Research
Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence
- † Equal contributors
1 Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
2 Department of Immunology and Infectious Diseases, Harvard School of Public Health, 677 Huntington Ave, Boston, MA 02115, USA
3 School for Health Studies, Simmons College, 300 The Fenway, Boston, MA 02115, USA
4 Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, BP 7325 Dakar, Senegal
5 Departamento de Parasitologia, Instituto de Ciencias Biomedicas da USP, Av. Prof. Lineu Prestes 1374, Cidade Universitaria, 05508-900 Sao Paulo, SP, Brazil
6 Instituto de Medicina Tropical de Sao Paulo, Universidade de Sao Paulo, Av Dr. Eneas de Carvalho Aguiar 470, 05403-907 Sao Paulo, SP, Brazil
7 National Institute of Malaria Research, 22, Sham Nath Marg, Delhi-110054, India
8 International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India
9 Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
Genome Biology 2008, 9:R171 doi:10.1186/gb-2008-9-12-r171
Published: 15 December 2008Additional files
Additional data file 1:
Lines indicate the number of SNPs exhibiting various call rates using the DM, BRLMM, and BRLMM-P SNP calling algorithms. BRLMM-P SNP calls were used for analysis.
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Additional data file 2:
Array performance in the presence of human DNA and malaria DNA from mixed (non-clonal) infections.
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Additional data file 3:
Reported results are for SNP loci known to exhibit different alleles between the HB3 and Dd2 lines. The highest proportion of heterozygous calls was observed for the even (1:1) mixture of malaria.
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Additional data file 4:
Concordance with known genotype can be improved using more stringent confidence cutoff values with the BRLMM-P calling algorithm.
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Additional data file 5:
Genomic location and genotype data for SNPs assayed on the array with a call rate of at least 80%.
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Additional data file 6:
(a) High MAF (MAF > 0.25) topology. (b) Low MAF (MAF < 0.25) topology. Nodes exhibiting bootstrap support levels of at least 50% or 90% are indicated by gray dots and black dots, respectively. Bootstrap support and branch length differ between the topologies, but the American and Asian parasites form congruent clades.
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Additional data file 7:
(a) Plot of the likelihood of the genotyping data given that the samples derive from K = 1-5 populations. (b) Plot of the posterior probability of population membership for each sample hybridized to the array, assuming three underlying populations.
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Additional data file 8:
(a) First two principal components for Brazil data; clusters suggest population structure. (b) First two components for worldwide data set. (c) First and third components for worldwide data set.
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Additional data file 9:
Significantly greater nonsynonymous divergence (determined by bootstrapping) is indicated by asterisks: **P < 0.001.
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Additional data file 10:
Nonsynonymous and silent SNP DAF correlation between Senegal and Thailand.
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