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Edited by Richard G. Klein, Stanford University, Stanford, CA, and approved August 12, 2016 (received for review July 6, 2016)
Article Figures & SI
Figures
- Fig. 1.
(A) Two of the Giemsa-stained slides analyzed in this study, labeled CM and CA (inferior stain). (B) Visualization of some Plasmodium parasites (arrows) in the CM slide under the microscope (400×).
- Fig. S1.
Damage pattern at the end of the DNA reads retrieved from the slides, consistent with those being ancient. Frequencies of C to T (red) and G to A (blue) misincorporations of the 5′ end (left) and 3′ end (right) are shown. From top to bottom: P. falciparum mtDNA reads; P. vivax mtDNA reads; and human reads.
- Fig. S2.
Fragment length distribution of the P. vivax and P. falciparum reads.
- Fig. 2.
Haplotype network constructed using NETWORK 5,0.0, incorporating 790 P. vivax mitochondrial DNA genomes previously published and the one retrieved in this study (arrow-marked European isolate). Size circles equal to the frequency of a given haplotype; lines separating haplotypes represent mutational steps. Each color shows the geographic origin of the samples.
- Fig. S3.
Maximum likelihood tree generated with a geographical diverse dataset of P. vivax mtDNA genomes (the green cross, marked with an arrow, corresponds to the European isolate). Red start represents a clade with 0.84 bootstrap support.
- Fig. 3.
Haplotype network constructed using NETWORK 5.0.0 incorporating 698 P. falciparum mitochondrial DNA genomes previously published and the one retrieved in this study (arrow-marked European isolate).
- Fig. S4.
Maximum likelihood tree generated with a geographical diverse dataset of P. falciparum mtDNA genomes (the green cross, marked with an arrow, corresponds to the European isolate). Red start represents a clade with 0.80 bootstrap support.
Tables
Sample Total reads Mapped reads (P. vivax/P .falciparum) Unique reads (P. vivax/P .falciparum) MtDNA coverage (P. vivax/P .falciparum) CA depletion 41,669,177 573/1,325 228/569 2.56/6.66 CM depletion 36,781,114 965/600 268/229 3.06/2.66 POS depletion 47,712,546 279/426 129/229 2.79/2.84 CA capture 52,310,688 474,175/1,093,502 336/814 3.86/9.73 CM capture 32,441,831 576,598/509,355 264/250 3.00/2.86 POS capture 32,323,796 38,160/178,290 112/210 1.32/2.56 Consensus mt DNA — — 459/1,220 5.02/14.75 Data were generated with two experimental approaches on the three slides (CM, CA, and POS). Depletion refers to the mapped reads from the genomic libraries depleted by whole human genome capture; capture refers to the mapped reads after capturing the genomic libraries with P. falciparum baits.
Sample Total reads Mapped reads Unique reads Nuclear coverage CA depletion 41,669,177 8,939 3,036 0.0000 CM depletion 36,781,114 40,047 35,072 0.0889 POS depletion 47,712,546 2,348 710 0.0000 CA capture 52,310,688 8,388 2,600 0.0053 CM capture 32,441,831 13,940 10,678 0.0259 POS capture 32,323,796 2,013 547 0.0010 Sample Total reads Mapped reads Unique reads Nuclear coverage CA depletion 41,669,177 90,132 80,570 0.0182 CM depletion 36,781,114 9,516 4,784 0.0130 POS depletion 47,712,546 6,653 4,965 0.0157 CA capture 52,310,688 24,196,904 132,642 0.4290 CM capture 32,441,831 78,769 3,559 0.0100 POS capture 32,323,796 489,464 2,792 0.0100 Sample Total reads Mapped reads Unique reads Nuclear coverage CA depletion 41,669,177 12,667,791 12,033,290 0.2116 CM depletion 36,781,114 6,221,402 5,841,497 0.1937 POS depletion 47,712,546 4,309,690 4,111,376 0.2290 CA capture 52,310,688 2,468,011 2,321,087 0.2073 CM capture 32,441,831 1,734,974 1,611,254 0.1881 POS capture 32,323,796 219,493 203,647 0.0451
Data supplements
Supporting Information
DNA from the eradicated European malaria parasites
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