{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T06:04:56Z","timestamp":1792044296331,"version":"4.4.0"},"reference-count":104,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2025,3,7]],"date-time":"2025-03-07T00:00:00Z","timestamp":1741305600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01 GM127480"],"award-info":[{"award-number":["R01 GM127480"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R35 GM136306"],"award-info":[{"award-number":["R35 GM136306"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,5,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The distribution of allelic effects on traits, along with their gene-by-gene and gene-by-environment interactions, contributes to the phenotypes available for selection and the trajectories of adaptive variants. Nonetheless, uncertainty persists regarding the effect sizes underlying adaptations and the importance of genetic interactions. Herein, we aimed to investigate the genetic architecture and the epistatic and environmental interactions involving loci that contribute to multiple adaptive traits using 2 new panels of Drosophila melanogaster recombinant inbred lines (RILs). To better fit our data, we re-implemented functions from R\/qtl using additive genetic models. We found 14 quantitative trait loci (QTLs) underlying melanism, wing size, song pattern, and ethanol resistance. By combining our mapping results with population genetic statistics, we identified potential new genes related to these traits. None of the detected QTLs showed clear evidence of epistasis, and our power analysis indicated that we should have seen at least 1 significant interaction if sign epistasis or strong positive epistasis played a pervasive role in trait evolution. In contrast, we did find roles for gene-by-environment interactions involving pigmentation traits. Overall, our data suggest that the genetic architecture of adaptive traits often involves alleles of detectable effect, that strong epistasis does not always play a role in adaptation, and that environmental interactions can modulate the effect size of adaptive alleles.<\/jats:p>","DOI":"10.1093\/g3journal\/jkaf051","type":"journal-article","created":{"date-parts":[[2025,3,7]],"date-time":"2025-03-07T19:59:26Z","timestamp":1741377566000},"source":"Crossref","is-referenced-by-count":5,"title":["Recombinant inbred line panels inform the genetic architecture and interactions of adaptive traits in <i>Drosophila melanogaster<\/i>"],"prefix":"10.1093","volume":"15","author":[{"given":"Tiago","family":"da Silva Ribeiro","sequence":"first","affiliation":[{"name":"Laboratory of Genetics, University of Wisconsin\u2013Madison , Madison, WI 53706 ,","place":["USA"]},{"name":"Department of Integrative Biology, University of Wisconsin\u2013Madison , Madison, WI 53706 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew J","family":"Lollar","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics, University of Wisconsin\u2013Madison , Madison, WI 53706 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quentin D","family":"Sprengelmeyer","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics, University of Wisconsin\u2013Madison , Madison, WI 53706 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1586-953X","authenticated-orcid":false,"given":"Yuheng","family":"Huang","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics, University of Wisconsin\u2013Madison , Madison, WI 53706 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Derek M","family":"Benson","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics, University of Wisconsin\u2013Madison , Madison, WI 53706 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Megan S","family":"Orr","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics, University of Wisconsin\u2013Madison , Madison, WI 53706 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zachary C","family":"Johnson","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics, University of Wisconsin\u2013Madison , Madison, WI 53706 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Russell B","family":"Corbett-Detig","sequence":"additional","affiliation":[{"name":"Genomics Institute, University of California, Santa Cruz , Santa Cruz, CA 95064 ,","place":["USA"]},{"name":"Department of Biomolecular Engineering, University of California, Santa Cruz , Santa Cruz, CA 95064 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2968-9545","authenticated-orcid":false,"given":"John E","family":"Pool","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics, University of Wisconsin\u2013Madison , Madison, WI 53706 ,","place":["USA"]},{"name":"Department of Integrative Biology, University of Wisconsin\u2013Madison , Madison, WI 53706 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,3,7]]},"reference":[{"issue":"7","key":"2025050809213710900_jkaf051-B1","first-page":"36","article-title":"Image processing with ImageJ","volume":"11","author":"Abramoff","year":"2004","journal-title":"Biophotonics Intern"},{"issue":"13","key":"2025050809213710900_jkaf051-B2","doi-asserted-by":"publisher","first-page":"e75","DOI":"10.1093\/nar\/gkaa450","article-title":"One fly\u2013one genome: chromosome-scale genome assembly of a single outbred Drosophila melanogaster","volume":"48","author":"Adams","year":"2020","journal-title":"Nucleic Acids Res."},{"issue":"4","key":"2025050809213710900_jkaf051-B3","doi-asserted-by":"publisher","first-page":"100260","DOI":"10.1016\/j.xgen.2023.100260","article-title":"Widespread epistasis among beneficial genetic variants revealed by high-throughput genome editing","volume":"3","author":"Ang","year":"2023","journal-title":"Cell Genom."},{"key":"2025050809213710900_jkaf051-B4","doi-asserted-by":"publisher","author":"Arthur","year":"2021","DOI":"10.1101\/2021.03.26.437280"},{"issue":"1","key":"2025050809213710900_jkaf051-B5","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1186\/1741-7007-11-11","article-title":"Multi-channel acoustic recording and automated analysis of Drosophila courtship songs","volume":"11","author":"Arthur","year":"2013","journal-title":"BMC Biol."},{"issue":"1","key":"2025050809213710900_jkaf051-B6","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1146\/annurev-ecolsys-102320-112153","article-title":"Epistasis and adaptation on fitness landscapes","volume":"53","author":"Bank","year":"2022","journal-title":"Annu Rev Ecol Evol Syst."},{"issue":"12","key":"2025050809213710900_jkaf051-B7","doi-asserted-by":"publisher","first-page":"769","DOI":"10.1038\/s41576-020-0250-z","article-title":"Polygenic adaptation: a unifying framework to understand positive selection","volume":"21","author":"Barghi","year":"2020","journal-title":"Nat Rev Genet."},{"issue":"1","key":"2025050809213710900_jkaf051-B8","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1038\/hdy.2016.109","article-title":"How does epistasis influence the response to selection?","volume":"118","author":"Barton","year":"2017","journal-title":"Heredity (Edinb)."},{"issue":"3","key":"2025050809213710900_jkaf051-B9","doi-asserted-by":"publisher","first-page":"1307","DOI":"10.1534\/genetics.116.192492","article-title":"A variable genetic architecture of melanic evolution in Drosophila melanogaster","volume":"204","author":"Bastide","year":"2016","journal-title":"Genetics"},{"issue":"1","key":"2025050809213710900_jkaf051-B10","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1186\/s12862-014-0179-y","article-title":"Pigmentation in Drosophila melanogaster reaches its maximum in Ethiopia and correlates most strongly with ultra-violet radiation in sub-Saharan Africa","volume":"14","author":"Bastide","year":"2014","journal-title":"BMC Evol Biol."},{"issue":"1","key":"2025050809213710900_jkaf051-B11","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1534\/genetics.107.081869","article-title":"A gain-of-function suppressor screen for genes involved in dorsal\u2013ventral boundary formation in the Drosophila wing","volume":"178","author":"Bejarano","year":"2008","journal-title":"Genetics"},{"issue":"1","key":"2025050809213710900_jkaf051-B12","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-213X-10-94","article-title":"Gene expression following induction of regeneration in Drosophila wing imaginal discs. Expression profile of regenerating wing discs","volume":"10","author":"Blanco","year":"2010","journal-title":"BMC Dev Biol."},{"issue":"30","key":"2025050809213710900_jkaf051-B13","doi-asserted-by":"publisher","first-page":"e2122152119","DOI":"10.1073\/pnas.2122152119","article-title":"Genetics of adaptation","volume":"119","author":"Bomblies","year":"2022","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"7","key":"2025050809213710900_jkaf051-B14","doi-asserted-by":"publisher","first-page":"889","DOI":"10.1093\/bioinformatics\/btg112","article-title":"R\/qtl: QTL mapping in experimental crosses","volume":"19","author":"Broman","year":"2003","journal-title":"Bioinformatics"},{"issue":"3","key":"2025050809213710900_jkaf051-B15","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1016\/j.tpb.2005.05.002","article-title":"The role of epistatic gene interactions in the response to selection and the evolution of evolvability","volume":"68","author":"Carter","year":"2005","journal-title":"Theor Popul Biol."},{"issue":"15","key":"2025050809213710900_jkaf051-B16","doi-asserted-by":"publisher","first-page":"2400","DOI":"10.1016\/j.cub.2018.06.011","article-title":"Discovery of a new song mode in Drosophila reveals hidden structure in the sensory and neural drivers of behavior","volume":"28","author":"Clemens","year":"2018","journal-title":"Curr Biol."},{"issue":"2","key":"2025050809213710900_jkaf051-B17","doi-asserted-by":"publisher","first-page":"278","DOI":"10.2307\/2408362","article-title":"Latitudinal cline in Drosophila melanogaster for knockdown resistance to ethanol fumes and for rates of response to selection for further resistance","volume":"39","author":"Cohan","year":"1985","journal-title":"Evolution"},{"issue":"4","key":"2025050809213710900_jkaf051-B18","doi-asserted-by":"publisher","first-page":"766","DOI":"10.2307\/2409305","article-title":"A test of the role of epistasis in divergence under uniform selection","volume":"43","author":"Cohan","year":"1989","journal-title":"Evolution"},{"issue":"10","key":"2025050809213710900_jkaf051-B19","doi-asserted-by":"publisher","first-page":"e1002905","DOI":"10.1371\/journal.pgen.1002905","article-title":"The many landscapes of recombination in Drosophila melanogaster","volume":"8","author":"Comeron","year":"2012","journal-title":"PLoS Genet."},{"issue":"1","key":"2025050809213710900_jkaf051-B20","doi-asserted-by":"publisher","first-page":"e1006529","DOI":"10.1371\/journal.pgen.1006529","article-title":"A hidden Markov model approach for simultaneously estimating local ancestry and admixture time using next generation sequence data in samples of arbitrary ploidy","volume":"13","author":"Corbett-Detig","year":"2017","journal-title":"PLoS Genet."},{"issue":"1544","key":"2025050809213710900_jkaf051-B21","doi-asserted-by":"publisher","first-page":"1241","DOI":"10.1098\/rstb.2009.0275","article-title":"On epistasis: why it is unimportant in polygenic directional selection","volume":"365","author":"Crow","year":"2010","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"issue":"10","key":"2025050809213710900_jkaf051-B22","doi-asserted-by":"publisher","first-page":"evac143","DOI":"10.1093\/gbe\/evac143","article-title":"Maximum SNP FST outperforms full-window statistics for detecting soft sweeps in local adaptation","volume":"14","author":"da Silva Ribeiro","year":"2022","journal-title":"Genome Biol Evol."},{"issue":"5\u20136","key":"2025050809213710900_jkaf051-B23","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1046\/j.1420-9101.1990.3050429.x","article-title":"Abdominal pigmentation and growth temperature in Drosophila melanogaster: similarities and differences in the norms of reaction of successive segments","volume":"3","author":"David","year":"1990","journal-title":"J Evol Biol."},{"issue":"13","key":"2025050809213710900_jkaf051-B24","doi-asserted-by":"publisher","first-page":"1208","DOI":"10.1016\/j.cub.2004.06.051","article-title":"Identification of the gene encoding bursicon, an insect neuropeptide responsible for cuticle sclerotization and wing spreading","volume":"14","author":"Dewey","year":"2004","journal-title":"Curr Biol."},{"issue":"17","key":"2025050809213710900_jkaf051-B25","doi-asserted-by":"publisher","first-page":"6178","DOI":"10.1073\/pnas.1308940110","article-title":"Beyond the single gene: how epistasis and gene-by-environment effects influence crop domestication","volume":"111","author":"Doust","year":"2014","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"4","key":"2025050809213710900_jkaf051-B26","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1007\/s00122-011-1734-1","article-title":"Towards the adaptation of grapevine varieties to climate change: QTLs and candidate genes for developmental stages","volume":"124","author":"Duch\u00eane","year":"2012","journal-title":"Theor Appl Genet."},{"issue":"3","key":"2025050809213710900_jkaf051-B27","doi-asserted-by":"publisher","first-page":"1417","DOI":"10.1534\/genetics.105.053868","article-title":"Epidermal growth factor receptor and transforming growth factor-\u03b2 signaling contributes to variation for wing shape in Drosophila melanogaster","volume":"173","author":"Dworkin","year":"2006","journal-title":"Genetics"},{"issue":"7","key":"2025050809213710900_jkaf051-B28","doi-asserted-by":"publisher","first-page":"282","DOI":"10.1016\/S0169-5347(97)81027-0","article-title":"Epistasis and its consequences for the evolution of natural populations","volume":"12","author":"Fenster","year":"1997","journal-title":"Trends Ecol Evol."},{"key":"2025050809213710900_jkaf051-B29","doi-asserted-by":"crossref","first-page":"xiv, 272","DOI":"10.5962\/bhl.title.27468","volume-title":"The Genetical Theory of Natural Selection","author":"Fisher","year":"1930"},{"key":"2025050809213710900_jkaf051-B30","doi-asserted-by":"publisher","first-page":"e53810","DOI":"10.7554\/eLife.53810","article-title":"Comprehensive fitness maps of Hsp90 show widespread environmental dependence","volume":"9","author":"Flynn","year":"2020","journal-title":"eLife"},{"issue":"7","key":"2025050809213710900_jkaf051-B31","doi-asserted-by":"publisher","first-page":"675","DOI":"10.1111\/gbb.12399","article-title":"Genetics of alcohol consumption in Drosophila melanogaster","volume":"16","author":"Fochler","year":"2017","journal-title":"Genes Brain Behav."},{"issue":"2","key":"2025050809213710900_jkaf051-B32","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1017\/S0016672398003176","article-title":"QTL mapping of genotype\u2013environment interaction for fitness in Drosophila melanogaster","volume":"71","author":"Fry","year":"1998","journal-title":"Genet Res (Camb)."},{"key":"2025050809213710900_jkaf051-B33","doi-asserted-by":"publisher","first-page":"e82824","DOI":"10.7554\/eLife.82824","article-title":"Polygenic adaptation from standing genetic variation allows rapid ecotype formation","volume":"12","author":"Fuhrmann","year":"2023","journal-title":"elife"},{"issue":"3","key":"2025050809213710900_jkaf051-B34","doi-asserted-by":"publisher","first-page":"394","DOI":"10.1111\/j.1365-2435.2007.01283.x","article-title":"Adaptive versus non-adaptive phenotypic plasticity and the potential for contemporary adaptation in new environments","volume":"21","author":"Ghalambor","year":"2007","journal-title":"Funct Ecol."},{"issue":"9","key":"2025050809213710900_jkaf051-B35","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1038\/nrg1426","article-title":"Uncovering cryptic genetic variation","volume":"5","author":"Gibson","year":"2004","journal-title":"Nat Rev Genet."},{"issue":"5","key":"2025050809213710900_jkaf051-B36","doi-asserted-by":"publisher","first-page":"e1004328","DOI":"10.1371\/journal.pgen.1004328","article-title":"Epistatically interacting substitutions are enriched during adaptive protein evolution","volume":"10","author":"Gong","year":"2014","journal-title":"PLoS Genet."},{"issue":"6","key":"2025050809213710900_jkaf051-B37","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1038\/sj.hdy.6800822","article-title":"Gene flow's effect on the genetic architecture of a local adaptation and its consequences for QTL analyses","volume":"96","author":"Griswold","year":"2006","journal-title":"Heredity (Edinb)."},{"issue":"12","key":"2025050809213710900_jkaf051-B38","doi-asserted-by":"publisher","first-page":"3501","DOI":"10.1111\/evo.12214","article-title":"Why epistasis is important for selection and adaptation","volume":"67","author":"Hansen","year":"2013","journal-title":"Evolution"},{"issue":"8","key":"2025050809213710900_jkaf051-B39","doi-asserted-by":"publisher","first-page":"1523","DOI":"10.1111\/j.0014-3820.2006.tb00498.x","article-title":"Evolution of genetic architecture under directional selection","volume":"60","author":"Hansen","year":"2006","journal-title":"Evolution"},{"issue":"2","key":"2025050809213710900_jkaf051-B40","doi-asserted-by":"publisher","first-page":"e1000008","DOI":"10.1371\/journal.pgen.1000008","article-title":"Data and theory point to mainly additive genetic variance for complex traits","volume":"4","author":"Hill","year":"2008","journal-title":"PLoS Genet."},{"issue":"4","key":"2025050809213710900_jkaf051-B41","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1111\/j.1095-8312.1997.tb01804.x","article-title":"Incipient reproductive isolation between two morphs of Drosophila elegans (Diptera: Drosophilidae)","volume":"61","author":"Hirai","year":"1997","journal-title":"Biol J Linn Soc Lond."},{"issue":"3","key":"2025050809213710900_jkaf051-B42","doi-asserted-by":"publisher","first-page":"iyab077","DOI":"10.1093\/genetics\/iyab077","article-title":"Parallel and population-specific gene regulatory evolution in cold-adapted fly populations","volume":"218","author":"Huang","year":"2021","journal-title":"Genetics"},{"issue":"39","key":"2025050809213710900_jkaf051-B43","doi-asserted-by":"publisher","first-page":"15553","DOI":"10.1073\/pnas.1213423109","article-title":"Epistasis dominates the genetic architecture of Drosophila quantitative traits","volume":"109","author":"Huang","year":"2012","journal-title":"Proc Natl Acad Sci U S A."},{"key":"2025050809213710900_jkaf051-B44","first-page":"1","volume-title":"Drosophila: Methods and Protocols","author":"Jenkins","year":"2022"},{"issue":"1\u20132","key":"2025050809213710900_jkaf051-B45","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1007\/s10709-003-2717-1","article-title":"Epistasis and genotype-environment interaction for quantitative trait loci affecting flowering time in Arabidopsis thaliana","volume":"123","author":"Juenger","year":"2005","journal-title":"Genetica"},{"issue":"5","key":"2025050809213710900_jkaf051-B46","doi-asserted-by":"publisher","first-page":"967","DOI":"10.1016\/0092-8674(93)90274-T","article-title":"Passover: a gene required for synaptic connectivity in the giant fiber system of Drosophila","volume":"73","author":"Krishnan","year":"1993","journal-title":"Cell"},{"issue":"4","key":"2025050809213710900_jkaf051-B47","doi-asserted-by":"publisher","first-page":"1775","DOI":"10.1534\/genetics.105.043125","article-title":"Identification of genetic loci that interact with cut during Drosophila wing-margin development","volume":"170","author":"Krupp","year":"2005","journal-title":"Genetics"},{"issue":"4","key":"2025050809213710900_jkaf051-B48","doi-asserted-by":"publisher","first-page":"1229","DOI":"10.1534\/genetics.115.174664","article-title":"The Drosophila genome nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population","volume":"199","author":"Lack","year":"2015","journal-title":"Genetics"},{"issue":"4","key":"2025050809213710900_jkaf051-B49","doi-asserted-by":"publisher","first-page":"1014","DOI":"10.1073\/pnas.1515964113","article-title":"Decanalization of wing development accompanied the evolution of large wings in high-altitude Drosophila","volume":"113","author":"Lack","year":"2016","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"2","key":"2025050809213710900_jkaf051-B50","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1111\/j.1558-5646.1992.tb02046.x","article-title":"Neutral theory of quantitative genetic variance in an island model with local extinction and colonization","volume":"46","author":"Lande","year":"1992","journal-title":"Evolution"},{"issue":"13","key":"2025050809213710900_jkaf051-B51","doi-asserted-by":"publisher","first-page":"3081","DOI":"10.1111\/mec.13671","article-title":"A haplotype method detects diverse scenarios of local adaptation from genomic sequence variation","volume":"25","author":"Lange","year":"2016","journal-title":"Mol Ecol."},{"issue":"10","key":"2025050809213710900_jkaf051-B52","doi-asserted-by":"publisher","first-page":"1826","DOI":"10.1101\/gr.276430.121","article-title":"Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels","volume":"32","author":"Lea","year":"2022","journal-title":"Genome Res."},{"key":"2025050809213710900_jkaf051-B53","author":"Li","year":"2013"},{"key":"2025050809213710900_jkaf051-B54","doi-asserted-by":"publisher","first-page":"jkaf050","DOI":"10.1093\/g3journal\/jkaf050","article-title":"Courtship song differs between African and European populations of Drosophila melanogaster and involves a strong effect locus","volume":"Accepted","author":"Lollar","year":"2025","journal-title":"G3"},{"issue":"12","key":"2025050809213710900_jkaf051-B55","doi-asserted-by":"publisher","first-page":"jkab349","DOI":"10.1093\/g3journal\/jkab349","article-title":"Genome-wide phenotypic RNAi screen in the Drosophila wing: phenotypic description of functional classes","volume":"11","author":"L\u00f3pez-Varea","year":"2021","journal-title":"G3 (Bethesda)"},{"issue":"26","key":"2025050809213710900_jkaf051-B56","doi-asserted-by":"publisher","first-page":"12933","DOI":"10.1073\/pnas.1821543116","article-title":"QTL \u00d7 environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient","volume":"116","author":"Lowry","year":"2019","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"11","key":"2025050809213710900_jkaf051-B57","doi-asserted-by":"publisher","first-page":"e1001162","DOI":"10.1371\/journal.pgen.1001162","article-title":"Pervasive cryptic epistasis in molecular evolution","volume":"6","author":"Lunzer","year":"2010","journal-title":"PLoS Genet."},{"issue":"1","key":"2025050809213710900_jkaf051-B58","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1146\/annurev.genet.35.102401.090633","article-title":"The genetic architecture of quantitative traits","volume":"35","author":"Mackay","year":"2001","journal-title":"Annu Rev Genet."},{"issue":"1","key":"2025050809213710900_jkaf051-B59","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1038\/nrg3627","article-title":"Epistasis and quantitative traits: using model organisms to study gene\u2013gene interactions","volume":"15","author":"Mackay","year":"2014","journal-title":"Nat Rev Genet."},{"issue":"2","key":"2025050809213710900_jkaf051-B60","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1017\/S0016672305007780","article-title":"QTL-based evidence for the role of epistasis in evolution","volume":"86","author":"Malmberg","year":"2005","journal-title":"Genet Res (Camb)."},{"issue":"12","key":"2025050809213710900_jkaf051-B61","doi-asserted-by":"publisher","first-page":"2413","DOI":"10.1111\/j.0014-3820.2006.tb01878.x","article-title":"The fitness effect of mutations across environments: a survey in light of fitness landscape models","volume":"60","author":"Martin","year":"2006","journal-title":"Evolution"},{"key":"2025050809213710900_jkaf051-B62","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1016\/bs.ctdb.2016.03.004","article-title":"The genetic basis of pigmentation differences within and between Drosophila species","volume":"119","author":"Massey","year":"2016","journal-title":"Curr Top Dev Biol."},{"issue":"7","key":"2025050809213710900_jkaf051-B63","doi-asserted-by":"publisher","first-page":"1077","DOI":"10.1007\/s00122-008-0846-8","article-title":"Multi-environment QTL mixed models for drought stress adaptation in wheat","volume":"117","author":"Mathews","year":"2008","journal-title":"Theor Appl Genet."},{"issue":"6","key":"2025050809213710900_jkaf051-B64","doi-asserted-by":"publisher","first-page":"305","DOI":"10.1016\/j.tree.2009.02.001","article-title":"Evolutionary consequences of cryptic genetic variation","volume":"24","author":"McGuigan","year":"2009","journal-title":"Trends Ecol Evol."},{"issue":"1","key":"2025050809213710900_jkaf051-B65","doi-asserted-by":"publisher","first-page":"12649","DOI":"10.1038\/ncomms12649","article-title":"Proteome-wide association studies identify biochemical modules associated with a wing-size phenotype in Drosophila melanogaster","volume":"7","author":"Okada","year":"2016","journal-title":"Nat Commun."},{"issue":"4","key":"2025050809213710900_jkaf051-B66","doi-asserted-by":"publisher","first-page":"935","DOI":"10.1111\/j.1558-5646.1998.tb01823.x","article-title":"The population genetics of adaptation: the distribution of factors fixed during adaptive evolution","volume":"52","author":"Orr","year":"1998","journal-title":"Evolution"},{"issue":"2","key":"2025050809213710900_jkaf051-B67","doi-asserted-by":"publisher","first-page":"875","DOI":"10.1093\/genetics\/157.2.875","article-title":"Haldane's sieve and adaptation from the standing genetic variation","volume":"157","author":"Orr","year":"2001","journal-title":"Genetics"},{"issue":"1","key":"2025050809213710900_jkaf051-B68","doi-asserted-by":"publisher","first-page":"iyad211","DOI":"10.1093\/genetics\/iyad211","article-title":"FlyBase: updates to the Drosophila genes and genomes database","volume":"227","author":"\u00d6zt\u00fcrk-\u00c7olak","year":"2024","journal-title":"Genetics"},{"issue":"3","key":"2025050809213710900_jkaf051-B69","doi-asserted-by":"publisher","first-page":"e57033","DOI":"10.1371\/journal.pone.0057033","article-title":"Multi-allelic major effect genes interact with minor effect QTLs to control adaptive color pattern variation in Heliconius erato","volume":"8","author":"Papa","year":"2013","journal-title":"PLoS One"},{"issue":"10","key":"2025050809213710900_jkaf051-B70","doi-asserted-by":"publisher","first-page":"e1002274","DOI":"10.1371\/journal.pbio.1002274","article-title":"Scaling the Drosophila wing: TOR-dependent target gene access by the hippo pathway transducer Yorkie","volume":"13","author":"Parker","year":"2015","journal-title":"PLoS Biol."},{"issue":"13","key":"2025050809213710900_jkaf051-B71","doi-asserted-by":"publisher","first-page":"5058","DOI":"10.1073\/pnas.1217538110","article-title":"Dpp-induced Egfr signaling triggers postembryonic wing development in Drosophila","volume":"110","author":"Paul","year":"2013","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"4","key":"2025050809213710900_jkaf051-B72","doi-asserted-by":"publisher","first-page":"1429","DOI":"10.1534\/genetics.118.301342","article-title":"A multivariate genome-wide association study of wing shape in Drosophila melanogaster","volume":"211","author":"Pitchers","year":"2019","journal-title":"Genetics"},{"issue":"3","key":"2025050809213710900_jkaf051-B73","doi-asserted-by":"publisher","first-page":"1295","DOI":"10.1534\/genetics.116.192484","article-title":"Genetic mapping by bulk segregant analysis in Drosophila: experimental design and simulation-based inference","volume":"204","author":"Pool","year":"2016","journal-title":"Genetics"},{"issue":"2","key":"2025050809213710900_jkaf051-B74","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1093\/molbev\/msw232","article-title":"Parallel evolution of cold tolerance within Drosophila melanogaster","volume":"34","author":"Pool","year":"2017","journal-title":"Mol Biol Evol."},{"issue":"4","key":"2025050809213710900_jkaf051-B75","doi-asserted-by":"publisher","first-page":"R208","DOI":"10.1016\/j.cub.2009.11.055","article-title":"The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation","volume":"20","author":"Pritchard","year":"2010","journal-title":"Curr Biol."},{"issue":"2","key":"2025050809213710900_jkaf051-B76","doi-asserted-by":"publisher","first-page":"781","DOI":"10.1534\/genetics.114.163857","article-title":"Systems genomics of metabolic phenotypes in wild-type Drosophila melanogaster","volume":"197","author":"Reed","year":"2014","journal-title":"Genetics"},{"issue":"3","key":"2025050809213710900_jkaf051-B77","doi-asserted-by":"publisher","first-page":"767","DOI":"10.1093\/genetics\/105.3.767","article-title":"Estimation of the coancestry coefficient: basis for a short-term genetic distance","volume":"105","author":"Reynolds","year":"1983","journal-title":"Genetics"},{"issue":"2","key":"2025050809213710900_jkaf051-B78","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1016\/j.ydbio.2013.11.013","article-title":"A survey of the trans-regulatory landscape for Drosophila melanogaster abdominal pigmentation","volume":"385","author":"Rogers","year":"2014","journal-title":"Dev Biol."},{"issue":"6709","key":"2025050809213710900_jkaf051-B79","doi-asserted-by":"publisher","first-page":"336","DOI":"10.1038\/24550","article-title":"Hsp90 as a capacitor for morphological evolution","volume":"396","author":"Rutherford","year":"1998","journal-title":"Nature"},{"issue":"11","key":"2025050809213710900_jkaf051-B80","doi-asserted-by":"publisher","first-page":"807","DOI":"10.1038\/nrg3522","article-title":"Ecological genomics of local adaptation","volume":"14","author":"Savolainen","year":"2013","journal-title":"Nat Rev Genet."},{"issue":"4","key":"2025050809213710900_jkaf051-B81","doi-asserted-by":"publisher","first-page":"514","DOI":"10.1101\/gr.181305.114","article-title":"A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development","volume":"25","author":"Schertel","year":"2015","journal-title":"Genome Res."},{"issue":"1877","key":"2025050809213710900_jkaf051-B82","doi-asserted-by":"publisher","first-page":"20220046","DOI":"10.1098\/rstb.2022.0046","article-title":"How predictable is adaptation from standing genetic variation? Experimental evolution in Drosophila highlights the central role of redundancy and linkage disequilibrium","volume":"378","author":"Schl\u00f6tterer","year":"2023","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"issue":"1","key":"2025050809213710900_jkaf051-B83","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1146\/annurev-genom-091416-035340","article-title":"On the evolution of lactase persistence in humans","volume":"18","author":"S\u00e9gurel","year":"2017","journal-title":"Annu Rev Genomics Hum Genet."},{"issue":"2","key":"2025050809213710900_jkaf051-B84","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1093\/genetics\/135.2.367","article-title":"Population structure in Daphnia obtusa: quantitative genetic and allozymic variation","volume":"135","author":"Spitze","year":"1993","journal-title":"Genetics"},{"issue":"3","key":"2025050809213710900_jkaf051-B85","doi-asserted-by":"publisher","first-page":"jkab454","DOI":"10.1093\/g3journal\/jkab454","article-title":"The evolution of larger size in high-altitude Drosophila melanogaster has a variable genetic architecture","volume":"12","author":"Sprengelmeyer","year":"2022","journal-title":"G3 (Bethesda)"},{"issue":"3","key":"2025050809213710900_jkaf051-B86","doi-asserted-by":"publisher","first-page":"627","DOI":"10.1093\/molbev\/msz271","article-title":"Recurrent collection of Drosophila melanogaster from wild African environments and genomic insights into species history","volume":"37","author":"Sprengelmeyer","year":"2020","journal-title":"Mol Biol Evol."},{"issue":"21","key":"2025050809213710900_jkaf051-B87","doi-asserted-by":"publisher","first-page":"15364","DOI":"10.1002\/ece3.8228","article-title":"Ethanol resistance in Drosophila melanogaster has increased in parallel cold-adapted populations and shows a variable genetic architecture within and between populations","volume":"11","author":"Sprengelmeyer","year":"2021","journal-title":"Ecol Evol."},{"issue":"7","key":"2025050809213710900_jkaf051-B88","doi-asserted-by":"publisher","first-page":"1204","DOI":"10.1002\/pro.2897","article-title":"Epistasis in protein evolution","volume":"25","author":"Starr","year":"2016","journal-title":"Protein Sci."},{"issue":"9","key":"2025050809213710900_jkaf051-B89","doi-asserted-by":"publisher","first-page":"e219","DOI":"10.1371\/journal.pbio.0050219","article-title":"Adaptive variation in beach mice produced by two interacting pigmentation genes","volume":"5","author":"Steiner","year":"2007","journal-title":"PLoS Biol."},{"issue":"2","key":"2025050809213710900_jkaf051-B90","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1111\/nph.15350","article-title":"Maize domestication and gene interaction","volume":"220","author":"Stitzer","year":"2018","journal-title":"New Phytol."},{"issue":"14","key":"2025050809213710900_jkaf051-B91","doi-asserted-by":"publisher","first-page":"e2205787119","DOI":"10.1073\/pnas.2205787119","article-title":"Epistatic QTLs for yield heterosis in tomato","volume":"120","author":"Torgeman","year":"2023","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"7","key":"2025050809213710900_jkaf051-B92","doi-asserted-by":"publisher","first-page":"e1000578","DOI":"10.1371\/journal.pgen.1000578","article-title":"Positive epistasis drives the acquisition of multidrug resistance","volume":"5","author":"Trindade","year":"2009","journal-title":"PLoS Genet."},{"key":"2025050809213710900_jkaf051-B93","volume-title":"Python 3 Reference Manual","author":"Van Rossum","year":"2009"},{"issue":"12","key":"2025050809213710900_jkaf051-B94","doi-asserted-by":"publisher","first-page":"2566","DOI":"10.1111\/jeb.12248","article-title":"Epistasis and maternal effects in experimental adaptation to chronic nutritional stress in Drosophila","volume":"26","author":"Vijendravarma","year":"2013","journal-title":"J Evol Biol."},{"issue":"1","key":"2025050809213710900_jkaf051-B95","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1146\/annurev.es.26.110195.003125","article-title":"Multiple fitness peaks and epistasis","volume":"26","author":"Whitlock","year":"1995","journal-title":"Annu Rev Ecol Syst."},{"issue":"2","key":"2025050809213710900_jkaf051-B96","doi-asserted-by":"publisher","first-page":"250","DOI":"10.1007\/BF00348047","article-title":"Field analyses of insect heat budgets: reflectance, size and heating rates","volume":"50","author":"Willmer","year":"1981","journal-title":"Oecologia"},{"issue":"2","key":"2025050809213710900_jkaf051-B97","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1093\/genetics\/16.2.97","article-title":"Evolution in Mendelian populations","volume":"16","author":"Wright","year":"1931","journal-title":"Genetics"},{"issue":"7","key":"2025050809213710900_jkaf051-B98","doi-asserted-by":"publisher","first-page":"2123","DOI":"10.1111\/j.1558-5646.2011.01277.x","article-title":"Establishment and maintenance of adaptive genetic divergence under migration, selection, and drift","volume":"65","author":"Yeaman","year":"2011","journal-title":"Evolution"},{"issue":"7","key":"2025050809213710900_jkaf051-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-selection balance","volume":"65","author":"Yeaman","year":"2011","journal-title":"Evolution"},{"issue":"9","key":"2025050809213710900_jkaf051-B100","doi-asserted-by":"publisher","first-page":"2215","DOI":"10.1111\/j.1558-5646.2008.00445.x","article-title":"Long-term adaptation of epistatic genetic networks","volume":"62","author":"Yukilevich","year":"2008","journal-title":"Evolution"},{"issue":"3","key":"2025050809213710900_jkaf051-B101","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1017\/S0016672399004255","article-title":"Estimating the genetic architecture of quantitative traits","volume":"74","author":"Zeng","year":"1999","journal-title":"Genet Res (Camb)."},{"issue":"4","key":"2025050809213710900_jkaf051-B102","doi-asserted-by":"publisher","first-page":"e1005965","DOI":"10.1371\/journal.pgen.1005965","article-title":"Functional regression models for epistasis analysis of multiple quantitative traits","volume":"12","author":"Zhang","year":"2016","journal-title":"PLoS Genet."},{"issue":"12","key":"2025050809213710900_jkaf051-B103","doi-asserted-by":"publisher","first-page":"3612","DOI":"10.1016\/j.celrep.2017.11.076","article-title":"Homeostatic control of Hpo\/MST kinase activity through autophosphorylation-dependent recruitment of the STRIPAK PP2A phosphatase complex","volume":"21","author":"Zheng","year":"2017","journal-title":"Cell Rep."},{"issue":"3","key":"2025050809213710900_jkaf051-B104","doi-asserted-by":"publisher","first-page":"e1002593","DOI":"10.1371\/journal.pgen.1002593","article-title":"Phenotypic plasticity of the Drosophila transcriptome","volume":"8","author":"Zhou","year":"2012","journal-title":"PLoS Genet."}],"container-title":["G3: Genes, Genomes, Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/g3journal\/advance-article-pdf\/doi\/10.1093\/g3journal\/jkaf051\/62340634\/jkaf051.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/g3journal\/article-pdf\/15\/5\/jkaf051\/62340634\/jkaf051.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/g3journal\/article-pdf\/15\/5\/jkaf051\/62340634\/jkaf051.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,8]],"date-time":"2025-05-08T13:21:45Z","timestamp":1746710505000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/g3journal\/article\/doi\/10.1093\/g3journal\/jkaf051\/8063644"}},"subtitle":[],"editor":[{"given":"L","family":"McIntyre","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,3,7]]},"references-count":104,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2025,3,7]]},"published-print":{"date-parts":[[2025,5,8]]}},"URL":"https:\/\/doi.org\/10.1093\/g3journal\/jkaf051","relation":{},"ISSN":["2160-1836"],"issn-type":[{"value":"2160-1836","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,5]]},"published":{"date-parts":[[2025,3,7]]},"article-number":"jkaf051"}}