M.-C., & Therrien, J.-C. (2018). Rapport d'activité 2016 au LARSA, Bilan récapitulatif des opérations, Programme de restauration des populations de saumons de la rivière Romaine. LARSA. Université Laval. Québec.

Layer, R. M., Chiang, C., Quinlan, A. R., & Hall, I. M. (2014). LUMPY: A probabilistic framework for structural variant discovery. *Genome Biology*, 15(6), R84. https://doi.org/10.1186/gb-2014-15-6-r84

Lehnert, S. J., Bentzen, P., Kess, T., Lien, S., Horne, J. B., Clément, M., & Bradbury, I. R. (2019). Chromosome polymorphisms track trans-Atlantic divergence and secondary contact in Atlantic salmon.

*Molecular Ecology*, 28(8), 2074-2087. https://doi.org/10.1111/mec.15065

Lemay, M.-A., Sibbesen, J. A., Torkamaneh, D., Hamel, J., Levesque, R. C., & Belzile, F. (2022). Combined use of Oxford Nanopore and Illumina sequencing yields insights into soybean structural variation biology. *BMC Biology*, 20(1), 53. https://doi.org/10.1186/s12915-022-01255-w

Levy-Sakin, M., Pastor, S., Mostovoy, Y., Li, L., Leung, A. K. Y., McCaffrey, J., Young, E., Lam, E. T., Hastie, A. R., Wong, K. H. Y., Chung, C. Y. L., Ma, W., Sibert, J., Rajagopalan, R., Jin, N., Chow, E. Y. C., Chu, C., Poon, A., Lin, C., ... Kwok, P. Y. (2019). Genome maps across 26 human populations reveal population-specific patterns of structural variation. *Nature Communications*, 10(1), 1025. https://doi.org/10.1038/s41467-019-08992-7

Li, H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. *ArXiv*, 1303.

Lien, S., Koop, B. F., Sandve, S. R., Miller, J. R., Kent, M. P., Nome, T., Hvidsten, T. R., Leong, J. S., Minkley, D. R., Zimin, A., Grammes, F., Grove, H., Gjuvsland, A., Walenz, B., Hermansen, R. A., von Schalburg, K., Rondeau, E. B., di Genova, A., Samy, J. K., ... Davidson, W. S. (2016). The Atlantic salmon genome provides insights into rediploidization. *Nature*, 533(7602), 200-205. https://doi.org/10.1038/nature17164

Lin, K., Smit, S., Bonnema, G., Sanchez-Perez, G., & de Ridder, D. (2015). Making the difference: Integrating structural variation detection tools. *Briefings in Bioinformatics*, 16(5), 852-864. https://doi.org/10.1093/bib/bbu047

Liu, S., Gao, G., Layer, R. M., Thorgaard, G. H., Wiens, G. D., Leeds, T. D., Martin, K. E., & Palti, Y. (2021). Identification of high-confidence structural variants in domesticated rainbow trout using whole-genome sequencing. *Frontiers in Genetics*, 12, 639355. https://doi.org/10.1038/fgene.2021.639355

Liu, Y., Huang, Y., Wang, G., & Wang, Y. (2020). A deep learning approach for filtering structural variants in short read sequencing data. *Briefings in Bioinformatics*, 22(4), bbaa370. https://doi.org/10.1093/bib/bbaa370

Lu, G., & Bernatchez, L. (1999). Correlated trophic specialization and genetic divergence in sympatric lake whitefish ecotypes (*Coregonus clupeaformis*): Support for the ecological speciation hypothesis. *Evolution*, 53(5), 1491-1505. https://doi.org/10.1111/j.1558-5646.1999.tb05413.x

Mahmoud, M., Gobet, N., Cruz-Davalos, D. I., Mounier, N., Dessimoz, C., & Sedlazeck, F. J. (2019). Structural variant calling: The long and the short of it. *Genome Biology*, 20(1), 14. https://doi.org/10.1186/s13059-019-1828-7

Marçais, G., Delcher, A. L., Phillippy, A. M., Coston, R., Salzberg, S. L., & Zimin, A. (2018). MUMmer4: A fast and versatile genome alignment system. *PLoS Computational Biology*, 14(1), e1005944. https://doi.org/10.1371/journal.pcbi.1005944

McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., & DePristo, M. (2010). The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. *Genome Research*, 20(9), 1297-1303. https://doi.org/10.1101/gr-107524.110

Meisner, J., & Albrechtsen, A. (2018). Inferring population structure and admixture proportions in low-depth NGS data. *Genetics*, 210(2), 719-731. https://doi.org/10.1534/genetics.118.301336

Mérot, C., Berdan, E. L., Babin, C., Normandeau, E., Wellenreuther, M., & Bernatchez, L. (2018). Intercontinental karyotype - environment parallelism supports a role for a chromosomal inversion in local adaptation in a seaweed fly. *Proceedings of the Royal Society B: Biological Sciences*, 285(1881), 10. https://doi.org/10.1098/rspb.2018.0519

Mérot, C., Oomen, R. A., Tigano, A., & Wellenreuther, M. (2020). A roadmap for understanding the evolutionary significance of structural
genomic variation. *Trends in Ecology & Evolution*, 35(7), 561-572.
https://doi.org/10.1016/j.tree.2020.03.002

Mérot, C., Stenløkk, K. S. R., Venney, C., Laporte, M., Moser, M., Normandeau, E., Árnyasi, M., Kent, M., Rougeux, C., Flynn, J. M., Lien, S., & Bernatchez, L. (2023). Genome assembly, structural variants, and genetic differentiation between lake whitefish young species pairs (Coregonus sp.) with long and short reads. *Molecular Ecology*, 32(6), 1458-1477. https://doi.org/10.1111/mec.16468

Mills, R. E., Walter, K., Stewart, C., Handsaker, R. E., Chen, K., Alkan, C., Abyzov, A., Yoon, S. C., Ye, K., Cheetham, R. K., Chinwalla, A., Conrad, D. F., Fu, Y., Grubert, F., Hajirasouliha, I., Hormozdiari, F., Iakoucheva, L. M., Iqbal, Z., Kang, S., ... 1000 Genomes Project. (2011). Mapping copy number variation by population-scale genome sequencing. *Nature*, 470(7332), 59-65. https://doi.org/10.1038/nature09708

Mohamed, A. R., Verbyla, K. L., al-Mamun, H. A., McWilliam, S., Evans, B., King, H., Kube, P., & Kijas, J. W. (2019). Polygenic and sex specific architecture for two maturation traits in farmed Atlantic salmon. *BMC Genomics*, 20(1), 139. https://doi.org/10.1186/s12864-019-5525-4

Nielsen, R., Paul, J. S., Albrechtsen, A., & Song, Y. S. (2011). Genotype and SNP calling from next-generation sequencing data. *Nature Reviews Genetics*, 12(6), 443-451. https://doi.org/10.1038/nrg2986

Norwegian University of Life Sciences. (2022). Ssal_Brian_v1.0 (GCA_923944775.1). https://www.ncbi.nlm.nih.gov/assembly/GCA_923944775.1/?shouldredirect=false

Oksanen, J., Simpson, G. L., Blanchet, F. G., Kindt, R., Legendre, P., Minchin, P. R., O'Hara, R. B., Solymos, P., Stevens, M. H. H., Szoecs, E., Wagner, H., Barbour, M., Bedward, M., Bolker, B., Borcard, D., Carvalho, G., Chirico, M., De Caceres, M., Durand, S., ... Weedon, J. (2022). *Vegan: Community ecology package (version 2.6-4)*. https://github.com/vegandevs/vegan

Outten, J., & Warren, A. (2021). Methods and developments in graphical pangenomics. *Journal of the Indian Institute of Science*, 101(3), 485-498. https://doi.org/10.1007/s41745-021-00255-z

Paten, B., Novak, A. M., Eizenga, J. M., & Garrison, E. (2017). Genome graphs and the evolution of genome inference. *Genome Research*, 27(5), 665-676. https://doi.org/10.1101/gr.214155.116

Pearse, D. E., Barson, N. J., Nome, T., Gao, G., Campbell, M. A., Abadía-Cardoso, A., Anderson, E. C., Rundio, D. E., Williams, T. H., Naish, K. A., Moen, T., Liu, S., Kent, M., Moser, M., Minkley, D. R., Rondeau, E. B., Brieuc, M. S. O., Sandve, S. R., Miller, M. R., ... Lien, S. (2019). Sex-dependent dominance maintains migration supergene in rainbow trout. *Nature Ecology & Evolution*, 3(12), 1731-1742. https://doi.org/10.1038/s41559-019-1044-6

Pearse, D. E., Miller, M. R., Abadía-Cardoso, A., & Garza, J. C. (2014). Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout. *Proceedings of the Royal Society B: Biological Sciences*, 281(1783), 20140012. https://doi.org/10.1098/rspb.2014.0012

Pedersen, B. S., Layer, R., & Quinlan, A. R. (2020). Smoove: Structural-variant calling and genotyping with existing tools. https://github.com/brentp/smoove

Topic, V., Rohlicek, C., Cunial, F., Hajirasouliha, I., Meleshko, D., Garimella, K., & Maheshwari, A. (2023). Cue: A deep-learning framework for structural variant discovery and genotyping. *Nature Methods*, 20(4), 559-568. https://doi.org/10.1038/s41592-023-01799-x

Quinlan, A. R., & Hall, I. M. (2010). BEDTools: A flexible suite of utilities for comparing genomic features. *Bioinformatics*, 26(6), 841-842. https://doi.org/10.1093/bioinformatics/btq033

R Core Team. (2021). R: A language and environment for statistical computing. R Foundation for Statistical Computing. https://www.R-projct.org/

Rang, F. J., Kloosterman, W. P., & de Ridder, J. (2018). From squiggle to basepair: Computational approaches for improving nanopore sequencing read accuracy. *Genome Biology*, 19(1), 90. https://doi.org/10.1186/s13059-018-1462-9

Rausch, T., Schlue, T., Schlattl, A., Stütz, A. M., Benes, V., & Korbel, J. O. (2012). DELLY: Structural variant discovery by integrated paired-end and split-read analysis. *Bioinformatics*, 28(18), i333-i339. https://doi.org/10.1093/bioinformatics/bts378

Reisle, C., Mungall, K. L., Choo, C., Paulino, D., Bleile, D. W., Muhammadzadeh, A., Mungall, A. J., Moore, R. A., Shlafman, I., Coope, R., Pleasance, S., Ma, Y., & Jones, S. J. M. (2019). MAVIS: Merging, annotation, validation, and illustration of structural variants. *Bioinformatics*, 35(3), 515-517. https://doi.org/10.1093/bioinformatics/bty621

Rellstab, C., Gugerli, F., Eckert, A. J., Hancock, A. M., & Holderegger, R. (2015). A practical guide to environmental association analysis in landscape genomics. *Molecular Ecology*, 24(17), 4348-4370. https://doi.org/10.1111/mec.13322

Rieseberg, L. H. (2001). Chromosomal rearrangements and speciation. *Trends in Ecology & Evolution*, 16(7), 351-358. https://doi.org/10.1016/s0169-5347(01)02187-5

Ritz, K. R., Noor, M. A. F., & Singh, N. D. (2017). Variation in recombination rate: Adaptive or not? *Trends in Genetics*, 33(5), 364-374. https://doi.org/10.1016/j.tig.2017.03.003

Rowan, B. A., Heavens, D., Feuerborn, T. R., Tock, A. J., Henderson, I. R., & Weigel, D. (2019). An ultra high-density *Arabidopsis thaliana* crossover map that refines the influences of structural variation and epigenetic features. *Genetics*, 213(3), 771-787. https://doi.org/10.1534/genetics.119.302406

Schieffer, K. (1975). *Atlantic salmon management study of the Romaine river*. Beak Consultants Ltd.

Sedlazeck, F. J., Lee, H., Darby, C. A., & Schatz, M. C. (2018). Piercing the dark matter: Bioinformatics of long-range sequencing and mapping. *Nature Reviews Genetics*, 19(6), 329-346. https://doi.org/10.1038/s41576-018-0003-4

Sedlazeck, F. J., Rescheneder, P., Smolka, M., Fang, H., Nattestad, M., von Haeseler, A., & Schatz, M. C. (2018). Accurate detection of complex structural variations using single-molecule sequencing. *Nature Methods*, 15(6), 461-468. https://doi.org/10.1038/s41592-018-0001-7

Sinclair-Waters, M., Ødegård, J., Korsvoll, S. A., Moen, T., Lien, S., Primmer, C. R., & Barson, N. J. (2020). Beyond large-effect loci: Large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon. *Genetics Selection Evolution*, 52(1), 9. https://doi.org/10.1186/s12711-020-0529-8

Sirén, J., Monlong, J., Chang, X., Novak, A. M., Eizenga, J. M., Markello, C., Sibbesen, J. A., Hickey, G., Chang, P. C., Carroll, A., Gupta, N., Gabriel, S., Blackwell, T. W., Ratan, A., Taylor, K. D., Rich, S. S., Rotter, J. I., Haussler, D., Garrison, E., & Paten, B. (2021). Pangenomics enables genotyping of known structural variants in 5202 diverse genomes. *Science*, 374(6574), abg8871. https://doi.org/10.1126/science.abg8871

Smit, A. F. A., Hubley, R., & Green, P. (2013). RepeatMasker Open-4.0.

Smolka, M., Paulin, L. F., Grochowski, C. M., Mahmoud, M., Behera, S., Gandhi, M., Hong, K., Pehlivan, D., Scholz, S. W., Carvalho, C. M. B., Proukakis, C., & Sedlazeck, F. J. (2022). Comprehensive structural variant detection: From mosaic to population-level. *bioRxiv*, 2022.004.2022.004.487055 https://doi.org/10.1101/2022.04.04.487055

Soderlund, C., Bomhoff, M., & Nelson, W. M. (2011). SyMAP v3.4: A turnkey synteny system with application to plant genomes. *Nucleic Acids Research*, 39(10), e68. https://doi.org/10.1093/nar/gkr123

Spielmann, M., Lupiáñez, D. G., & Mundlos, S. (2018). Structural variation in the 3D genome. *Nature Reviews Genetics*, 19(7), 453-467. https://doi.org/10.1038/s41576-018-0007-0

Spies, N., Zook, J. M., Salit, M., & Sidow, A. (2015). Svviz: A read viewer for validating structural variants. *Bioinformatics*, 31(24), 3994-3996. https://doi.org/10.1093/bioinformatics/btv478
genomic variation. *Trends in Ecology & Evolution*, 35(7), 561-572.
https://doi.org/10.1016/j.tree.2020.03.002

Mérot, C., Stenløkk, K. S. R., Venney, C., Laporte, M., Moser, M., Normandeau, E., Árnyasi, M., Kent, M., Rougeux, C., Flynn, J. M., Lien, S., & Bernatchez, L. (2023). Genome assembly, structural variants, and genetic differentiation between lake whitefish young species pairs (Coregonus sp.) with long and short reads. *Molecular Ecology*, 32(6), 1458-1477. https://doi.org/10.1111/mec.16468

Mills, R. E., Walter, K., Stewart, C., Handsaker, R. E., Chen, K., Alkan, C., Abyzov, A., Yoon, S. C., Ye, K., Cheetham, R. K., Chinwalla, A., Conrad, D. F., Fu, Y., Grubert, F., Hajirasouliha, I., Hormozdiari, F., Iakoucheva, L. M., Iqbal, Z., Kang, S., ... 1000 Genomes Project. (2011). Mapping copy number variation by population-scale genome sequencing. *Nature*, 470(7332), 59-65. https://doi.org/10.1038/nature09708

Mohamed, A. R., Verbyla, K. L., al-Mamun, H. A., McWilliam, S., Evans, B., King, H., Kube, P., & Kijas, J. W. (2019). Polygenic and sex specific architecture for two maturation traits in farmed Atlantic salmon. *BMC Genomics*, 20(1), 139. https://doi.org/10.1186/s12864-019-5525-4

Nielsen, R., Paul, J. S., Albrechtsen, A., & Song, Y. S. (2011). Genotype and SNP calling from next-generation sequencing data. *Nature Reviews Genetics*, 12(6), 443-451. https://doi.org/10.1038/nrg2986

Norwegian University of Life Sciences. (2022). Ssal_Brian_v1.0 (GCA_923944775.1). https://www.ncbi.nlm.nih.gov/assembly/ GCA_923944775.1/?shouldredirect=false

Oksanen, J., Simpson, G. L., Blanchet, F. G., Kindt, R., Legendre, P., Minchin, P. R., O'Hara, R. B., Solymos, P., Stevens, M. H. H., Szoecs, E., Wagner, H., Barbour, M., Bedward, M., Bolker, B., Borcard, D., Carvalho, G., Chirico, M., De Caceres, M., Durand, S., ... Weedon, J. (2022). *Vegan: Community ecology package (version 2.6-4)*. https:// github.com/vegandevs/vegan

Outten, J., & Warren, A. (2021). Methods and developments in graphical pangenomics. *Journal of the Indian Institute of Science*, 101(3), 485-498. https://doi.org/10.1007/s41745-021-00255-z

Paten, B., Novak, A. M., Eizenga, J. M., & Garrison, E. (2017). Genome graphs and the evolution of genome inference. *Genome Research*, 27(5), 665-676. https://doi.org/10.1101/gr.214155.116

Pearse, D. E., Barson, N. J., Nome, T., Gao, G., Campbell, M. A., Abadía-Cardoso, A., Anderson, E. C., Rundio, D. E., Williams, T. H., Naish, K. A., Moen, T., Liu, S., Kent, M., Moser, M., Minkley, D. R., Rondeau, E. B., Brieuc, M. S. O., Sandve, S. R., Miller, M. R., ... Lien, S. (2019). Sex-dependent dominance maintains migration supergene in rainbow trout. *Nature Ecology & Evolution*, 3(12), 1731-1742. https:// doi.org/10.1038/s41559-019-1044-6

Pearse, D. E., Miller, M. R., Abadía-Cardoso, A., & Garza, J. C. (2014). Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout. *Proceedings of the Royal Society B: Biological Sciences*, 281(1783), 20140012. https://doi.org/10.1098/rspb.2014.0012

Pedersen, B. S., Layer, R., & Quinlan, A. R. (2020). Smoove: Structural-variant calling and genotyping with existing tools. https://github.com/ brentp/smoove

Topic, V., Rohlicek, C., Cunial, F., Hajirasouliha, I., Meleshko, D., Garimella, K., & Maheshwari, A. (2023). Cue: A deep-learning framework for structural variant discovery and genotyping. *Nature Methods*, 20(4), 559-568. https://doi.org/10.1038/s41592-023-01799-x

Quinlan, A. R., & Hall, I. M. (2010). BEDTools: A flexible suite of utilities for comparing genomic features. *Bioinformatics*, 26(6), 841-842. https://doi.org/10.1093/bioinformatics/btq033

R Core Team. (2021). R: A language and environment for statistical computing. R Foundation for Statistical Computing. https://www.R-projct.org/

Rang, F. J., Kloosterman, W. P., & de Ridder, J. (2018). From squiggle to basepair: Computational approaches for improving nanopore sequencing read accuracy. *Genome Biology*, 19(1), 90. https://doi.org/10.1186/s13059-018-1462-9

Rausch, T., Schlue, T., Schlattl, A., Stütz, A. M., Benes, V., & Korbel, J. O. (2012). DELLY: Structural variant discovery by integrated paired-end and split-read analysis. *Bioinformatics*, 28(18), i333-i339. https://doi.org/10.1093/bioinformatics/bts378

Reisle, C., Mungall, K. L., Choo, C., Paulino, D., Bleile, D. W., Muhammadzadeh, A., Mungall, A. J., Moore, R. A., Shlafman, I., Coope, R., Pleasance, S., Ma, Y., & Jones, S. J. M. (2019). MAVIS: Merging, annotation, validation, and illustration of structural variants. *Bioinformatics*, 35(3), 515-517. https://doi.org/10.1093/bioinformatics/bty621

Rellstab, C., Gugerli, F., Eckert, A. J., Hancock, A. M., & Holderegger, R. (2015). A practical guide to environmental association analysis in landscape genomics. *Molecular Ecology*, 24(17), 4348-4370. https://doi.org/10.1111/mec.13322

Rieseberg, L. H. (2001). Chromosomal rearrangements and speciation. *Trends in Ecology & Evolution*, 16(7), 351-358. https://doi.org/10.1016/s0169-5347(01)02187-5

Ritz, K. R., Noor, M. A. F., & Singh, N. D. (2017). Variation in recombination rate: Adaptive or not? *Trends in Genetics*, 33(5), 364-374. https://doi.org/10.1016/j.tig.2017.03.003

Rowan, B. A., Heavens, D., Feuerborn, T. R., Tock, A. J., Henderson, I. R., & Weigel, D. (2019). An ultra high-density *Arabidopsis thaliana* crossover map that refines the influences of structural variation and epigenetic features. *Genetics*, 213(3), 771-787. https://doi.org/10.1534/genetics.119.302406

Schieffer, K. (1975). *Atlantic salmon management study of the Romaine river*. Beak Consultants Ltd.

Sedlazeck, F. J., Lee, H., Darby, C. A., & Schatz, M. C. (2018). Piercing the dark matter: Bioinformatics of long-range sequencing and mapping. *Nature Reviews Genetics*, 19(6), 329-346. https://doi.org/10.1038/s41576-018-0003-4

Sedlazeck, F. J., Rescheneder, P., Smolka, M., Fang, H., Nattestad, M., von Haeseler, A., & Schatz, M. C. (2018). Accurate detection of complex structural variations using single-molecule sequencing. *Nature Methods*, 15(6), 461-468. https://doi.org/10.1038/s41592-018-0001-7

Sinclair-Waters, M., Ødegård, J., Korsvoll, S. A., Moen, T., Lien, S., Primmer, C. R., & Barson, N. J. (2020). Beyond large-effect loci: Large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon. *Genetics Selection Evolution*, 52(1), 9. https://doi.org/10.1186/s12711-020-0529-8

Sirén, J., Monlong, J., Chang, X., Novak, A. M., Eizenga, J. M., Markello, C., Sibbesen, J. A., Hickey, G., Chang, P. C., Carroll, A., Gupta, N., Gabriel, S., Blackwell, T. W., Ratan, A., Taylor, K. D., Rich, S. S., Rotter, J. I., Haussler, D., Garrison, E., & Paten, B. (2021). Pangenomics enables genotyping of known structural variants in 5202 diverse genomes. *Science*, 374(6574), abg8871. https://doi.org/10.1126/science.abg8871

Smit, A. F. A., Hubley, R., & Green, P. (2013). RepeatMasker Open-4.0.

Smolka, M., Paulin, L. F., Grochowski, C. M., Mahmoud, M., Behera, S., Gandhi, M., Hong, K., Pehlivan, D., Scholz, S. W., Carvalho, C. M. B., Proukakis, C., & Sedlazeck, F. J. (2022). Comprehensive structural variant detection: From mosaic to population-level. *bioRxiv*, 2022.004.2022.0487055 https://doi.org/10.1101/2022.04.04.487055

Soderlund, C., Bomhoff, M., & Nelson, W. M. (2011). SyMAP v3.4: A turnkey synteny system with application to plant genomes. *Nucleic Acids Research*, 39(10), e68. https://doi.org/10.1093/nar/gkr123

Spielmann, M., Lupiáñez, D. G., & Mundlos, S. (2018). Structural variation in the 3D genome. *Nature Reviews Genetics*, 19(7), 453-467. https://doi.org/10.1038/s41576-018-0007-0

Spies, N., Zook, J. M., Salit, M., & Sidow, A. (2015). Svviz: A read viewer for validating structural variants. *Bioinformatics*, 31(24), 3994-3996. https://doi.org/10.1093/bioinformatics/btv478
Stefansson, S. O., Björnsson, B. T., Ebbesson, L. O., & McCormick, S. D. (2008). Smoltification. In R. N. Finn (Ed.), *Fish larval physiology* (pp. 639–681). CRC Press. https://doi.org/10.1201/9780429061608

Stenløkk, K. S. R. (2023). *Genomic structural variations as drivers of adaptation in salmonid fishes*. (Philosophiae Doctor (PhD)). Norwegian University of Life Sciences, (2023:26).

Stuart, K. C., Edwards, R. J., Sherwin, W. B., & Rollins, L. A. (2023). Contrasting patterns of single nucleotide polymorphisms and structural variation across multiple invasions. *Molecular Biology and Evolution*, 40(3), msad046. https://doi.org/10.1093/molbev/msad046

Sudmant, P. H., Mallick, S., Nelson, B. J., Hormozdiari, F., Krumm, N., Huddleston, J., Coe, B. P., Baker, C., Nordenfelt, S., Bamshad, M., Jorde, L. B., Posukh, O. L., Sahakyan, H., Watkins, W. S., Yepiskoposyan, L., Abdullah, M. S., Bravi, C. M., Capelli, C., Hervig, T., ... Eichler, E. E. (2015). Global diversity, population stratification, and selection of human copy-number variation. *Science*, 349(6253), aab3761. https://doi.org/10.1126/science.aab3761

Sudmant, P. H., Rausch, T., Gardner, E. J., Handsaker, R. E., Abyzov, A., Huddleston, J., Zhang, Y., Ye, K., Jun, G., Fritz, M. H., Konkel, M. K., Malhotra, A., Stütz, A. M., Shi, X., Casale, F. P., Chen, J., Hormozdiari, F., Dayama, G., Chen, K., ... Korbel, J. O. (2015). An integrated map of structural variation in 2,504 human genomes. *Nature*, 526(7571), 75–81. https://doi.org/10.1038/nature15394

Supek, F., Bošnjak, M., Škunca, N., & Šmuc, T. (2011). REVIGO summarizes and visualizes long lists of gene ontology terms. *PLoS One*, 6(7), e21800. https://doi.org/10.1371/journal.pone.0021800

T. Dion, M.-C., Chayer, M., Proulx, E., Langlois-Parisé, I., & Therrien, J.-C. (2020). *Rapport d'activité 2017 au LARSA, Bilan récapitulatif des opérations, Programme de restauration des populations de saumons de la rivière Romaine*. LARSA. Université Laval. Québec.

T. Dion, M.-C., Langlois-Parisé, I., & Proulx, E. (2020). *Rapport d'activité 2018 au LARSA, Bilan récapitulatif des opérations, Programme de restauration des populations de saumons de la rivière Romaine*. Université Laval.

Taylor, E. B. (1991). A review of local adaptation in Salmonidae, with particular reference to Pacific and Atlantic salmon. *Aquaculture*, 98(1), 185–207. https://doi.org/10.1016/0044-8486(91)90383-1

Tham, C. Y., Tirado-Magallanes, R., Goh, Y., Fullwood, M. J., Koh, B. T. H., Wang, W., Ng, C. H., Chng, W. J., Thiery, A., Tenen, D. G., & Benoukraf, T. (2020). NanoVar: Accurate characterization of patients' genomic structural variants using low-depth nanopore sequencing. *Genome Biology*, 21(1), 56. https://doi.org/10.1186/s13059-020-01968-7

Therrien, J.-C., T. Dion, M.-C., Ouellet-Cauchon, G., & Langlois-Parisé, I. (2017). *Rapport d'activité 2014–2015 au LARSA, Bilan récapitulatif des opérations, Programme de restauration des populations de saumons de la rivière Romaine*. LARSA. Université Laval.

Thompson, M. J., & Jiggins, C. D. (2014). Supergenes and their role in evolution. *Heredity*, 113(1), 1–8. https://doi.org/10.1038/hdy.2014.20

Tuttle, E. M. (2003). Alternative reproductive strategies in the white-throated sparrow: Behavioral and genetic evidence. *Behavioral Ecology*, 14(3), 425–432. https://doi.org/10.1093/beheco/14.3.425

van't Hof, A., Campagne, P., Rigden, D. J., Yung, C. J., Lingley, J., Quail, M. A., Hall, N., Darby, A. C., & Saccheri, I. J. (2016). The industrial melanism mutation in British peppered moths is a transposable element. *Nature*, 534(7605), 102–105. https://doi.org/10.1038/nature17951

Waters, C. D., Clemento, A., Aykanat, T., Garza, J. C., Naish, K. A., Narum, S., & Primmer, C. R. (2021). Heterogeneous genetic basis of age at maturity in salmonid fishes. *Molecular Ecology*, 30(6), 1435–1456. https://doi.org/10.1111/mec.15822

Watson, K. B., Lehnert, S. J., Bentzen, P., Kess, T., Einfeldt, A., Duffy, S., Perriman, B., Lien, S., Kent, M., & Bradbury, I. R. (2022). Environmentally associated chromosomal structural variation influences fine-scale population structure of Atlantic Salmon (*Salmo salar*). *Molecular Ecology*, 31(4), 1057–1075. https://doi.org/10.1111/mec.16307

Weir, B. S., & Cockerham, C. C. (1984). Estimating F-statistics for the analysis of population structure. *Evolution*, 38(6), 1358–1370. https://doi.org/10.2307/2408641

Weissensteiner, M. H., Bunikis, I., Catalán, A., Francoijs, K.-J., Knief, U., Heim, W., Peona, V., Pophaly, S. D., Sedlazeck, F. J., Suh, A., Warmuth, V. M., & Wolf, J. B. W. (2020). Discovery and population genomics of structural variation in a songbird genus. *Nature Communications*, 11(1), 3403. https://doi.org/10.1038/s41467-020-17195-4

Wellband, K., Mérot, C., Linnansaari, T., Elliott, J. A. K., Curry, R. A., & Bernatchez, L. (2019). Chromosomal fusion and life history-associated genomic variation contribute to within-river local adaptation of Atlantic salmon. *Molecular Ecology*, 28(6), 1439–1459. https://doi.org/10.1111/mec.14965

Wellenreuther, M., & Bernatchez, L. (2018). Eco-evolutionary genomics of chromosomal inversions. *Trends in Ecology & Evolution*, 33(6), 427–440. https://doi.org/10.1016/j.tree.2018.04.002

Wellenreuther, M., Mérot, C., Berdan, E., & Bernatchez, L. (2019). Going beyond SNPs: The role of structural genomic variants in adaptive evolution and species diversification. *Molecular Ecology*, 28(6), 1203–1209. https://doi.org/10.1111/mec.15066

Wold, J. R., Guhlin, J. G., Dearden, P. K., Santure, A. W., & Steeves, T. E. (2023). The promise and challenges of characterizing genome-wide structural variants: A case study in a critically endangered parrot. *Molecular Ecology Resources*, Advance online publication. https://doi.org/10.1111/1755-0998.13783

Wolf, J. B. W., & Ellegren, H. (2017). Making sense of genomic islands of differentiation in light of speciation. *Nature Reviews Genetics*, 18(2), 87–100. https://doi.org/10.1038/nrg.2016.133

Wright, S. (1984). *Evolution and the genetics of populations, Volume 4: Variability within and among natural populations*. University of Chicago Press.

WSP Global. (2019). *Complexe de la Romaine - Suivi environnemental 2017 en phase exploitation: Suivi de la population de saumon atlantique*. https://www.ree.environnement.gouv.qc.ca/dossiers/3211-12-086/3211-12-086-16.pdf

Yan, S. M., Sherman, R. M., Taylor, D. J., Nair, D. R., Bortvin, A. N., Schatz, M. C., & McCoy, R. C. (2021). Local adaptation and archaic introduction shape global diversity at human structural variant loci. *eLife*, 10, e67615. https://doi.org/10.7554/eLife.67615

Zhou, Y., Minio, A., Massonnet, M., Solares, E., Lv, Y., Beridze, T., Cantu, D., & Gaut, B. S. (2019). The population genetics of structural variants in grapevine domestication. *Nature Plants*, 5(9), 965–979. https://doi.org/10.1038/s41477-019-0507-8

## SUPPORTING INFORMATION

Additional supporting information can be found online in the Supporting Information section at the end of this article.

**How to cite this article:** Lecomte, L., Árnyasi, M., Ferchaud, A.-L., Kent, M., Lien, S., Stenløkk, K., Sylvestre, F., Bernatchez, L., & Mérot, C. (2024). Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations. *Evolutionary Applications*, 17, e13653. https://doi.org/10.1111/eva.13653
Stefansson, S. O., Björnsson, B. T., Ebbesson, L. O., & McCormick, S. D. (2008). Smoltification. In R. N. Finn (Ed.), *Fish larval physiology* (pp. 639–681). CRC Press. https://doi.org/10.1201/9780429061608

Stenløkk, K. S. R. (2023). *Genomic structural variations as drivers of adaptation in salmonid fishes*. (Philosophiae Doctor (PhD)). Norwegian University of Life Sciences, (2023:26).

Stuart, K. C., Edwards, R. J., Sherwin, W. B., & Rollins, L. A. (2023). Contrasting patterns of single nucleotide polymorphisms and structural variation across multiple invasions. *Molecular Biology and Evolution*, 40(3), msad046. https://doi.org/10.1093/molbev/msad046

Sudmant, P. H., Mallick, S., Nelson, B. J., Hormozdiari, F., Krumm, N., Huddleston, J., Coe, B. P., Baker, C., Nordenfelt, S., Bamshad, M., Jorde, L. B., Posukh, O. L., Sahakyan, H., Watkins, W. S., Yepiskoposyan, L., Abdullah, M. S., Bravi, C. M., Capelli, C., Hervig, T., ... Eichler, E. E. (2015). Global diversity, population stratification, and selection of human copy-number variation. *Science*, 349(6253), aab3761. https://doi.org/10.1126/science.aab3761

Sudmant, P. H., Rausch, T., Gardner, E. J., Handsaker, R. E., Abyzov, A., Huddleston, J., Zhang, Y., Ye, K., Jun, G., Fritz, M. H., Konkel, M. K., Malhotra, A., Stütz, A. M., Shi, X., Casale, F. P., Chen, J., Hormozdiari, F., Dayama, G., Chen, K., ... Korbel, J. O. (2015). An integrated map of structural variation in 2,504 human genomes. *Nature*, 526(7571), 75–81. https://doi.org/10.1038/nature15394

Supek, F., Bošnjak, M., Škunca, N., & Šmuc, T. (2011). REVIGO summarizes and visualizes long lists of gene ontology terms. *PLoS One*, 6(7), e21800. https://doi.org/10.1371/journal.pone.0021800

T. Dion, M.-C., Chayer, M., Proulx, E., Langlois-Parisé, I., & Therrien, J.-C. (2020). *Rapport d'activité 2017 au LARSA, Bilan récapitulatif des opérations, Programme de restauration des populations de saumons de la rivière Romaine*. LARSA. Université Laval. Québec.

T. Dion, M.-C., Langlois-Parisé, I., & Proulx, E. (2020). *Rapport d'activité 2018 au LARSA, Bilan récapitulatif des opérations, Programme de restauration des populations de saumons de la rivière Romaine*. Université Laval.

Taylor, E. B. (1991). A review of local adaptation in Salmonidae, with particular reference to Pacific and Atlantic salmon. *Aquaculture*, 98(1), 185–207. https://doi.org/10.1016/0044-8486(91)90383-1

Tham, C. Y., Tirado-Magallanes, R., Goh, Y., Fullwood, M. J., Koh, B. T. H., Wang, W., Ng, C. H., Chng, W. J., Thiery, A., Tenen, D. G., & Benoukraf, T. (2020). NanoVar: Accurate characterization of patients' genomic structural variants using low-depth nanopore sequencing. *Genome Biology*, 21(1), 56. https://doi.org/10.1186/s13059-020-01968-7

Therrien, J.-C., T. Dion, M.-C., Ouellet-Cauchon, G., & Langlois-Parisé, I. (2017). *Rapport d'activité 2014–2015 au LARSA, Bilan récapitulatif des opérations, Programme de restauration des populations de saumons de la rivière Romaine*. LARSA. Université Laval.

Thompson, M. J., & Jiggins, C. D. (2014). Supergenes and their role in evolution. *Heredity*, 113(1), 1–8. https://doi.org/10.1038/hdy.2014.20

Tuttle, E. M. (2003). Alternative reproductive strategies in the white-throated sparrow: Behavioral and genetic evidence. *Behavioral Ecology*, 14(3), 425–432. https://doi.org/10.1093/beheco/14.3.425

van't Hof, A., Campagne, P., Rigden, D. J., Yung, C. J., Lingley, J., Quail, M. A., Hall, N., Darby, A. C., & Saccheri, I. J. (2016). The industrial melanism mutation in British peppered moths is a transposable element. *Nature*, 534(7605), 102–105. https://doi.org/10.1038/nature17951

Waters, C. D., Clemento, A., Aykanat, T., Garza, J. C., Naish, K. A., Narum, S., & Primmer, C. R. (2021). Heterogeneous genetic basis of age at maturity in salmonid fishes. *Molecular Ecology*, 30(6), 1435–1456. https://doi.org/10.1111/mec.15822

Watson, K. B., Lehnert, S. J., Bentzen, P., Kess, T., Einfeldt, A., Duffy, S., Perriman, B., Lien, S., Kent, M., & Bradbury, I. R. (2022). Environmentally associated chromosomal structural variation influences fine-scale population structure of Atlantic Salmon (*Salmo salar*). *Molecular Ecology*, 31(4), 1057–1075. https://doi.org/10.1111/mec.16307

Weir, B. S., & Cockerham, C. C. (1984). Estimating F-statistics for the analysis of population structure. *Evolution*, 38(6), 1358–1370. https://doi.org/10.2307/2408641

Weissensteiner, M. H., Bunikis, I., Catalán, A., Francoijs, K.-J., Knief, U., Heim, W., Peona, V., Pophaly, S. D., Sedlazeck, F. J., Suh, A., Warmuth, V. M., & Wolf, J. B. W. (2020). Discovery and population genomics of structural variation in a songbird genus. *Nature Communications*, 11(1), 3403. https://doi.org/10.1038/s41467-020-17195-4

Wellband, K., Mérot, C., Linnansaari, T., Elliott, J. A. K., Curry, R. A., & Bernatchez, L. (2019). Chromosomal fusion and life history-associated genomic variation contribute to within-river local adaptation of Atlantic salmon. *Molecular Ecology*, 28(6), 1439–1459. https://doi.org/10.1111/mec.14965

Wellenreuther, M., & Bernatchez, L. (2018). Eco-evolutionary genomics of chromosomal inversions. *Trends in Ecology & Evolution*, 33(6), 427–440. https://doi.org/10.1016/j.tree.2018.04.002

Wellenreuther, M., Mérot, C., Berdan, E., & Bernatchez, L. (2019). Going beyond SNPs: The role of structural genomic variants in adaptive evolution and species diversification. *Molecular Ecology*, 28(6), 1203–1209. https://doi.org/10.1111/mec.15066

Wold, J. R., Guhlin, J. G., Dearden, P. K., Santure, A. W., & Steeves, T. E. (2023). The promise and challenges of characterizing genome-wide structural variants: A case study in a critically endangered parrot. *Molecular Ecology Resources*, Advance online publication. https://doi.org/10.1111/1755-0998.13783

Wolf, J. B. W., & Ellegren, H. (2017). Making sense of genomic islands of differentiation in light of speciation. *Nature Reviews Genetics*, 18(2), 87–100. https://doi.org/10.1038/nrg.2016.133

Wright, S. (1984). *Evolution and the genetics of populations, Volume 4: Variability within and among natural populations*. University of Chicago Press.

WSP Global. (2019). *Complexe de la Romaine – Suivi environnemental 2017 en phase exploitation: Suivi de la population de saumon atlantique*. https://www.ree.environnement.gouv.qc.ca/dossiers/3211-12-086/3211-12-086-16.pdf

Yan, S. M., Sherman, R. M., Taylor, D. J., Nair, D. R., Bortvin, A. N., Schatz, M. C., & McCoy, R. C. (2021). Local adaptation and archaic introduction shape global diversity at human structural variant loci. *eLife*, 10, e67615. https://doi.org/10.7554/eLife.67615

Zhou, Y., Minio, A., Massonnet, M., Solares, E., Lv, Y., Beridze, T., Cantu, D., & Gaut, B. S. (2019). The population genetics of structural variants in grapevine domestication. *Nature Plants*, 5(9), 965–979. https://doi.org/10.1038/s41477-019-0507-8

## SUPPORTING INFORMATION

Additional supporting information can be found online in the Supporting Information section at the end of this article.

**How to cite this article:** Lecomte, L., Árnyasi, M., Ferchaud, A.-L., Kent, M., Lien, S., Stenløkk, K., Sylvestre, F., Bernatchez, L., & Mérot, C. (2024). Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations. *Evolutionary Applications*, 17, e13653. https://doi.org/10.1111/eva.13653