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In this study, we analyzed whole-genome sequences of 614\n                    <jats:italic>Y. pestis<\/jats:italic>\n                    strains, with 141 strains newly sequenced, collected over 96 years across Madagascar. All isolates emerged in 1898 and belong to the phylogroup 1.ORI3, supporting a single introduction event to Madagascar, followed by local diversification. We identified 23 distinct subgroups, including eight previously undescribed. Although most novel subgroups were rarely detected or rapidly extinguished, the \u0263 subgroup circulated between 2016 and 2019 in southeastern Madagascar\u2014an area historically plague-free for 64 years. Our analysis revealed extensive strain diversity and subgroup persistence, with some subgroups, such as \u03b1 and \u03b2, persisting silently for decades before reemerging during the 2017 pneumonic plague epidemic. These findings uncover deep, previously underestimated phylogenetic diversity and long-term dynamics of\n                    <jats:italic>Y. pestis<\/jats:italic>\n                    in Madagascar, providing critical insights for understanding transmission patterns and informing future plague surveillance and control efforts.\n                  <\/jats:p>","DOI":"10.1038\/s42003-025-09109-1","type":"journal-article","created":{"date-parts":[[2025,11,26]],"date-time":"2025-11-26T12:36:49Z","timestamp":1764160609000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Evaluating the early diversification of Yersinia pestis and its phylogeographic expansion over 96 years of evolution in Madagascar"],"prefix":"10.1038","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4776-2662","authenticated-orcid":false,"given":"Lovasoa Nomena","family":"Randriantseheno","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason W.","family":"Sahl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adrien","family":"Rieux","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4024-3002","authenticated-orcid":false,"given":"Guillem","family":"Mas Fiol","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dawn","family":"Birdsell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivier","family":"Gorg\u00e9","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric","family":"Valade","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4343-0508","authenticated-orcid":false,"given":"Javier","family":"Pizarro-Cerd\u00e0","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Voahangy","family":"Andrianaivoarimanana","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2684-6007","authenticated-orcid":false,"given":"David M.","family":"Wagner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minoarisoa","family":"Rajerison","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,11,26]]},"reference":[{"key":"9109_CR1","doi-asserted-by":"publisher","first-page":"109278","DOI":"10.1016\/j.celrep.2021.109278","volume":"35","author":"J Susat","year":"2021","unstructured":"Susat, J. et al. 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