{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T22:20:03Z","timestamp":1792016403660,"version":"4.4.0"},"reference-count":85,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2025,12,16]],"date-time":"2025-12-16T00:00:00Z","timestamp":1765843200000},"content-version":"vor","delay-in-days":18,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002341","name":"Research Council of Finland","doi-asserted-by":"publisher","award":["343022"],"award-info":[{"award-number":["343022"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002341","name":"Research Council of Finland","doi-asserted-by":"publisher","award":["328961"],"award-info":[{"award-number":["328961"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002341","name":"Research Council of Finland","doi-asserted-by":"publisher","award":["346805"],"award-info":[{"award-number":["346805"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"publisher","award":["310030-207642"],"award-info":[{"award-number":["310030-207642"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,11,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Some of the most striking examples of phenotypic variation within species are controlled by supergenes. However, most research on supergenes has focused on their emergence and long-term maintenance, leaving the later stages of their life cycle largely unexplored. Specifically, what happens to a derived supergene haplotype when the trait it controls reaches fixation? Here we answer this question using the ancient supergene system of Formica ants, where (monogynous) single-queen colonies typically carry only the ancestral haplotype M while the derived haplotype P is exclusive to (polygynous) colonies with multiple queens. Through comparative population genomics of 264 individuals from all seven European wood ant species, we found that the P haplotype was present in only 1\/3 obligately polygynous species (Formica polyctena). In the two others (Formica aquilonia and Formica paralugubris), the P haplotype was completely missing except for duplicated P-specific paralogs of two genes, Zasp52 and TTLL2, with Zasp52 being directly involved in wing muscle development. We hypothesize that these genes play a direct role in polygyny and contribute to differences in body size and\/or dispersal behavior between monogynous and polygynous queens. A complete lack of P\/P genotypes among the 261 workers suggests strong selection against such genotypes. While our analyses did not reveal evidence of increased mutation load on the P, it is possible that this skew in genotype distributions is driven by a few loci with strong fitness effects. We propose that selection to escape P-associated fitness costs underlies the loss of this haplotype in obligately polygynous wood ants.<\/jats:p>","DOI":"10.1093\/molbev\/msaf320","type":"journal-article","created":{"date-parts":[[2025,12,15]],"date-time":"2025-12-15T12:28:50Z","timestamp":1765801730000},"source":"Crossref","is-referenced-by-count":6,"title":["The loss of a supergene in obligately polygynous\n                    <i>Formica<\/i>\n                    wood ant species"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1457-4174","authenticated-orcid":false,"given":"Hanna","family":"Sigeman","sequence":"first","affiliation":[{"name":"Ecology and Genetics Research Unit, University of Oulu , Oulu ,","place":["Finland"]},{"name":"Department of Medical Biochemistry and Microbiology, Uppsala University , Uppsala ,","place":["Sweden"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2553-1487","authenticated-orcid":false,"given":"Ina","family":"Satokangas","sequence":"additional","affiliation":[{"name":"Organismal and Evolutionary Biology Research Programme, University of Helsinki , Helsinki ,","place":["Finland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-9666-3380","authenticated-orcid":false,"given":"Matthieu","family":"de Lamarre","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolution, University of Lausanne , Lausanne ,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1625-4473","authenticated-orcid":false,"given":"Patrick","family":"Krapf","sequence":"additional","affiliation":[{"name":"Organismal and Evolutionary Biology Research Programme, University of Helsinki , Helsinki ,","place":["Finland"]},{"name":"Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam , Amsterdam ,","place":["Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4923-0993","authenticated-orcid":false,"given":"Pierre","family":"Nouhaud","sequence":"additional","affiliation":[{"name":"Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki ,","place":["Finland"]},{"name":"UMR CBGP, INRAE, CIRAD, IRD, Institut Agro, Universit\u00e9 Montpellier , Montpellier ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7634-2029","authenticated-orcid":false,"given":"Riddhi","family":"Deshmukh","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolution, University of Lausanne , Lausanne ,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6468-5956","authenticated-orcid":false,"given":"Heikki","family":"Helanter\u00e4","sequence":"additional","affiliation":[{"name":"Department of Medical Biochemistry and Microbiology, Uppsala University , Uppsala ,","place":["Sweden"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7207-199X","authenticated-orcid":false,"given":"Michel","family":"Chapuisat","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolution, University of Lausanne , Lausanne ,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8852-0793","authenticated-orcid":false,"given":"Jonna","family":"Kulmuni","sequence":"additional","affiliation":[{"name":"Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki ,","place":["Finland"]},{"name":"Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam , Amsterdam ,","place":["Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6587-6156","authenticated-orcid":false,"given":"Lumi","family":"Viljakainen","sequence":"additional","affiliation":[{"name":"Ecology and Genetics Research Unit, University of Oulu , Oulu ,","place":["Finland"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,12,16]]},"reference":[{"key":"2025122405571343200_msaf320-B1","doi-asserted-by":"publisher","first-page":"1062","DOI":"10.1111\/mec.16821","article-title":"Cryptic recessive lethality of a supergene controlling social organization in ants","volume":"32","author":"Blacher","year":"2023","journal-title":"Mol Ecol"},{"key":"2025122405571343200_msaf320-B2","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2025122405571343200_msaf320-B3","doi-asserted-by":"publisher","first-page":"304","DOI":"10.1016\/j.cub.2019.11.032","article-title":"An ancient and eroded social supergene is widespread across Formica ants","volume":"30","author":"Brelsford","year":"2020","journal-title":"Curr Biol"},{"key":"2025122405571343200_msaf320-B4","doi-asserted-by":"publisher","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"Trimal: a tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","author":"Capella-Guti\u00e9rrez","year":"2009","journal-title":"Bioinformatics"},{"key":"2025122405571343200_msaf320-B5","doi-asserted-by":"publisher","first-page":"1064","DOI":"10.1111\/j.0014-3820.2004.tb00440.x","article-title":"Variable queen number in ant colonies: no impact on queen turnover, inbreeding, and population genetic differentiation in the ant Formica selysi","volume":"58","author":"Chapuisat","year":"2004","journal-title":"Evol Int J Org Evol"},{"key":"2025122405571343200_msaf320-B6","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1111\/j.1558-5646.1997.tb02435.x","article-title":"Microsatellites reveal high population viscosity and limited dispersal in the ant Formica paralugubris","volume":"51","author":"Chapuisat","year":"1997","journal-title":"Evolution"},{"key":"2025122405571343200_msaf320-B7","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1007\/s002650050636","article-title":"Extended family structure in the ant Formica paralugubris: the role of the breeding system","volume":"46","author":"Chapuisat","year":"1999","journal-title":"Behav Ecol Sociobiol"},{"key":"2025122405571343200_msaf320-B8","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1111\/eva.12291","article-title":"The status of supergenes in the 21st century: recombination suppression in Batesian mimicry and sex chromosomes and other complex adaptations","volume":"9","author":"Charlesworth","year":"2016","journal-title":"Evol Appl"},{"key":"2025122405571343200_msaf320-B9","doi-asserted-by":"publisher","first-page":"3718","DOI":"10.1074\/jbc.M112.401794","article-title":"The Drosophila Z-disc protein Z(210) is an adult muscle isoform of Zasp52, which is required for normal myofibril organization in indirect flight muscles","volume":"288","author":"Chechenova","year":"2013","journal-title":"J Biol Chem"},{"key":"2025122405571343200_msaf320-B10","doi-asserted-by":"publisher","first-page":"3317","DOI":"10.1093\/bioinformatics\/btu530","article-title":"Quartet inference from SNP data under the coalescent model","volume":"30","author":"Chifman","year":"2014","journal-title":"Bioinformatics"},{"key":"2025122405571343200_msaf320-B11","doi-asserted-by":"publisher","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly (Austin)"},{"key":"2025122405571343200_msaf320-B12","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1038\/hdy.1960.15","article-title":"Super-genes and mimicry","volume":"14","author":"Clarke","year":"1960","journal-title":"Heredity (Edinb)"},{"key":"2025122405571343200_msaf320-B13","author":"Dainat"},{"key":"2025122405571343200_msaf320-B14","doi-asserted-by":"publisher","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and VCFtools","volume":"27","author":"Danecek","year":"2011","journal-title":"Bioinformatics"},{"key":"2025122405571343200_msaf320-B15","doi-asserted-by":"publisher","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"GigaScience"},{"key":"2025122405571343200_msaf320-B16","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1007\/s00040-004-0745-1","article-title":"Population genetics of the socially polymorphic ant Formica podzolica","volume":"51","author":"DeHeer","year":"2004","journal-title":"Insectes Soc"},{"key":"2025122405571343200_msaf320-B17","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2025122405571343200_msaf320-B18","doi-asserted-by":"publisher","first-page":"4660","DOI":"10.1038\/s41467-019-12493-y","article-title":"Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing","volume":"10","author":"Edge","year":"2019","journal-title":"Nat Commun"},{"key":"2025122405571343200_msaf320-B19","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","article-title":"OrthoFinder: phylogenetic orthology inference for comparative genomics","volume":"20","author":"Emms","year":"2019","journal-title":"Genome Biol"},{"key":"2025122405571343200_msaf320-B20","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1074\/mcp.M113.035600","article-title":"Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics","volume":"13","author":"Fagerberg","year":"2014","journal-title":"Mol Cell Proteomics"},{"key":"2025122405571343200_msaf320-B21","doi-asserted-by":"publisher","first-page":"2807","DOI":"10.1046\/j.0962-1083.2001.01410.x","article-title":"Social and genetic characteristics of geographically isolated populations in the ant Formica cinerea","volume":"10","author":"Goropashnaya","year":"2001","journal-title":"Mol Ecol"},{"key":"2025122405571343200_msaf320-B22","doi-asserted-by":"publisher","first-page":"2896","DOI":"10.1093\/bioinformatics\/btaa025","article-title":"Identifying and removing haplotypic duplication in primary genome assemblies","volume":"36","author":"Guan","year":"2020","journal-title":"Bioinformatics"},{"key":"2025122405571343200_msaf320-B23","doi-asserted-by":"publisher","first-page":"1947","DOI":"10.1111\/j.1420-9101.2012.02591.x","article-title":"Cryptic recombination in the ever-young sex chromosomes of hylid frogs","volume":"25","author":"Guerrero","year":"2012","journal-title":"J Evol Biol"},{"key":"2025122405571343200_msaf320-B24","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1007\/s00040-003-0720-2","article-title":"Genetic differentiation in sympatric wood ants, Formica rufa and F. polyctena","volume":"51","author":"Gyllenstrand","year":"2004","journal-title":"Insectes Soc"},{"key":"2025122405571343200_msaf320-B25","volume-title":"Social polymorphism and dispersal in Formica ants","author":"Hakala","year":"2020"},{"key":"2025122405571343200_msaf320-B26","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1186\/1471-2148-9-69","article-title":"Genetic clusters and sex-biased gene flow in a unicolonial Formica ant","volume":"9","author":"Holzer","year":"2009","journal-title":"BMC Evol Biol"},{"key":"2025122405571343200_msaf320-B27","doi-asserted-by":"publisher","first-page":"189","DOI":"10.25849\/myrmecol.news_035:189","article-title":"Isolated hybrid wood-ant population Formica aquilonia x F. lugubris in subarctic Finland","volume":"35","author":"J\u00e4rvinen","year":"2025","journal-title":"Myrmecol News"},{"key":"2025122405571343200_msaf320-B28","doi-asserted-by":"publisher","first-page":"288","DOI":"10.1038\/s41588-020-00771-1","article-title":"Mutation load at a mimicry supergene sheds new light on the evolution of inversion polymorphisms","volume":"53","author":"Jay","year":"2021","journal-title":"Nat Genet"},{"key":"2025122405571343200_msaf320-B29","first-page":"225","article-title":"Development of alary muscles in single- and multiple-queen populations of the wood ant Formica truncorum","volume":"42","author":"Johnson","year":"2005","journal-title":"Ann Zool Fenn"},{"key":"2025122405571343200_msaf320-B30","doi-asserted-by":"publisher","first-page":"e303","DOI":"10.1371\/journal.pbio.0040303","article-title":"A conserved supergene locus controls colour pattern diversity in Heliconius butterflies","volume":"4","author":"Joron","year":"2006","journal-title":"PLoS Biol"},{"key":"2025122405571343200_msaf320-B31","doi-asserted-by":"publisher","first-page":"e1003342","DOI":"10.1371\/journal.pgen.1003342","article-title":"Alp\/Enigma family proteins cooperate in Z-disc formation and myofibril assembly","volume":"9","author":"Katzemich","year":"2013","journal-title":"PLoS Genet"},{"key":"2025122405571343200_msaf320-B32","first-page":"161","volume-title":"Gene prediction: methods and protocols","author":"Keilwagen","year":"2019"},{"key":"2025122405571343200_msaf320-B33","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1080\/08927014.1991.9525359","article-title":"Queen number, mode of colony founding, and queen reproductive success in ants (Hymenoptera Formicidae)","volume":"3","author":"Keller","year":"1991","journal-title":"Ethol Ecol Evol"},{"key":"2025122405571343200_msaf320-B34","doi-asserted-by":"publisher","first-page":"177","DOI":"10.2307\/3545107","article-title":"The assessment of reproductive success of queens in ants and other social insects","volume":"67","author":"Keller","year":"1993","journal-title":"Oikos"},{"key":"2025122405571343200_msaf320-B35","doi-asserted-by":"publisher","first-page":"278","DOI":"10.1111\/j.1558-5646.1956.tb02852.x","article-title":"A model of a genetic system which leads to closer linkage by natural selection","volume":"10","author":"Kimura","year":"1956","journal-title":"Evolution"},{"key":"2025122405571343200_msaf320-B36","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","article-title":"Assembly of long, error-prone reads using repeat graphs","volume":"37","author":"Kolmogorov","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2025122405571343200_msaf320-B37","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1038\/ng.3443","article-title":"A supergene determines highly divergent male reproductive morphs in the ruff","volume":"48","author":"K\u00fcpper","year":"2016","journal-title":"Nat Genet"},{"key":"2025122405571343200_msaf320-B38","doi-asserted-by":"publisher","first-page":"D445","DOI":"10.1093\/nar\/gkac998","article-title":"OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity","volume":"51","author":"Kuznetsov","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025122405571343200_msaf320-B39","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1093\/jeb\/voaf023","article-title":"Unexpected absence of a multiple-queen supergene haplotype from supercolonial populations of Formica ants","volume":"38","author":"Lagunas-Robles","year":"2025","journal-title":"J Evol Biol"},{"key":"2025122405571343200_msaf320-B40","doi-asserted-by":"publisher","first-page":"e2101427118","DOI":"10.1073\/pnas.2101427118","article-title":"Linked supergenes underlie split sex ratio and social organization in an ant","volume":"118","author":"Lagunas-Robles","year":"2021","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2025122405571343200_msaf320-B41","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1038\/ng.3430","article-title":"Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)","volume":"48","author":"Lamichhaney","year":"2016","journal-title":"Nat Genet"},{"key":"2025122405571343200_msaf320-B42","doi-asserted-by":"publisher","first-page":"e1006400","DOI":"10.1371\/journal.pgen.1006400","article-title":"Zasp52, a core Z-disc protein in Drosophila indirect flight muscles, interacts with \u03b1-actinin via an extended PDZ domain","volume":"12","author":"Liao","year":"2016","journal-title":"PLOS Genet"},{"key":"2025122405571343200_msaf320-B43","doi-asserted-by":"publisher","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","article-title":"featureCounts: an efficient general purpose program for assigning sequence reads to genomic features","volume":"30","author":"Liao","year":"2014","journal-title":"Bioinformatics"},{"key":"2025122405571343200_msaf320-B44","unstructured":"Lindenbaum P . JVarkit: java-based utilities for Bioinformatics. Figshare. \u00a02015. 10.6084\/m9.figshare.1425030."},{"key":"2025122405571343200_msaf320-B45","doi-asserted-by":"publisher","first-page":"2430","DOI":"10.1111\/mec.14051","article-title":"Genetic architecture and balancing selection: the life and death of differentiated variants","volume":"26","author":"Llaurens","year":"2017","journal-title":"Mol Ecol"},{"key":"2025122405571343200_msaf320-B46","doi-asserted-by":"publisher","first-page":"733","DOI":"10.1111\/j.1365-294X.2005.02444.x","article-title":"Genetic changes associated to declining populations of Formica ants in fragmented forest landscape","volume":"14","author":"M\u00e4ki-Pet\u00e4ys","year":"2005","journal-title":"Mol Ecol"},{"key":"2025122405571343200_msaf320-B47","doi-asserted-by":"publisher","first-page":"3165","DOI":"10.3390\/ani12223165","article-title":"Assessing molecular diversity in native and introduced populations of red wood ant Formica paralugubris","volume":"12","author":"Masoni","year":"2022","journal-title":"Animals (Basel)"},{"key":"2025122405571343200_msaf320-B48","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1186\/s12862-022-02001-0","article-title":"A novel distribution of supergene genotypes is present in the socially polymorphic ant Formica neoclara","volume":"22","author":"McGuire","year":"2022","journal-title":"BMC Ecol Evol"},{"key":"2025122405571343200_msaf320-B49","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol Biol Evol"},{"key":"2025122405571343200_msaf320-B50","author":"Monaghan"},{"key":"2025122405571343200_msaf320-B51","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1093\/jhered\/esac019","article-title":"Assembly of a hybrid Formica aquilonia \u00d7 F. polyctena ant genome from a haploid male","volume":"113","author":"Nouhaud","year":"2022","journal-title":"J Hered"},{"key":"2025122405571343200_msaf320-B52","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1038\/hdy.1982.10","article-title":"Genetic population structure in polygynous Formica ants","volume":"48","author":"Pamilo","year":"1982","journal-title":"Heredity (Edinb)"},{"key":"2025122405571343200_msaf320-B54","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1007\/BF01240528","article-title":"Genetic differentiation of disjunct populations of the ants Formica aquilonia and Formica lugubris in Europe","volume":"39","author":"Pamilo","year":"1992","journal-title":"Insectes Soc"},{"key":"2025122405571343200_msaf320-B53","first-page":"179","article-title":"Genetic patchwork of network-building wood ant populations","volume":"42","author":"Pamilo","year":"2005","journal-title":"Ann Zool Fenn"},{"key":"2025122405571343200_msaf320-B55","doi-asserted-by":"publisher","first-page":"ISCB Comm J-304","DOI":"10.12688\/f1000research.23297.1","article-title":"GFF utilities: GffRead and GffCompare","volume":"9","author":"Pertea","year":"2020","journal-title":"F1000Res"},{"key":"2025122405571343200_msaf320-B56","doi-asserted-by":"publisher","first-page":"1031","DOI":"10.1111\/jeb.14038","article-title":"A socially polymorphic Formica ant species exhibits a novel distribution of social supergene genotypes","volume":"35","author":"Pierce","year":"2022","journal-title":"J Evol Biol"},{"key":"2025122405571343200_msaf320-B57","doi-asserted-by":"publisher","first-page":"983","DOI":"10.1038\/nbt.4235","article-title":"A universal SNP and small-indel variant caller using deep neural networks","volume":"36","author":"Poplin","year":"2018","journal-title":"Nat Biotechnol"},{"key":"2025122405571343200_msaf320-B58","doi-asserted-by":"publisher","first-page":"3416","DOI":"10.1111\/mec.16481","article-title":"Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European ranges","volume":"31","author":"Portinha","year":"2022","journal-title":"Mol Ecol"},{"key":"2025122405571343200_msaf320-B59","doi-asserted-by":"publisher","first-page":"2728","DOI":"10.1016\/j.cub.2014.09.071","article-title":"Convergent genetic architecture underlies social organization in ants","volume":"24","author":"Purcell","year":"2014","journal-title":"Curr Biol"},{"key":"2025122405571343200_msaf320-B60","doi-asserted-by":"publisher","first-page":"6246","DOI":"10.1111\/mec.16196","article-title":"The maintenance of polymorphism in an ancient social supergene","volume":"30","author":"Purcell","year":"2021","journal-title":"Mol Ecol"},{"key":"2025122405571343200_msaf320-B61","volume-title":"R: a language and environment for statistical computing","author":"R Core Team","year":"2022"},{"key":"2025122405571343200_msaf320-B62","first-page":"65","article-title":"The evolution of polygyny and polydomy in mound-building formica ants","volume":"42","author":"Rosengren","year":"1983","journal-title":"Acta Entomol Fenn"},{"key":"2025122405571343200_msaf320-B63","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1007\/s10682-006-9139-3","article-title":"Alternative life-histories in a socially polymorphic ant","volume":"21","author":"Rosset","year":"2007","journal-title":"Evol Ecol"},{"key":"2025122405571343200_msaf320-B64","doi-asserted-by":"publisher","first-page":"4329","DOI":"10.1111\/mec.16992","article-title":"Semipermeable species boundaries create opportunities for gene flow and adaptive potential","volume":"32","author":"Satokangas","year":"2023","journal-title":"Mol Ecol"},{"key":"2025122405571343200_msaf320-B65","doi-asserted-by":"publisher","first-page":"5085","DOI":"10.1016\/j.cub.2023.10.049","article-title":"Social antagonism facilitates supergene expansion in ants","volume":"33","author":"Scarparo","year":"2023","journal-title":"Curr Biol"},{"key":"2025122405571343200_msaf320-B66","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1093\/aesa\/saae020","article-title":"Broad host use and frequent polyandry in the facultative dulotic species Formica aserva (Hymenoptera: Formicidae)","volume":"117","author":"Scarparo","year":"2024","journal-title":"Ann Entomol Soc Am"},{"key":"2025122405571343200_msaf320-B67","doi-asserted-by":"publisher","first-page":"R288","DOI":"10.1016\/j.cub.2014.01.056","article-title":"Supergenes and Complex phenotypes","volume":"24","author":"Schwander","year":"2014","journal-title":"Curr Biol"},{"key":"2025122405571343200_msaf320-B68","volume-title":"The ants of central and North Europe. 1. Auflage","author":"Seifert","year":"2018"},{"key":"2025122405571343200_msaf320-B69","doi-asserted-by":"publisher","first-page":"1219","DOI":"10.1007\/s10682-010-9371-8","article-title":"Independent hybrid populations of Formica polyctena X rufa wood ants (Hymenoptera: Formicidae) abound under conditions of forest fragmentation","volume":"24","author":"Seifert","year":"2010","journal-title":"Evol Ecol"},{"key":"2025122405571343200_msaf320-B70","doi-asserted-by":"publisher","first-page":"2462","DOI":"10.1111\/j.0014-3820.2004.tb00875.x","article-title":"Coexistence of the social types: genetic population structure in the ant Formica Exsecta","volume":"58","author":"Sepp\u00e4","year":"2004","journal-title":"Evolution"},{"key":"2025122405571343200_msaf320-B71","doi-asserted-by":"publisher","first-page":"e0163962","DOI":"10.1371\/journal.pone.0163962","article-title":"SeqKit: a cross-platform and ultrafast toolkit for FASTA\/Q file manipulation","volume":"11","author":"Shen","year":"2016","journal-title":"PLoS One"},{"key":"2025122405571343200_msaf320-B72","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1002\/pro.3290","article-title":"Clustal Omega for making accurate alignments of many protein sequences","volume":"27","author":"Sievers","year":"2018","journal-title":"Protein Sci"},{"key":"2025122405571343200_msaf320-B73","doi-asserted-by":"publisher","first-page":"1180","DOI":"10.1038\/s41467-022-28806-7","article-title":"Recurring adaptive introgression of a supergene variant that determines social organization","volume":"13","author":"Stolle","year":"2022","journal-title":"Nat Commun"},{"key":"2025122405571343200_msaf320-B74","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1007\/BF00172934","article-title":"Genetic population structure and sociogenetic organisation in Formica truncorum (Hymenoptera; Formicidae)","volume":"33","author":"Sundstr\u00f6m","year":"1993","journal-title":"Behav Ecol Sociobiol"},{"key":"2025122405571343200_msaf320-B75","first-page":"163","article-title":"Genetic population structure and dispersal patterns in Formica ants - a review","volume":"42","author":"Sundstr\u00f6m","year":"2005","journal-title":"Ann Zool Fenn"},{"key":"2025122405571343200_msaf320-B76","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1017\/CBO9780511819049.010","volume-title":"The phylogenetic handbook: a practical approach to phylogenetic analysis and hypothesis testing","author":"Swofford","year":"2009"},{"key":"2025122405571343200_msaf320-B77","doi-asserted-by":"publisher","first-page":"20210197","DOI":"10.1098\/rstb.2021.0197","article-title":"Unbalanced selection: the challenge of maintaining a social polymorphism when a supergene is selfish","volume":"377","author":"Tafreshi","year":"2022","journal-title":"Philos Trans R Soc B Biol Sci"},{"key":"2025122405571343200_msaf320-B78","doi-asserted-by":"publisher","first-page":"2032","DOI":"10.1093\/bioinformatics\/btv098","article-title":"Sambamba: fast processing of NGS alignment formats","volume":"31","author":"Tarasov","year":"2015","journal-title":"Bioinformatics"},{"key":"2025122405571343200_msaf320-B79","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/hdy.2014.20","article-title":"Supergenes and their role in evolution","volume":"113","author":"Thompson","year":"2014","journal-title":"Heredity (Edinb)"},{"key":"2025122405571343200_msaf320-B80","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1086\/282485","article-title":"On supergenes. I. The evolution of supergenes","volume":"101","author":"Turner","year":"1967","journal-title":"Am Nat"},{"key":"2025122405571343200_msaf320-B81","volume-title":"Genomics in the cloud: using Docker, GATK, and WDL in Terra","author":"Van der Auwera","year":"2000"},{"key":"2025122405571343200_msaf320-B82","doi-asserted-by":"publisher","first-page":"853","DOI":"10.1007\/s10592-014-0584-1","article-title":"Population genetics of Formica aquilonia wood ants in Scotland: the effects of long-term forest fragmentation and recent reforestation","volume":"15","author":"Vanhala","year":"2014","journal-title":"Conserv Genet"},{"key":"2025122405571343200_msaf320-B83","doi-asserted-by":"publisher","first-page":"664","DOI":"10.1038\/nature11832","article-title":"A Y-like social chromosome causes alternative colony organization in fire ants","volume":"493","author":"Wang","year":"2013","journal-title":"Nature"},{"key":"2025122405571343200_msaf320-B84","doi-asserted-by":"publisher","first-page":"5582","DOI":"10.1093\/bioinformatics\/btaa1081","article-title":"Accurate, scalable cohort variant calls using DeepVariant and GLnexus","volume":"36","author":"Yun","year":"2021","journal-title":"Bioinformatics"},{"key":"2025122405571343200_msaf320-B85","doi-asserted-by":"publisher","first-page":"1269","DOI":"10.1038\/s41467-017-01370-1","article-title":"Tracing the origin and evolution of supergene mimicry in butterflies","volume":"8","author":"Zhang","year":"2017","journal-title":"Nat Commun"}],"container-title":["Molecular Biology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/mbe\/advance-article-pdf\/doi\/10.1093\/molbev\/msaf320\/65925450\/msaf320.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/mbe\/article-pdf\/42\/12\/msaf320\/65925450\/msaf320.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/mbe\/article-pdf\/42\/12\/msaf320\/65925450\/msaf320.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,24]],"date-time":"2025-12-24T10:57:24Z","timestamp":1766573844000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/mbe\/article\/doi\/10.1093\/molbev\/msaf320\/8381686"}},"subtitle":[],"editor":[{"given":"Russell","family":"Corbett-Detig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,11,28]]},"references-count":85,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2025,11,28]]}},"URL":"https:\/\/doi.org\/10.1093\/molbev\/msaf320","relation":{},"ISSN":["0737-4038","1537-1719"],"issn-type":[{"value":"0737-4038","type":"print"},{"value":"1537-1719","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,12]]},"published":{"date-parts":[[2025,11,28]]},"article-number":"msaf320"}}