{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,3]],"date-time":"2026-11-03T06:24:11Z","timestamp":1793687051760,"version":"4.5.1"},"reference-count":48,"publisher":"Springer Science and Business Media LLC","issue":"9","license":[{"start":{"date-parts":[[2023,9,1]],"date-time":"2023-09-01T00:00:00Z","timestamp":1693526400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2023,9,14]],"date-time":"2023-09-14T00:00:00Z","timestamp":1694649600000},"content-version":"vor","delay-in-days":13,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"UK Department of Health and Social Care"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Med"],"published-print":{"date-parts":[[2023,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    The 2022 global mpox outbreak raises questions about how this zoonotic disease established effective human-to-human transmission and its potential for further adaptation. The 2022 outbreak virus is related to an ongoing outbreak in Nigeria originally reported in 2017, but the evolutionary path linking the two remains unclear due to a lack of genomic data between 2018, when virus exportations from Nigeria were first recorded, and 2022, when the global mpox outbreak began. Here, 18 viral genomes obtained from patients across southern Nigeria in 2019\u20132020 reveal multiple lineages of monkeypox virus (MPXV) co-circulated in humans for several years before 2022, with progressive accumulation of mutations consistent with APOBEC3 activity over time. We identify Nigerian A.2 lineage isolates, confirming the lineage that has been multiply exported to North America independently of the 2022 outbreak originated in Nigeria, and that it has persisted by human-to-human transmission in Nigeria for more than 2 years before its latest exportation. Finally, we identify a lineage-defining APOBEC3-style mutation in all A.2 isolates that disrupts gene\n                    <jats:italic>A46R<\/jats:italic>\n                    , encoding a viral innate immune modulator. Collectively, our data demonstrate MPXV capacity for sustained diversification within humans, including mutations that may be consistent with established mechanisms of poxvirus adaptation.\n                  <\/jats:p>","DOI":"10.1038\/s41591-023-02456-8","type":"journal-article","created":{"date-parts":[[2023,9,14]],"date-time":"2023-09-14T12:03:52Z","timestamp":1694693032000},"page":"2317-2324","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":88,"title":["Distinct monkeypox virus lineages co-circulating in humans before 2022"],"prefix":"10.1038","volume":"29","author":[{"given":"Nnaemeka","family":"Ndodo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan","family":"Ashcroft","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kuiama","family":"Lewandowski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adesola","family":"Yinka-Ogunleye","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2411-0290","authenticated-orcid":false,"given":"Chimaobi","family":"Chukwu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adama","family":"Ahmad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0093-6549","authenticated-orcid":false,"given":"David","family":"King","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1837-6255","authenticated-orcid":false,"given":"Afolabi","family":"Akinpelu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4712-4601","authenticated-orcid":false,"given":"Carlos","family":"Maluquer de Motes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5599-3933","authenticated-orcid":false,"given":"Paolo","family":"Ribeca","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0735-8649","authenticated-orcid":false,"given":"Rebecca P.","family":"Sumner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4337-3707","authenticated-orcid":false,"given":"Andrew","family":"Rambaut","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Chester","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3037-624X","authenticated-orcid":false,"given":"Tom","family":"Maishman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2730-4031","authenticated-orcid":false,"given":"Oluwafemi","family":"Bamidele","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nwando","family":"Mba","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olajumoke","family":"Babatunde","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olusola","family":"Aruna","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven T.","family":"Pullan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benedict","family":"Gannon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4776-3403","authenticated-orcid":false,"given":"Colin S.","family":"Brown","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chikwe","family":"Ihekweazu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2556-9407","authenticated-orcid":false,"given":"Ifedayo","family":"Adetifa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7493-3159","authenticated-orcid":false,"given":"David O.","family":"Ulaeto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2023,9,14]]},"reference":[{"key":"2456_CR1","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1016\/S1473-3099(23)00055-5","volume":"23","author":"D Ulaeto","year":"2023","unstructured":"Ulaeto, D. et al. New nomenclature for mpox (monkeypox) and monkeypox virus clades. Lancet Infect. Dis. 23, 273\u2013275 (2023).","journal-title":"Lancet Infect. Dis."},{"key":"2456_CR2","doi-asserted-by":"crossref","unstructured":"Jezek, Z. & Fenner, F. Human monkeypox (Karger, 1988).","DOI":"10.1016\/B978-0-12-253045-6.50011-0"},{"key":"2456_CR3","doi-asserted-by":"publisher","first-page":"16262","DOI":"10.1073\/pnas.1005769107","volume":"107","author":"AW Rimoin","year":"2010","unstructured":"Rimoin, A. W. et al. Major increase in human monkeypox incidence 30 years after smallpox vaccination campaigns cease in the Democratic Republic of Congo. Proc. Natl Acad. Sci. USA 107, 16262\u201316267 (2010).","journal-title":"Proc. Natl Acad. Sci."},{"key":"2456_CR4","doi-asserted-by":"publisher","first-page":"e210","DOI":"10.1093\/cid\/ciaa143","volume":"71","author":"D Ogoina","year":"2020","unstructured":"Ogoina, D. et al. Clinical course and outcome of human monkeypox in Nigeria. Clin. Infect. Dis. 71, e210\u2013e214 (2020).","journal-title":"Clin. Infect. Dis."},{"key":"2456_CR5","doi-asserted-by":"publisher","first-page":"872","DOI":"10.1016\/S1473-3099(19)30294-4","volume":"19","author":"A Yinka-Ogunleye","year":"2019","unstructured":"Yinka-Ogunleye, A. et al. Outbreak of human monkeypox in Nigeria in 2017\u201318: a clinical and epidemiological report. Lancet Infect. Dis. 19, 872\u2013879 (2019).","journal-title":"Lancet Infect. Dis."},{"key":"2456_CR6","doi-asserted-by":"publisher","first-page":"1367","DOI":"10.1093\/infdis\/jiaa559","volume":"225","author":"MR Mauldin","year":"2022","unstructured":"Mauldin, M. R. et al. Exportation of monkeypox virus from the African continent. J. Infect. Dis. 225, 1367\u20131376 (2022).","journal-title":"J. Infect. Dis."},{"key":"2456_CR7","doi-asserted-by":"publisher","first-page":"1166","DOI":"10.1016\/S1473-3099(19)30537-7","volume":"19","author":"OT Ng","year":"2019","unstructured":"Ng, O. T. et al. A case of imported Monkeypox in Singapore. Lancet Infect. Dis. 19, 1166 (2019).","journal-title":"Lancet Infect. Dis."},{"key":"2456_CR8","doi-asserted-by":"publisher","first-page":"1800509","DOI":"10.2807\/1560-7917.ES.2018.23.38.1800509","volume":"23","author":"A Vaughan","year":"2018","unstructured":"Vaughan, A. et al. Two cases of monkeypox imported to the United Kingdom, September 2018. Euro Surveill. 23, 1800509 (2018).","journal-title":"Euro Surveill."},{"key":"2456_CR9","doi-asserted-by":"publisher","first-page":"2200422","DOI":"10.2807\/1560-7917.ES.2022.27.22.2200422","volume":"27","author":"R Vivancos","year":"2022","unstructured":"Vivancos, R. et al. Community transmission of monkeypox in the United Kingdom, April to May 2022. Euro Surveill. 27, 2200422 (2022).","journal-title":"Euro Surveill."},{"key":"2456_CR10","doi-asserted-by":"publisher","first-page":"980\u2013983","DOI":"10.3201\/eid2505.190076","volume":"25","author":"N Erez","year":"2019","unstructured":"Erez, N. et al. Diagnosis of imported monkeypox, Israel, 2018. Emerg. Infect. Dis. 25, 980\u2013983 (2019).","journal-title":"Emerg. Infect. Dis."},{"key":"2456_CR11","first-page":"2200424","volume":"27","author":"MP Duque","year":"2022","unstructured":"Duque, M. P. et al. Ongoing monkeypox virus outbreak, Portugal, 29 April to 23 May 2022. Euro Surveill. 27, 2200424 (2022).","journal-title":"Euro Surveill."},{"key":"2456_CR12","doi-asserted-by":"publisher","first-page":"e639","DOI":"10.1016\/S2666-5247(22)00194-X","volume":"3","author":"DO Ulaeto","year":"2022","unstructured":"Ulaeto, D. O., Dunning, J. & Carroll, M. W. Evolutionary implications of human transmission of monkeypox: the importance of sequencing multiple lesions. Lancet Microbe 3, e639\u2013e640 (2022).","journal-title":"Lancet Microbe"},{"key":"2456_CR13","doi-asserted-by":"publisher","first-page":"1569","DOI":"10.1038\/s41591-022-01907-y","volume":"28","author":"J Isidro","year":"2022","unstructured":"Isidro, J. et al. Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus. Nat. Med. 28, 1569\u20131572 (2022).","journal-title":"Nat. Med."},{"key":"2456_CR14","doi-asserted-by":"publisher","first-page":"560","DOI":"10.1126\/science.add4153","volume":"378","author":"CM Gigante","year":"2022","unstructured":"Gigante, C. M. et al. Multiple lineages of monkeypox virus detected in the United States, 2021\u20132022. Science 378, 560\u2013565 (2022).","journal-title":"Science"},{"key":"2456_CR15","doi-asserted-by":"publisher","first-page":"e3001769","DOI":"10.1371\/journal.pbio.3001769","volume":"20","author":"C Happi","year":"2022","unstructured":"Happi, C. et al. Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus. PLoS Biol. 20, e3001769 (2022).","journal-title":"PLoS Biol."},{"key":"2456_CR16","doi-asserted-by":"publisher","first-page":"2661","DOI":"10.1099\/vir.0.81215-0","volume":"86","author":"AM Likos","year":"2005","unstructured":"Likos, A. M. et al. A tale of two clades: monkeypox viruses. J. Gen. Virol. 86, 2661\u20132672 (2005).","journal-title":"J. Gen. Virol."},{"key":"2456_CR17","first-page":"569\u2013576","volume":"46","author":"SO Foster","year":"1972","unstructured":"Foster, S. O. et al. Human monkeypox. Bull. World Health Organ. 46, 569\u2013576 (1972).","journal-title":"Bull. World Health Organ."},{"key":"2456_CR18","doi-asserted-by":"publisher","first-page":"2168","DOI":"10.3390\/v7042168","volume":"7","author":"Y Nakazawa","year":"2015","unstructured":"Nakazawa, Y. et al. A phylogeographic investigation of African monkeypox. Viruses 7, 2168\u20132184 (2015).","journal-title":"Viruses"},{"key":"2456_CR19","unstructured":"O\u2019Toole, \u00c1. & Rambaut, A. Initial observations about putative APOBEC3 deaminase editing driving short-term evolution of MPXV since 2017. https:\/\/virological.org\/t\/initial-observations-about-putative-apobec3-deaminase-editing-driving-short-term-evolution-of-mpxv-since-2017\/830"},{"key":"2456_CR20","unstructured":"O\u2019Toole, \u00c1. & Rambaut, A. An APOBEC3 molecular clock to estimate the date of emergenceof hMPXV. https:\/\/virological.org\/t\/an-apobec3-molecular-clock-to-estimate-the-date-of-emergence-of-hmpxv\/885"},{"key":"2456_CR21","doi-asserted-by":"publisher","first-page":"e01524","DOI":"10.1128\/MRA.01524-19","volume":"9","author":"I Cohen-Gihon","year":"2020","unstructured":"Cohen-Gihon, I. et al. Identification and whole-genome sequencing of a Monkeypox virus strain isolated in Israel. Microbiol. Resour. Announc. 9, e01524\u201301519 (2020).","journal-title":"Microbiol. Resour. Announc."},{"key":"2456_CR22","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1016\/0042-6822(90)90294-2","volume":"179","author":"SJ Goebel","year":"1990","unstructured":"Goebel, S. J. et al. The complete DNA sequence of vaccinia virus. Virology 179, 247\u2013266 (1990).","journal-title":"Virology"},{"key":"2456_CR23","doi-asserted-by":"publisher","first-page":"1007","DOI":"10.1084\/jem.20041442","volume":"201","author":"J Stack","year":"2005","unstructured":"Stack, J. et al. Vaccinia virus protein A46R targets multiple Toll-like\u2013interleukin-1 receptor adaptors and contributes to virulence. J. Exp. Med. 201, 1007\u20131018 (2005).","journal-title":"J. Exp. Med."},{"key":"2456_CR24","doi-asserted-by":"publisher","first-page":"10162","DOI":"10.1073\/pnas.160027697","volume":"97","author":"A Bowie","year":"2000","unstructured":"Bowie, A. et al. A46R and A52R from vaccinia virus are antagonists of host IL-1 and toll-like receptor signaling. Proc. Natl Acad. Sci. USA 97, 10162\u201310167 (2000).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2456_CR25","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1016\/0014-5793(93)80455-4","volume":"335","author":"A Alcami","year":"1993","unstructured":"Alcami, A. & Smith, G. L. Comment on the paper by Shchelkunov et al. (1993) FEBS Lett. 319, 80\u201383. Two genes encoding poxvirus cytokine receptors are disrupted or deleted in variola virus. FEBS Lett. 335, 136\u2013137 (1993).","journal-title":"FEBS Lett."},{"key":"2456_CR26","doi-asserted-by":"publisher","first-page":"eaaw8977","DOI":"10.1126\/science.aaw8977","volume":"369","author":"B M\u00fchlemann","year":"2020","unstructured":"M\u00fchlemann, B. et al. Diverse variola virus (smallpox) strains were widespread in northern Europe in the Viking Age. Science 369, eaaw8977 (2020).","journal-title":"Science"},{"key":"2456_CR27","doi-asserted-by":"publisher","first-page":"1933","DOI":"10.3390\/v2091933","volume":"2","author":"RC Hendrickson","year":"2010","unstructured":"Hendrickson, R. C., Wang, C., Hatcher, E. L. & Lefkowitz, E. J. Orthopoxvirus genome evolution: the role of gene loss. Viruses 2, 1933\u20131967 (2010).","journal-title":"Viruses"},{"key":"2456_CR28","unstructured":"Centers for Disease Control and Prevention. Update on mpox in Nigeria (Nigeria CDC, 2022)."},{"key":"2456_CR29","unstructured":"Centers for Disease Control and Prevention. Outbreak Brief 25: mpox in Africa Union Member States (Africa CDC, 2023)."},{"key":"2456_CR30","unstructured":"Centers for Disease Control and Prevention. Outbreak Brief 26: mpox in Africa Union Member States (Africa CDC, 2023)."},{"key":"2456_CR31","doi-asserted-by":"publisher","first-page":"1367","DOI":"10.1093\/jac\/dku545","volume":"70","author":"S Duraffour","year":"2015","unstructured":"Duraffour, S. et al. ST-246 is a key antiviral to inhibit the viral F13L phospholipase, one of the essential proteins for orthopoxvirus wrapping. J. Antimicrob. Chemother. 70, 1367\u20131380 (2015).","journal-title":"J. Antimicrob. Chemother."},{"key":"2456_CR32","doi-asserted-by":"publisher","first-page":"2740","DOI":"10.3390\/v2122740","volume":"2","author":"R Lanier","year":"2010","unstructured":"Lanier, R. et al. Development of CMX001 for the treatment of poxvirus infections. Viruses 2, 2740\u20132762 (2010).","journal-title":"Viruses"},{"key":"2456_CR33","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1038\/nature01709","volume":"424","author":"B Mangeat","year":"2003","unstructured":"Mangeat, B. et al. Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts. Nature 424, 99\u2013103 (2003).","journal-title":"Nature"},{"key":"2456_CR34","doi-asserted-by":"publisher","unstructured":"Suspene, R. et al. APOBEC3F is a mutational driver of the human monkeypox virus identified in the 2022 outbreak. J. Infect. Dis. https:\/\/doi.org\/10.1093\/infdis\/jiad165 (2023).","DOI":"10.1093\/infdis\/jiad165"},{"key":"2456_CR35","doi-asserted-by":"publisher","first-page":"783","DOI":"10.1038\/s41587-019-0156-5","volume":"37","author":"T Charalampous","year":"2019","unstructured":"Charalampous, T. et al. Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection. Nat. Biotechnol. 37, 783\u2013792 (2019).","journal-title":"Nat. Biotechnol."},{"key":"2456_CR36","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1186\/s13073-015-0220-9","volume":"7","author":"AL Greninger","year":"2015","unstructured":"Greninger, A. L. et al. Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome Med. 7, 99 (2015).","journal-title":"Genome Med."},{"key":"2456_CR37","doi-asserted-by":"publisher","first-page":"1800228","DOI":"10.2807\/1560-7917.ES.2018.23.50.1800228","volume":"23","author":"LE Kafetzopoulou","year":"2018","unstructured":"Kafetzopoulou, L. E. et al. Assessment of metagenomic Nanopore and Illumina sequencing for recovering whole genome sequences of chikungunya and dengue viruses directly from clinical samples. Euro Surveill. 23, 1800228 (2018).","journal-title":"Euro Surveill."},{"key":"2456_CR38","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1016\/j.meegid.2015.03.018","volume":"32","author":"MS Wright","year":"2015","unstructured":"Wright, M. S. et al. SISPA-seq for rapid whole genome surveys of bacterial isolates. Infect. Genet. Evol. 32, 191\u2013198 (2015).","journal-title":"Infect. Genet. Evol."},{"key":"2456_CR39","doi-asserted-by":"publisher","unstructured":"Quick, J. One-pot ligation protocol for Oxford Nanopore libraries. https:\/\/doi.org\/10.17504\/protocols.io.k9acz2e (2018).","DOI":"10.17504\/protocols.io.k9acz2e"},{"key":"2456_CR40","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1101\/gr.215087.116","volume":"27","author":"S Koren","year":"2017","unstructured":"Koren, S. et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27, 722\u2013736 (2017).","journal-title":"Genome Res."},{"key":"2456_CR41","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403\u2013410 (1990).","journal-title":"J. Mol. Biol."},{"key":"2456_CR42","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","volume":"26","author":"AR Quinlan","year":"2010","unstructured":"Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841\u2013842 (2010).","journal-title":"Bioinformatics"},{"key":"2456_CR43","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","volume":"30","author":"K Katoh","year":"2013","unstructured":"Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. evolution 30, 772\u2013780 (2013).","journal-title":"Mol. Biol. evolution"},{"key":"2456_CR44","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/molbev\/msu300","volume":"32","author":"L-T Nguyen","year":"2015","unstructured":"Nguyen, L.-T., Schmidt, H. A., Von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. evolution 32, 268\u2013274 (2015).","journal-title":"Mol. Biol. evolution"},{"key":"2456_CR45","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1186\/1745-6150-3-20","volume":"3","author":"Y Kapustin","year":"2008","unstructured":"Kapustin, Y., Souvorov, A., Tatusova, T. & Lipman, D. Splign: algorithms for computing spliced alignments with identification of paralogs. Biol. direct 3, 20 (2008).","journal-title":"Biol. direct"},{"key":"2456_CR46","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","volume":"30","author":"A Stamatakis","year":"2014","unstructured":"Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312\u20131313 (2014).","journal-title":"Bioinformatics"},{"key":"2456_CR47","unstructured":"R Core Team. R: a language and environment for statistical computing (R Foundation for Statistical Computing, 2019)."},{"key":"2456_CR48","unstructured":"Ogle, D. H., Doll, J. C., Wheeler, A. P. & Dinno, A. FSA: fisheries stock analysis. R package version 0.8.30. (2022)."}],"container-title":["Nature Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41591-023-02456-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41591-023-02456-8","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41591-023-02456-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T07:18:01Z","timestamp":1783667881000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41591-023-02456-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,9]]},"references-count":48,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2023,9]]}},"alternative-id":["2456"],"URL":"https:\/\/doi.org\/10.1038\/s41591-023-02456-8","relation":{},"ISSN":["1078-8956","1546-170X"],"issn-type":[{"value":"1078-8956","type":"print"},{"value":"1546-170X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,9]]},"assertion":[{"value":"13 January 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 June 2023","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 September 2023","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}