Neutral polymorphisms in putative housekeeping genes and tandem repeats unravels the population genetics and evolutionary history of Plasmodium vivax in India
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. Analy...
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| description | 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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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.</description><identifier>ISSN: 1935-2735</identifier><identifier>ISSN: 1935-2727</identifier><identifier>EISSN: 1935-2735</identifier><identifier>DOI: 10.1371/journal.pntd.0002425</identifier><identifier>PMID: 24069480</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Animals ; Evolution, Molecular ; Genes ; Genes, Essential - genetics ; Genetic aspects ; Genetics, Population ; Genomics ; Health aspects ; Humans ; India - epidemiology ; Kinases ; Malaria ; Malaria, Vivax - epidemiology ; Malaria, Vivax - parasitology ; Medical research ; Microbiology ; Parasites ; Phylogeography ; Plasmodium vivax ; Plasmodium vivax - genetics ; Polymorphism, Single Nucleotide ; Population genetics ; Single nucleotide polymorphisms ; Studies ; Tandem Repeat Sequences</subject><ispartof>PLoS neglected tropical diseases, 2013-09, Vol.7 (9), p.e2425-e2425</ispartof><rights>COPYRIGHT 2013 Public Library of Science</rights><rights>2013 Prajapati et al 2013 Prajapati et al</rights><rights>2013 Prajapati et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Prajapati SK, Joshi H, Carlton JM, Rizvi MA (2013) Neutral Polymorphisms in Putative Housekeeping Genes and Tandem Repeats Unravels the Population Genetics and Evolutionary History of Plasmodium vivax in India. 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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.</description><subject>Analysis</subject><subject>Animals</subject><subject>Evolution, Molecular</subject><subject>Genes</subject><subject>Genes, Essential - genetics</subject><subject>Genetic aspects</subject><subject>Genetics, Population</subject><subject>Genomics</subject><subject>Health aspects</subject><subject>Humans</subject><subject>India - epidemiology</subject><subject>Kinases</subject><subject>Malaria</subject><subject>Malaria, Vivax - epidemiology</subject><subject>Malaria, Vivax - parasitology</subject><subject>Medical research</subject><subject>Microbiology</subject><subject>Parasites</subject><subject>Phylogeography</subject><subject>Plasmodium vivax</subject><subject>Plasmodium vivax - genetics</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Population genetics</subject><subject>Single nucleotide polymorphisms</subject><subject>Studies</subject><subject>Tandem Repeat Sequences</subject><issn>1935-2735</issn><issn>1935-2727</issn><issn>1935-2735</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>DOA</sourceid><recordid>eNptUl2L1DAULaK46-o_EA0I4suMaZM0zYuwLH4MLOqDPoekvZ1mTJOatMX9M_5W053usgMSyA0355z7mWUvc7zNCc_fH_wUnLLbwY3NFmNc0II9ys5zQdim4IQ9fvA-y57FeMCYCVblT7OzguJS0AqfZ3-_wjQGZdHg7U3vw9CZ2EdkHBqmUY1mBtT5KcIvgMG4PdqDg4iUa9CYLuhRgAHUGNHkgprBRjR2kMSGySa2d7eE0dRHDszeTotbhRuUIo0-Wd-i71bF3jdm6tFsZvVnib9zjVHPsyetshFerPYi-_np44-rL5vrb593V5fXm5qJctzoGhOtNQZWV1xpTJuKNaKkreZNpaEugWpdElJjaJq8EJiLVjSlpiJPHCXIRfb6qDtYH-Xa2ihzSgtKKcM0IXZHROPVQQ7B9KkG6ZWRtw4f9lKFVKgFSahoK10RIVROhSJaFJzlggpSaJ7XZdL6sEabdA9NDW4ZwYno6Y8zndz7WRLOecV5Eni3CgT_e4I4yt7EGqxVDtK0Ut6EswqziiXomyN0r1JqxrU-KdYLXF4SyktGhVgEt_9BpZNGbGrvoDXJf0J4-4DQgbJjF9fhxlMgPQLr4GMM0N6XmWO5LPJdt-WyyHJd5ER79bBF96S7zSX_ACjx9Q0</recordid><startdate>20130901</startdate><enddate>20130901</enddate><creator>Prajapati, Surendra K</creator><creator>Joshi, Hema</creator><creator>Carlton, Jane M</creator><creator>Rizvi, M Alam</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20130901</creationdate><title>Neutral polymorphisms in putative housekeeping genes and tandem repeats unravels the population genetics and evolutionary history of Plasmodium vivax in India</title><author>Prajapati, Surendra K ; Joshi, Hema ; Carlton, Jane M ; Rizvi, M Alam</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c596t-bc03bbb0e5c87ab04d85d964fb7d8bec6e4bb633c0edd129079f9d6b4910e5a93</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Analysis</topic><topic>Animals</topic><topic>Evolution, Molecular</topic><topic>Genes</topic><topic>Genes, Essential - genetics</topic><topic>Genetic aspects</topic><topic>Genetics, Population</topic><topic>Genomics</topic><topic>Health aspects</topic><topic>Humans</topic><topic>India - epidemiology</topic><topic>Kinases</topic><topic>Malaria</topic><topic>Malaria, Vivax - epidemiology</topic><topic>Malaria, Vivax - parasitology</topic><topic>Medical research</topic><topic>Microbiology</topic><topic>Parasites</topic><topic>Phylogeography</topic><topic>Plasmodium vivax</topic><topic>Plasmodium vivax - genetics</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Population genetics</topic><topic>Single nucleotide polymorphisms</topic><topic>Studies</topic><topic>Tandem Repeat Sequences</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Prajapati, Surendra K</creatorcontrib><creatorcontrib>Joshi, Hema</creatorcontrib><creatorcontrib>Carlton, Jane M</creatorcontrib><creatorcontrib>Rizvi, M Alam</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PLoS neglected tropical diseases</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Prajapati, Surendra K</au><au>Joshi, Hema</au><au>Carlton, Jane M</au><au>Rizvi, M Alam</au><au>del Portillo, Hernando A.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Neutral polymorphisms in putative housekeeping genes and tandem repeats unravels the population genetics and evolutionary history of Plasmodium vivax in India</atitle><jtitle>PLoS neglected tropical diseases</jtitle><addtitle>PLoS Negl Trop Dis</addtitle><date>2013-09-01</date><risdate>2013</risdate><volume>7</volume><issue>9</issue><spage>e2425</spage><epage>e2425</epage><pages>e2425-e2425</pages><issn>1935-2735</issn><issn>1935-2727</issn><eissn>1935-2735</eissn><abstract>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.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>24069480</pmid><doi>10.1371/journal.pntd.0002425</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Analysis Animals Evolution, Molecular Genes Genes, Essential - genetics Genetic aspects Genetics, Population Genomics Health aspects Humans India - epidemiology Kinases Malaria Malaria, Vivax - epidemiology Malaria, Vivax - parasitology Medical research Microbiology Parasites Phylogeography Plasmodium vivax Plasmodium vivax - genetics Polymorphism, Single Nucleotide Population genetics Single nucleotide polymorphisms Studies Tandem Repeat Sequences |
| title | Neutral polymorphisms in putative housekeeping genes and tandem repeats unravels the population genetics and evolutionary history of Plasmodium vivax in India |
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