{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T04:42:25Z","timestamp":1791434545450,"version":"4.3.3"},"reference-count":100,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T00:00:00Z","timestamp":1775001600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,6,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Populations often adapt to their local environments despite the homogenizing effects of gene flow, but the genomic mechanisms enabling this process remain unclear. Theory predicts that adaptive divergence under high connectivity is favored when beneficial alleles cluster in regions of reduced recombination, a pattern that can be reinforced by structural variants (SVs). We investigated this in three-spined sticklebacks (Gasterosteus aculeatus) from the St. Lawrence Estuary, where distinct freshwater and marine ecotypes meet and interbreed along a short ecological gradient. Using long- and short-read whole-genome sequencing, we mapped fine-scale recombination landscapes, cataloged SVs, and examined their relationship with adaptive genomic regions. Recombination landscapes differed between populations, with population-specific shifts in recombination rate estimated by an LD-based method. Putatively adaptive regions were not confined to low-recombination regions, yet SVs (inversions, insertions, and deletions) frequently coincided with local recombination suppression and elevated differentiation, suggesting they may contribute to local adaptation. Differentiated regions also overlapped disproportionately with previously-identified regions involved in repeated local adaptation across the species range, which tended to be strongly enriched on chromosomes IV, VII and XXI. These repeated regions were associated with lower recombination rates, suggesting that recombination suppression may contribute to their reuse across populations. As found in stickleback populations from other regions, the St. Lawrence populations exhibit elements suggestive of concentrated architectures clustered in a few genomic regions, along with relatively diffuse patterns of highly differentiated regions distributed genome-wide, across a wide range of recombination rates. These results highlight the intertwined roles of recombination variation and structural variation in shaping evolutionary trajectories in connected populations.<\/jats:p>","DOI":"10.1093\/g3journal\/jkag086","type":"journal-article","created":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T17:32:35Z","timestamp":1775064755000},"source":"Crossref","is-referenced-by-count":1,"title":["The genomic architecture of local adaptation in two connected populations of three-spined stickleback"],"prefix":"10.1093","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-4178-1937","authenticated-orcid":false,"given":"Sann","family":"Delaive","sequence":"first","affiliation":[{"name":"D\u00e9partement de Biologie, Institut de Biologie Int\u00e9grative et Des Syst\u00e8mes (IBIS), Universit\u00e9 Laval , Qu\u00e9bec, Quebec , G1V 0A6","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicolas","family":"Der\u00f4me","sequence":"additional","affiliation":[{"name":"D\u00e9partement de Biologie, Institut de Biologie Int\u00e9grative et Des Syst\u00e8mes (IBIS), Universit\u00e9 Laval , Qu\u00e9bec, Quebec , G1V 0A6","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sam","family":"Yeaman","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Calgary , Calgary, Alberta , T2N 1N4","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,4,1]]},"reference":[{"key":"2026060312382314200_jkag086-B1","doi-asserted-by":"publisher","first-page":"388","DOI":"10.1093\/icb\/icac071","article-title":"Freshwater colonization, adaptation, and genomic divergence in threespine stickleback","volume":"62","author":"Aguirre","year":"2022","journal-title":"Integr Comp Biol"},{"key":"2026060312382314200_jkag086-B2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msaf092","article-title":"Genetic differentiation is constrained to chromosomal inversions and putative centromeres in locally adapted populations with higher gene flow","volume":"42","author":"Akopyan","year":"2025","journal-title":"Mol Biol Evol"},{"key":"2026060312382314200_jkag086-B3","doi-asserted-by":"publisher","first-page":"1655","DOI":"10.1101\/gr.094052.109","article-title":"Fast model-based estimation of ancestry in unrelated individuals","volume":"19","author":"Alexander","year":"2009","journal-title":"Genome Res"},{"key":"2026060312382314200_jkag086-B4","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1098\/rspb.2010.0923","article-title":"Rapid evolution of cold tolerance in stickleback","volume":"278","author":"Barrett","year":"2011","journal-title":"Proc Biol Sci"},{"key":"2026060312382314200_jkag086-B5","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/iyab229","article-title":"Efficient ancestry and mutation simulation with msprime 1.0","volume":"220","author":"Baumdicker","year":"2022","journal-title":"Genetics"},{"key":"2026060312382314200_jkag086-B6","first-page":"377","article-title":"Contemporary evolution, allelic recycling, and adaptive radiation of the threespine stickleback","volume":"15","author":"Bell","year":"2013","journal-title":"Evol Ecol Res"},{"key":"2026060312382314200_jkag086-B7","doi-asserted-by":"publisher","first-page":"4274","DOI":"10.1111\/mec.15501","article-title":"Variation in recombination rate affects detection of outliers in genome scans under neutrality","volume":"29","author":"Booker","year":"2020","journal-title":"Mol Ecol"},{"key":"2026060312382314200_jkag086-B8","doi-asserted-by":"publisher","first-page":"684","DOI":"10.1128\/mcb.5.4.684-691.1985","article-title":"Effect of insertions, deletions, and double-strand breaks on homologous recombination in mouse L cells","volume":"5","author":"Brenner","year":"1985","journal-title":"Mol Cell Biol"},{"key":"2026060312382314200_jkag086-B9","doi-asserted-by":"publisher","author":"Casale","year":"2024","DOI":"10.1101\/2024.07.22.604552"},{"key":"2026060312382314200_jkag086-B10","doi-asserted-by":"publisher","first-page":"2379","DOI":"10.1111\/mec.15499","article-title":"Shared ancestral polymorphisms and chromosomal rearrangements as potential drivers of local adaptation in a marine fish","volume":"29","author":"Cayuela","year":"2020","journal-title":"Mol Ecol"},{"key":"2026060312382314200_jkag086-B11","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1004830","article-title":"Extensive copy-number variation of young genes across stickleback populations","volume":"10","author":"Chain","year":"2014","journal-title":"PLoS Genet"},{"key":"2026060312382314200_jkag086-B12","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/s13742-015-0047-8","article-title":"Second-generation PLINK: rising to the challenge of larger and richer datasets","volume":"4","author":"Chang","year":"2015","journal-title":"Gigascience"},{"key":"2026060312382314200_jkag086-B13","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1534\/genetics.111.134288","article-title":"The effects of deleterious mutations on evolution at linked sites","volume":"190","author":"Charlesworth","year":"2012","journal-title":"Genetics"},{"key":"2026060312382314200_jkag086-B14","doi-asserted-by":"publisher","first-page":"632","DOI":"10.1111\/jeb.14137","article-title":"Why and how do Y chromosome stop recombining?","volume":"36","author":"Charlesworth","year":"2023","journal-title":"J Evol Biol"},{"key":"2026060312382314200_jkag086-B15","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1017\/S0016672397002954","article-title":"The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations","volume":"70","author":"Charlesworth","year":"1997","journal-title":"Genet Res"},{"key":"2026060312382314200_jkag086-B16","doi-asserted-by":"publisher","first-page":"S30","DOI":"10.1038\/ng2042","article-title":"The population genetics of structural variation","volume":"39","author":"Conrad","year":"2007","journal-title":"Nat Genet."},{"key":"2026060312382314200_jkag086-B17","doi-asserted-by":"publisher","first-page":"3133","DOI":"10.1111\/mec.12796","article-title":"Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow","volume":"23","author":"Cruickshank","year":"2014","journal-title":"Mol Ecol"},{"key":"2026060312382314200_jkag086-B18","article-title":"Population genetic structure of three-spined sticklebacks in the St. Lawrence: a gradient of change","author":"Delaive","year":"2025","journal-title":"NCBI BioProject. Accession: PRJNA1327819"},{"key":"2026060312382314200_jkag086-B19","doi-asserted-by":"publisher","first-page":"4765","DOI":"10.1111\/mec.15565","article-title":"Copy number variants outperform SNPs to reveal genotype\u2013temperature association in a marine species","volume":"29","author":"Dorant","year":"2020","journal-title":"Mol Ecol"},{"key":"2026060312382314200_jkag086-B20","doi-asserted-by":"publisher","DOI":"10.1111\/mec.17126","article-title":"Conserved islands of divergence associated with adaptive variation in sockeye salmon are maintained by multiple mechanisms","volume":"33","author":"Euclide","year":"2024","journal-title":"Mol Ecol"},{"key":"2026060312382314200_jkag086-B21","doi-asserted-by":"publisher","first-page":"613","DOI":"10.1016\/j.ympev.2018.06.008","article-title":"Worldwide phylogeny of three-spined sticklebacks","volume":"127","author":"Fang","year":"2018","journal-title":"Mol Phylogenet Evol"},{"key":"2026060312382314200_jkag086-B22","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1016\/j.tig.2012.03.009","article-title":"The genomics of speciation-with-gene-flow","volume":"28","author":"Feder","year":"2012","journal-title":"Trends Genet"},{"key":"2026060312382314200_jkag086-B23","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1111\/ele.12388","article-title":"Locally adapted traits maintained in the face of high gene flow","volume":"18","author":"Fitzpatrick","year":"2015","journal-title":"Ecol Lett"},{"key":"2026060312382314200_jkag086-B24","doi-asserted-by":"publisher","DOI":"10.1111\/eva.13675","article-title":"Adaptation to seasonal reproduction and environment-associated factors drive temporal and spatial differentiation in northwest Atlantic herring despite gene flow","volume":"17","author":"Fuentes-Pardo","year":"2024","journal-title":"Evol Appl"},{"key":"2026060312382314200_jkag086-B25","doi-asserted-by":"publisher","first-page":"1139","DOI":"10.1093\/oxfordjournals.molbev.a003886","article-title":"Local rates of recombination are positively correlated with GC content in the human genome","volume":"18","author":"Fullerton","year":"2001","journal-title":"Mol Biol Evol"},{"key":"2026060312382314200_jkag086-B26","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1002\/edn3.221","article-title":"Fish community shifts along a strong fluvial environmental gradient revealed by eDNA metabarcoding","volume":"4","author":"Garc\u00eda-Machado","year":"2022","journal-title":"Environmental DNA"},{"key":"2026060312382314200_jkag086-B27","doi-asserted-by":"publisher","first-page":"1965","DOI":"10.1038\/s41559-022-01890-0","article-title":"Chromosomal inversion polymorphisms shape the genomic landscape of deer mice","volume":"6","author":"Harringmeyer","year":"2022","journal-title":"Nat Ecol Evol"},{"key":"2026060312382314200_jkag086-B28","doi-asserted-by":"publisher","DOI":"10.1126\/science.adj7026","article-title":"Patterns of recombination in snakes reveal a tug-of-war between PRDM9 and promoter-like features","volume":"383","author":"Hoge","year":"2024","journal-title":"Science"},{"key":"2026060312382314200_jkag086-B29","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1000862","article-title":"Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags","volume":"6","author":"Hohenlohe","year":"2010","journal-title":"PLoS Genet"},{"key":"2026060312382314200_jkag086-B30","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1007\/13836_2019_67","volume-title":"Population genomics: marine organisms","author":"Hohenlohe","year":"2020"},{"key":"2026060312382314200_jkag086-B31","doi-asserted-by":"publisher","first-page":"1240","DOI":"10.1111\/nph.13643","article-title":"Evidence for extensive parallelism but divergent genomic architecture of adaptation along altitudinal and latitudinal gradients in Populus trichocarpa","volume":"209","author":"Holliday","year":"2016","journal-title":"New Phytol"},{"key":"2026060312382314200_jkag086-B32","doi-asserted-by":"publisher","first-page":"3840","DOI":"10.1111\/mec.15996","article-title":"Intraspecific genetic variation matters when predicting seagrass distribution under climate change","volume":"30","author":"Hu","year":"2021","journal-title":"Mol Ecol"},{"key":"2026060312382314200_jkag086-B33","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2427312122","article-title":"Polymorphic transposable elements contribute to variation in recombination landscapes","volume":"122","author":"Huang","year":"2025","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026060312382314200_jkag086-B34","doi-asserted-by":"publisher","first-page":"2735","DOI":"10.1111\/evo.12771","article-title":"Quantitative genetic variance in experimental fly populations evolving with or without environmental heterogeneity","volume":"69","author":"Huang","year":"2015","journal-title":"Evolution"},{"key":"2026060312382314200_jkag086-B35","doi-asserted-by":"publisher","first-page":"1916","DOI":"10.1093\/evolut\/qpae117","article-title":"Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure","volume":"78","author":"Ishigohoka","year":"2024","journal-title":"Evolution"},{"key":"2026060312382314200_jkag086-B36","doi-asserted-by":"publisher","DOI":"10.1111\/mec.17297","article-title":"The interplay of local adaptation and gene flow may lead to the formation of supergenes","volume":"33","author":"Jay","year":"2018","journal-title":"Mol Ecol"},{"key":"2026060312382314200_jkag086-B37","doi-asserted-by":"publisher","first-page":"625","DOI":"10.1038\/ng.346","article-title":"The rise and fall of a human recombination hot spot","volume":"41","author":"Jeffreys","year":"2009","journal-title":"Nat Genet"},{"key":"2026060312382314200_jkag086-B38","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msae112","article-title":"Understanding the genetic basis of variation in meiotic recombination: past, present, and future","volume":"41","author":"Johnston","year":"2024","journal-title":"Mol Biol Evol"},{"key":"2026060312382314200_jkag086-B39","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1038\/nature10944","article-title":"The genomic basis of adaptive evolution in threespine sticklebacks","volume":"484","author":"Jones","year":"2012","journal-title":"Nature"},{"key":"2026060312382314200_jkag086-B40","doi-asserted-by":"publisher","first-page":"1381","DOI":"10.1534\/genetics.115.184820","article-title":"Two-locus likelihoods under variable population size and fine-scale recombination rate estimation","volume":"203","author":"Kamm","year":"2016","journal-title":"Genetics"},{"key":"2026060312382314200_jkag086-B41","doi-asserted-by":"publisher","first-page":"111431","DOI":"10.1016\/j.jtbi.2023.111431","article-title":"Effect of beneficial sweeps and background selection on genetic diversity in changing environments","volume":"562","author":"Kaushik","year":"2023","journal-title":"J Theor Biol"},{"key":"2026060312382314200_jkag086-B42","doi-asserted-by":"publisher","first-page":"1225","DOI":"10.1111\/j.1461-0248.2004.00684.x","article-title":"Conceptual issues in local adaptation","volume":"7","author":"Kawecki","year":"2004","journal-title":"Ecol Lett"},{"key":"2026060312382314200_jkag086-B43","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.1000501","article-title":"How and why chromosome inversions evolve","volume":"8","author":"Kirkpatrick","year":"2010","journal-title":"PLoS Biol"},{"key":"2026060312382314200_jkag086-B44","doi-asserted-by":"publisher","DOI":"10.1111\/eva.13653","article-title":"Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations","volume":"17","author":"Lecomte","year":"2024","journal-title":"Evol Appl"},{"key":"2026060312382314200_jkag086-B45","doi-asserted-by":"publisher","first-page":"E7204","DOI":"10.1073\/pnas.1512020112","article-title":"Evolution of stickleback in 50 years on earthquake-uplifted islands","volume":"112","author":"Lescak","year":"2015","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026060312382314200_jkag086-B46","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1016\/0040-5809(74)90022-7","article-title":"Stable linkage disequilibrium without epistasis in subdivided populations","volume":"6","author":"Li","year":"1974","journal-title":"Theor Popul Biol"},{"key":"2026060312382314200_jkag086-B47","doi-asserted-by":"publisher","first-page":"3686","DOI":"10.1111\/j.1365-294X.2012.05639.x","article-title":"Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus)","volume":"21","author":"Limborg","year":"2012","journal-title":"Mol Ecol"},{"key":"2026060312382314200_jkag086-B48","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0040224","article-title":"Investigation of inversion polymorphisms in the human genome using principal components analysis","volume":"7","author":"Ma","year":"2012","journal-title":"PLoS One"},{"key":"2026060312382314200_jkag086-B49","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1016\/j.tree.2019.02.008","article-title":"A combinatorial view on speciation and adaptive radiation","volume":"34","author":"Marques","year":"2019","journal-title":"Trends Ecol Evol"},{"key":"2026060312382314200_jkag086-B50","doi-asserted-by":"publisher","first-page":"362","DOI":"10.1038\/hdy.2015.104","article-title":"On the importance of being structured: instantaneous coalescence rates and human evolution\u2014lessons for ancestral population size inference?","volume":"116","author":"Mazet","year":"2016","journal-title":"Heredity (Edinb)."},{"key":"2026060312382314200_jkag086-B51","doi-asserted-by":"publisher","first-page":"3901","DOI":"10.1111\/j.1365-294X.2008.03884.x","article-title":"Landscape genetic analyses reveal cryptic population structure and putative selection gradients in a large-scale estuarine environment","volume":"17","author":"McCairns","year":"2008","journal-title":"Mol Ecol"},{"key":"2026060312382314200_jkag086-B52","doi-asserted-by":"publisher","first-page":"1097","DOI":"10.1111\/j.1420-9101.2012.02496.x","article-title":"Plasticity and heritability of morphological variation within and between parapatric stickleback demes","volume":"25","author":"Mccairns","year":"2012","journal-title":"J Evol Biol"},{"key":"2026060312382314200_jkag086-B53","doi-asserted-by":"publisher","first-page":"2513","DOI":"10.1111\/mec.15500","article-title":"Making the most of population genomic data to understand the importance of chromosomal inversions for adaptation and speciation","volume":"29","author":"M\u00e9rot","year":"2020","journal-title":"Mol Ecol"},{"key":"2026060312382314200_jkag086-B54","doi-asserted-by":"publisher","first-page":"3953","DOI":"10.1093\/molbev\/msab143","article-title":"Locally adaptive inversions modulate genetic variation at different geographic scales in a seaweed fly","volume":"38","author":"M\u00e9rot","year":"2021","journal-title":"Mol Biol Evol"},{"key":"2026060312382314200_jkag086-B55","doi-asserted-by":"publisher","first-page":"561","DOI":"10.1016\/j.tree.2020.03.002","article-title":"A roadmap for understanding the evolutionary significance of structural genomic variation","volume":"35","author":"M\u00e9rot","year":"2020","journal-title":"Trends Ecol Evol"},{"key":"2026060312382314200_jkag086-B56","doi-asserted-by":"publisher","DOI":"10.1111\/mec.17277","article-title":"Divergence and gene flow history at two large chromosomal inversions underlying ecotype differentiation in the long-snouted seahorse","volume":"33","author":"Meyer","year":"2024","journal-title":"Mol Ecol"},{"key":"2026060312382314200_jkag086-B57","doi-asserted-by":"publisher","first-page":"603","DOI":"10.1534\/genetics.116.197988","article-title":"Structural variation shapes the landscape of recombination in mouse","volume":"206","author":"Morgan","year":"2017","journal-title":"Genetics"},{"key":"2026060312382314200_jkag086-B58","doi-asserted-by":"publisher","first-page":"561","DOI":"10.1111\/mec.12624","article-title":"Local adaptation with high gene flow: temperature parameters drive adaptation to altitude in the common frog (Rana temporaria)","volume":"23","author":"Muir","year":"2014","journal-title":"Mol Ecol"},{"key":"2026060312382314200_jkag086-B59","doi-asserted-by":"publisher","first-page":"jkab007","DOI":"10.1093\/g3journal\/jkab007","article-title":"Improved contiguity of the threespine stickleback genome using long-read sequencing","volume":"11","author":"Nath","year":"2021","journal-title":"G3 (Bethesda)"},{"key":"2026060312382314200_jkag086-B60","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1002\/evl3.37","article-title":"Ancient genomic variation underlies repeated ecological adaptation in young stickleback populations","volume":"2","author":"Nelson","year":"2018","journal-title":"Evol Lett"},{"key":"2026060312382314200_jkag086-B61","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1038\/hdy.2009.151","article-title":"Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species","volume":"103","author":"Noor","year":"2009","journal-title":"Heredity (Edinb)."},{"key":"2026060312382314200_jkag086-B62","doi-asserted-by":"publisher","first-page":"1940","DOI":"10.1073\/pnas.79.6.1940","article-title":"Linkage disequilibrium due to random genetic drift in finite subdivided populations","volume":"79","author":"Ohta","year":"1982","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026060312382314200_jkag086-B63","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1006\/tpbi.1997.1301","article-title":"Deleterious mutations, variable epistatic interactions, and the evolution of recombination","volume":"51","author":"Otto","year":"1997","journal-title":"Theor Popul Biol"},{"key":"2026060312382314200_jkag086-B64","doi-asserted-by":"publisher","first-page":"msae273","DOI":"10.1093\/molbev\/msae273","article-title":"Selection can favor a recombination landscape that limits polygenic adaptation","volume":"42","author":"Par\u00e9e","year":"2025","journal-title":"Mol Biol Evol"},{"key":"2026060312382314200_jkag086-B65","doi-asserted-by":"publisher","first-page":"20150486","DOI":"10.1098\/rstb.2015.0486","article-title":"The genetic and molecular architecture of phenotypic diversity in sticklebacks","volume":"372","author":"Peichel","year":"2017","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"key":"2026060312382314200_jkag086-B66","doi-asserted-by":"publisher","first-page":"476","DOI":"10.1038\/s41576-020-0240-1","article-title":"From molecules to populations: appreciating and estimating recombination rate variation","volume":"21","author":"Pe\u00f1alba","year":"2020","journal-title":"Nat Rev Genet"},{"key":"2026060312382314200_jkag086-B67","doi-asserted-by":"publisher","first-page":"3580","DOI":"10.1111\/mec.12337","article-title":"Signals of selection in outlier loci in a widely dispersing species across an environmental mosaic","volume":"22","author":"Pespeni","year":"2013","journal-title":"Mol Ecol"},{"key":"2026060312382314200_jkag086-B68","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1093\/gbe\/evv250","article-title":"Construction of ultradense linkage maps with lep-MAP2: stickleback F2 recombinant crosses as an example","volume":"8","author":"Rastas","year":"2016","journal-title":"Genome Biol Evol"},{"key":"2026060312382314200_jkag086-B69","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3002950","article-title":"PRDM9 drives the location and rapid evolution of recombination hotspots in salmonid fish","volume":"23","author":"Raynaud","year":"2025","journal-title":"PLoS Biol"},{"key":"2026060312382314200_jkag086-B70","doi-asserted-by":"publisher","first-page":"article no. e27","DOI":"10.24072\/pcjournal.254","article-title":"Performance and limitations of linkage-disequilibrium-based methods for inferring the genomic landscape of recombination and detecting hotspots: a simulation study","volume":"3","author":"Raynaud","year":"2023","journal-title":"Peer Community J"},{"key":"2026060312382314200_jkag086-B71","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1146\/annurev-genom-111720-081402","article-title":"Threespine stickleback: a model system for evolutionary genomics","volume":"22","author":"Reid","year":"2021","journal-title":"Annu Rev Genomics Hum Genet"},{"key":"2026060312382314200_jkag086-B72","doi-asserted-by":"publisher","first-page":"1081","DOI":"10.1163\/156853900502448","article-title":"Predator handling failures of lateral plate morphs in Gasterosteus Aculeatus: functional implications for the ancestral plate condition","volume":"137","author":"Reimchen","year":"2000","journal-title":"Behaviour"},{"key":"2026060312382314200_jkag086-B73","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abg5285","article-title":"Predicting future from past: the genomic basis of recurrent and rapid stickleback evolution","volume":"7","author":"Roberts Kingman","year":"2021","journal-title":"Sci Adv"},{"key":"2026060312382314200_jkag086-B74","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1038\/s41437-025-00784-8","article-title":"Experimental test of the fitness effects of divergent marine\u2013freshwater chromosomal inversions in stickleback under different salinity conditions","volume":"135","author":"Rodr\u00edguez-Fuentes","year":"2025","journal-title":"Heredity (Edinb)"},{"key":"2026060312382314200_jkag086-B75","doi-asserted-by":"publisher","first-page":"8767","DOI":"10.1038\/ncomms9767","article-title":"The genomics of ecological vicariance in threespine stickleback fish","volume":"6","author":"Roesti","year":"2015","journal-title":"Nat Commun"},{"key":"2026060312382314200_jkag086-B76","doi-asserted-by":"publisher","first-page":"962","DOI":"10.1111\/mec.70027","article-title":"Inversions dominate evolution in the European sardine (Sardina pilchardus) amid strong gene flow","volume":"34","author":"Sabatino","year":"2025","journal-title":"Mol Ecol"},{"key":"2026060312382314200_jkag086-B77","doi-asserted-by":"publisher","first-page":"4378","DOI":"10.1111\/mec.14226","article-title":"Gene flow and selection interact to promote adaptive divergence in regions of low recombination","volume":"26","author":"Samuk","year":"2017","journal-title":"Mol Ecol"},{"key":"2026060312382314200_jkag086-B78","doi-asserted-by":"publisher","first-page":"699","DOI":"10.2307\/1940797","article-title":"Adaptive radiation in sticklebacks: size, shape, and habitat use efficiency","volume":"74","author":"Schluter","year":"1993","journal-title":"Ecology"},{"key":"2026060312382314200_jkag086-B79","doi-asserted-by":"publisher","first-page":"1552","DOI":"10.1093\/gbe\/evz090","article-title":"Divergent fine-scale recombination landscapes between a freshwater and marine population of threespine stickleback fish","volume":"11","author":"Shanfelter","year":"2019","journal-title":"Genome Biol Evol"},{"key":"2026060312382314200_jkag086-B80","doi-asserted-by":"publisher","first-page":"1549","DOI":"10.1111\/mec.16317","article-title":"Gene flow influences the genomic architecture of local adaptation in six riverine fish species","volume":"32","author":"Shi","year":"2023","journal-title":"Mol Ecol"},{"key":"2026060312382314200_jkag086-B81","doi-asserted-by":"publisher","first-page":"2427","DOI":"10.1105\/tpc.15.00391","article-title":"DNA crossover motifs associated with epigenetic modifications delineate open chromatin regions in Arabidopsis","volume":"27","author":"Shilo","year":"2015","journal-title":"Plant Cell"},{"key":"2026060312382314200_jkag086-B82","doi-asserted-by":"publisher","first-page":"8568","DOI":"10.1038\/s41598-024-59157-6","article-title":"Putative climate adaptation in American pikas (Ochotona princeps) is associated with copy number variation across environmental gradients","volume":"14","author":"Sjodin","year":"2024","journal-title":"Sci Rep"},{"key":"2026060312382314200_jkag086-B83","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1038\/hdy.2011.44","article-title":"Recombination rate variation in closely related species","volume":"107","author":"Smukowski","year":"2011","journal-title":"Heredity (Edinb)"},{"key":"2026060312382314200_jkag086-B84","doi-asserted-by":"publisher","first-page":"RP88604","DOI":"10.7554\/eLife.88604.2","article-title":"Repeatability of adaptation in sunflowers: genomic regions harbouring inversions also drive adaptation in species lacking an inversion","volume":"12","author":"Soudi","year":"2023","journal-title":"eLife"},{"key":"2026060312382314200_jkag086-B85","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.aaw9206","article-title":"Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations","volume":"5","author":"Spence","year":"2019","journal-title":"Sci Adv"},{"key":"2026060312382314200_jkag086-B86","doi-asserted-by":"publisher","first-page":"830","DOI":"10.1093\/gbe\/evr081","article-title":"Effects of inversions on within- and between-species recombination and divergence","volume":"3","author":"Stevison","year":"2011","journal-title":"Genome Biol Evol"},{"key":"2026060312382314200_jkag086-B87","author":"Stuart","year":"2026"},{"key":"2026060312382314200_jkag086-B88","doi-asserted-by":"publisher","first-page":"1667","DOI":"10.1093\/evolut\/qpad075","article-title":"Searching for intralocus sexual conflicts in the three-spined stickleback (Gasterosteus aculeatus) genome","volume":"77","author":"Sylvestre","year":"2023","journal-title":"Evolution"},{"key":"2026060312382314200_jkag086-B89","doi-asserted-by":"publisher","first-page":"364","DOI":"10.1093\/evolut\/qpae169","article-title":"Rapid evolution of recombination landscapes during the divergence of cichlid ecotypes in Lake Masoko","volume":"79","author":"Talbi","year":"2025","journal-title":"Evolution"},{"key":"2026060312382314200_jkag086-B90","doi-asserted-by":"publisher","first-page":"13412","DOI":"10.1002\/ece3.6945","article-title":"Allometric relationships in morphological traits associated with foraging, swimming ability, and predator defense reveal adaptations toward brackish and freshwater environments in the threespine stickleback","volume":"10","author":"Taugb\u00f8l","year":"2020","journal-title":"Ecol Evol"},{"key":"2026060312382314200_jkag086-B91","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1004696","article-title":"Fast evolution from precast bricks: genomics of young freshwater populations of threespine stickleback Gasterosteus aculeatus","volume":"10","author":"Terekhanova","year":"2014","journal-title":"PLoS Genet"},{"key":"2026060312382314200_jkag086-B92","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1038\/ng.3748","article-title":"Robust and scalable inference of population history from hundreds of unphased whole genomes","volume":"49","author":"Terhorst","year":"2017","journal-title":"Nat Genet"},{"key":"2026060312382314200_jkag086-B93","doi-asserted-by":"publisher","first-page":"2144","DOI":"10.1111\/mec.13606","article-title":"Genomics of local adaptation with gene flow","volume":"25","author":"Tigano","year":"2016","journal-title":"Mol Ecol"},{"key":"2026060312382314200_jkag086-B94","doi-asserted-by":"publisher","first-page":"1337","DOI":"10.1038\/s41559-024-02434-4","article-title":"Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish","volume":"8","author":"Venu","year":"2024","journal-title":"Nat Ecol Evol"},{"key":"2026060312382314200_jkag086-B95","doi-asserted-by":"publisher","first-page":"503","DOI":"10.1101\/gr.103663.109","article-title":"Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution","volume":"20","author":"V\u00f6lker","year":"2010","journal-title":"Genome Res"},{"key":"2026060312382314200_jkag086-B96","doi-asserted-by":"publisher","first-page":"1203","DOI":"10.1111\/mec.15066","article-title":"Going beyond SNPs: the role of structural genomic variants in adaptive evolution and species diversification","volume":"28","author":"Wellenreuther","year":"2019","journal-title":"Mol Ecol"},{"key":"2026060312382314200_jkag086-B97","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2413587122","article-title":"Copy number variation contributes to parallel local adaptation in an invasive plant","volume":"122","author":"Wilson","year":"2025","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026060312382314200_jkag086-B98","doi-asserted-by":"publisher","first-page":"iyab134","DOI":"10.1093\/genetics\/iyab134","article-title":"Evolution of polygenic traits under global vs local adaptation","volume":"220","author":"Yeaman","year":"2022","journal-title":"Genetics"},{"key":"2026060312382314200_jkag086-B99","doi-asserted-by":"publisher","first-page":"1897","DOI":"10.1111\/j.1558-5646.2011.01269.x","article-title":"The genetic architecture of adaptation under migration\u2013selection balance","volume":"65","author":"Yeaman","year":"2011","journal-title":"Evolution"},{"key":"2026060312382314200_jkag086-B100","doi-asserted-by":"publisher","first-page":"msad192","DOI":"10.1093\/molbev\/msad192","article-title":"De novo mutation rates in sticklebacks","volume":"40","author":"Zhang","year":"2023","journal-title":"Mol Biol Evol"}],"container-title":["G3: Genes, Genomes, Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/g3journal\/advance-article-pdf\/doi\/10.1093\/g3journal\/jkag086\/67713503\/jkag086.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/g3journal\/article-pdf\/16\/6\/jkag086\/67713503\/jkag086.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/g3journal\/article-pdf\/16\/6\/jkag086\/67713503\/jkag086.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T16:38:28Z","timestamp":1780504708000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/g3journal\/article\/doi\/10.1093\/g3journal\/jkag086\/8571313"}},"subtitle":[],"editor":[{"given":"A","family":"Whitehead","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,4,1]]},"references-count":100,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2026,4,1]]},"published-print":{"date-parts":[[2026,6,3]]}},"URL":"https:\/\/doi.org\/10.1093\/g3journal\/jkag086","relation":{},"ISSN":["2160-1836"],"issn-type":[{"value":"2160-1836","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,6]]},"published":{"date-parts":[[2026,4,1]]},"article-number":"jkag086"}}