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However, the genomic make-up of\n                    <jats:italic>P. knowlesi<\/jats:italic>\n                    in Sabah was previously poorly understood. To inform on local patterns of transmission and putative adaptive drivers, we conduct population-level genetic analyses of\n                    <jats:italic>P. knowlesi<\/jats:italic>\n                    human infections using 52 new whole genomes from Sabah, Malaysia, in combination with publicly available data. We identify the emergence of distinct geographical subpopulations within the macaque-associated clusters using identity-by-descent-based connectivity analysis. Secondly, we report on introgression events between the clusters, which may be linked to differentiation of the subpopulations, and that overlap genes critical for survival in human and mosquito hosts. Using village-level locations from\n                    <jats:italic>P. knowlesi<\/jats:italic>\n                    infections, we also identify associations between several introgressed regions and both intact forest perimeter-area ratio and mosquito vector habitat suitability. Our findings provide further evidence of the complex role of changing ecosystems and sympatric macaque hosts in Malaysia driving distinct genetic changes seen in\n                    <jats:italic>P. knowlesi<\/jats:italic>\n                    populations. Future expanded analyses of evolving\n                    <jats:italic>P. knowlesi<\/jats:italic>\n                    genetics and environmental drivers of transmission will be important to guide public health surveillance and control strategies.\n                  <\/jats:p>","DOI":"10.1371\/journal.pntd.0012885","type":"journal-article","created":{"date-parts":[[2025,3,12]],"date-time":"2025-03-12T13:25:19Z","timestamp":1741785919000},"page":"e0012885","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":7,"title":["Genomic epidemiology of Plasmodium knowlesi reveals putative genetic drivers of adaptation in Malaysia"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5171-819X","authenticated-orcid":true,"given":"Jacob A. 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