Michel 2024

[jfy133]

Publication DOI or URL

https://www.nature.com/articles/s41586-024-07546-2

Additional context

Data availability

Raw sequencing data from 36 malaria-positive individuals, as well as newly reported data from 41 ancient individuals enriched at human ancestry-informative SNP positions, have been deposited at the European Nucleotide Archive (accession number PRJEB73276). Ancient and modern P. vivax and P. falciparum nuclear genotypes are available in eigenstrat format (https://figshare.com/projects/Ancient_Plasmodium_genomes_shed_light_on_the_history_of_human_malaria/196711). This study used modern P. falciparum and P. vivax genotype datasets available through the Pf6 data release of the MalariaGEN P. falciparum Community Project (ftp://ngs.sanger.ac.uk/production/malaria/pfcommunityproject/Pf6/) and the Pv4 data release of the MalariaGEN P. vivax Genome Variation project (ftp://ngs.sanger.ac.uk/production/malaria/Resource/30). Previously published raw sequencing datasets from Indian P. falciparum strains and the Ebro Delta blood slide can be obtained from the European Nucleotide Archive under accession numbers PRJNA322219 and PRJEB30878, respectively. This study used previously published ancient human genotype datasets obtained from the Reich laboratory’s Allen Ancient DNA Resource v.54.1 (https://reich.hms.harvard.edu/allen-ancient-dna-resource-aadr-downloadable-genotypes-present-day-and-ancient-dna-data). Previously published modern P. falciparum and P. vivax mitochondrial datasets, as well as genomic sequences used in our probe design and metagenomic screening database, are available via the National Center for Biotechnology Information (accession numbers can be found in Supplementary Tables 9, 10, 11 and 13). The following whole-genome sequencing datasets obtained from the NCBI Sequence Read Archive were used for phylogenetic dating: SAMN02677154, SAMN02677164, SAMN02677167, SAMN03274512, SAMN02677169, SAMN02677170, SAMN02677171, SAMN02677180, SAMN02677183, SAMN02677184, SAMN02677185, SAMN02677186, SAMN02677187, SAMN02677195 and SAMN00710542. The following genome assemblies and chromosome sequences available via the NCBI were used as references in this study: P. falciparum mitochondria: LR605957.1; P. vivax mitochondria: LT635627.1; P. malariae mitochondria: LT594637.1; P. falciparum nuclear chromosomes: GCA_000002765.3; P. vivax nuclear chromosomes: GCA_900093555.1; P. vivax-like nuclear chromosomes: GCA_003402215.1; Plasmodium cynomolgi nuclear chromosomes: GCA_900180395.1; P. praefalciparum nuclear chromosomes: GCA_900095595.1; and the Genome Reference Consortium Human Build 37 (GRCh37): PRJNA31257. Maps presented in the main text and Extended Data figures were produced using the following resources: Cartopy (v.0.20.3, https://github.com/SciTools/cartopy/tree/v0.20.3); Natural Earth (naturalearthdata.com); and World Shaded Relief map (Esri, 2009).