Replication Data for: Identification of two genomic cryptotypes of Plasmodium malariae in Africa

These data and scripts are accompanying the manuscript: "Identification of two genomic cryptotypes of Plasmodium malariae in Africa" by Margaux J. M. Lefebvre*, Céline Arnathau, Sandrine Houzé, Benoit de Thoisy, Camila González, Silvia Rondón, Arnab Pain, Michael C. Fontaine§*, Franck Prugnolle§* & Virginie Rougeron§* (*, contact person; § co-supervisors and co-last authors). The archive here includes: malariae_brasi.filt.core.ploidy2.vcf.gz: the SNP polymorphism data in VCF format. Scripts_WGSPmalariae.tar all the scripts and explanations that are provided in the GitHub repository accompanying the manuscript (github.com) in a zipped folder. README.txt: additional explanations related to the data. Context and scientific goals: Plasmodium malariae is a human malaria parasite widely distributed across Africa, yet its population structure and genomic diversity remain incompletely characterized because of limited whole-genome data from the continent. In addition, the evolutionary and genetic relationships between P. malariae and the closely related simian parasite from South America, Plasmodium brasilianum, are still not fully understood due to the scarcity of genomic resources. To address these knowledge gaps, this study analyzed parasite genomes obtained from infected humans and non-human primates to investigate genetic diversity, population structure, and signatures of adaptation. Specifically, the objectives were to expand and strengthen the African whole-genome dataset for P. malariae and to generate additional genomic data for P. brasilianum, thereby improving our understanding of their genetic relationships and evolutionary history. See the manuscript for further details.