TY - JOUR
T1 - Neutral Polymorphisms in Putative Housekeeping Genes and Tandem Repeats Unravels the Population Genetics and Evolutionary History of Plasmodium vivax in India
AU - Prajapati, Surendra K.
AU - Joshi, Hema
AU - Carlton, Jane M.
AU - Rizvi, M. Alam
N1 - Funding Information:
This work was supported by the Department of Biotechnology and Indian Council of Medical Research, New Delhi, and with funds from a National Institutes of Health/Fogarty International Center, Global Infectious Disease training grant (D43 TW007884). SKP is an ICMR-Postdoctoral Fellow. The authors thank Dr. Steven Sullivan for proof reading, Dr. Simon Kang'a for technical support, and NIMR scientists, staff in the Molecular Biology Division, and at NIMR field units for their support and cooperation during the study. The authors would like to dedicate this manuscript to the memory of Dr. Hema Joshi (deceased). The content is solely the responsibility of the authors and does not necessarily represent the official views of the Fogarty International Center or the National Institutes of Health.
PY - 2013/9
Y1 - 2013/9
N2 - The evolutionary history and age of Plasmodium vivax has been inferred as both recent and ancient by several studies, mainly using mitochondrial genome diversity. Here we address the age of P. vivax on the Indian subcontinent using selectively neutral housekeeping genes and tandem repeat loci. Analysis of ten housekeeping genes revealed a substantial number of SNPs (n = 75) from 100 P. vivax isolates collected from five geographical regions of India. Neutrality tests showed a majority of the housekeeping genes were selectively neutral, confirming the suitability of housekeeping genes for inferring the evolutionary history of P. vivax. In addition, a genetic differentiation test using housekeeping gene polymorphism data showed a lack of geographical structuring between the five regions of India. The coalescence analysis of the time to the most recent common ancestor estimate yielded an ancient TMRCA (232,228 to 303,030 years) and long-term population history (79,235 to 104,008) of extant P. vivax on the Indian subcontinent. Analysis of 18 tandem repeat loci polymorphisms showed substantial allelic diversity and heterozygosity per locus, and analysis of potential bottlenecks revealed the signature of a stable P. vivax population, further corroborating our ancient age estimates. For the first time we report a comparable evolutionary history of P. vivax inferred by nuclear genetic markers (putative housekeeping genes) to that inferred from mitochondrial genome diversity.
AB - The evolutionary history and age of Plasmodium vivax has been inferred as both recent and ancient by several studies, mainly using mitochondrial genome diversity. Here we address the age of P. vivax on the Indian subcontinent using selectively neutral housekeeping genes and tandem repeat loci. Analysis of ten housekeeping genes revealed a substantial number of SNPs (n = 75) from 100 P. vivax isolates collected from five geographical regions of India. Neutrality tests showed a majority of the housekeeping genes were selectively neutral, confirming the suitability of housekeeping genes for inferring the evolutionary history of P. vivax. In addition, a genetic differentiation test using housekeeping gene polymorphism data showed a lack of geographical structuring between the five regions of India. The coalescence analysis of the time to the most recent common ancestor estimate yielded an ancient TMRCA (232,228 to 303,030 years) and long-term population history (79,235 to 104,008) of extant P. vivax on the Indian subcontinent. Analysis of 18 tandem repeat loci polymorphisms showed substantial allelic diversity and heterozygosity per locus, and analysis of potential bottlenecks revealed the signature of a stable P. vivax population, further corroborating our ancient age estimates. For the first time we report a comparable evolutionary history of P. vivax inferred by nuclear genetic markers (putative housekeeping genes) to that inferred from mitochondrial genome diversity.
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U2 - 10.1371/journal.pntd.0002425
DO - 10.1371/journal.pntd.0002425
M3 - Article
C2 - 24069480
AN - SCOPUS:84884679367
SN - 1935-2727
VL - 7
JO - PLoS neglected tropical diseases
JF - PLoS neglected tropical diseases
IS - 9
M1 - e2425
ER -