title: Plasmodium vivax synonymous substitution frequencies, evolution and population structure deduced from diversity in AMA 1 and MSP 1 genes.
abstract: Polymorphic regions of the genes encoding Plasmodium vivax apical membrane antigen 1 (PvAMA1) and P. vivax merozoite surface protein 1 (PvMSP1) were sequenced to examine population diversity both within and between geographical areas. Sequences were obtained for 219 isolates for PvAMA1 and for 175 isolates for PvMSP1 from Africa, China, India, Indonesia, Philippines, Papua New Guinea, Solomon Islands and Thailand. Over half of the isolates were obtained from different regions within the Philippines, and this was used to look at the diversity within a country. Sixty nine haplotypes and 22 polymorphic sites in a 414-bp region of PvAMA1 and 41 haplotypes and 34 polymorphic sites in a 249-bp fragment of PvMSP1 were detected. For both PvAMA1 and PvMSP1, four previously unreported polymorphic nucleotide positions were identified. Population analysis indicated that there were significant differences in allele frequencies between different regions but these differences were small compared to the diversity within populations (Fixation index, F(ST), of 0.126 and 0.078 for PvAMA1 and PvMSP1, respectively). PvAMA1 and PvMSP1 had similar nonsynonymous substitution frequencies but surprisingly, the synonymous substitution frequency for PvMSP1 was eight times the frequency for PvAMA1 suggesting that synonymous substitutions in at least PvAMA1 are not neutral.
authors.affiliation: University of Sydney, Sydney, Australia.
authors.forename: M
authors.initials: M
authors.lastname: Figtree
authors.forename: C J
authors.initials: CJ
authors.lastname: Pasay
authors.forename: R
authors.initials: R
authors.lastname: Slade
authors.forename: Q
authors.initials: Q
authors.lastname: Cheng
authors.forename: N
authors.initials: N
authors.lastname: Cloonan
authors.forename: J
authors.initials: J
authors.lastname: Walker
authors.forename: A
authors.initials: A
authors.lastname: Saul
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000953:Antigens, Protozoan; D001483:Base Sequence; D019143:Evolution, Molecular; D017125:Genes, Protozoan; D014644:Genetic Variation; D005828:Genetics, Population; D006801:Humans; D016780:Malaria, Vivax / Q000469:parasitology; D008565:Membrane Proteins / Q000235:genetics*; D020066:Merozoite Surface Protein 1 / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D010966:Plasmodium vivax / Q000235:genetics* / Q000378:metabolism; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D015800:Protozoan Proteins / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D000953:Antigens, Protozoan; D008565:Membrane Proteins; D020066:Merozoite Surface Protein 1; D015800:Protozoan Proteins; C090077:apical membrane antigen I, Plasmodium