110
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: not found

      African origin of the malaria parasite Plasmodium vivax

      research-article
      1 , 1 , 3 , 1 , 4 , 1 , 1 , 2 , 1 , 1 , 1 , 1 , 5 , 5 , 5 , 5 , 5 , 5 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 15 , 18 , 15 , 19 , 20 , 21 , 21 , 22 , 23 , 23 , 24 , 24 , 25 , 26 , 26 , 27 , 28 , 26 , 26 , 26 , 29 , 5 , 30 , 31 , 32 , 1 , 2 ,   33 , 5 , 1 , 2 , 4 , 31
      Nature communications
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Plasmodium vivax is the leading cause of human malaria in Asia and Latin America but is absent from most of central Africa due to the near fixation of a mutation that inhibits the expression of its receptor, the Duffy antigen, on human erythrocytes. The emergence of this protective allele is not understood because P. vivax is believed to have originated in Asia. Here we show, using a non-invasive approach, that wild chimpanzees and gorillas throughout central Africa are endemically infected with parasites that are closely related to human P. vivax. Sequence analyses reveal that ape parasites lack host specificity and are much more diverse than human parasites, which form a monophyletic lineage within the ape parasite radiation. These findings indicate that human P. vivax is of African origin and likely selected for the Duffy-negative mutation. All extant human P. vivax parasites are derived from a single ancestor that escaped out of Africa.

          Related collections

          Most cited references65

          • Record: found
          • Abstract: found
          • Article: not found

          New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

          PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            Clustal W and Clustal X version 2.0.

            The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems. The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              MrBayes 3: Bayesian phylogenetic inference under mixed models.

              MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types-e.g. morphological, nucleotide, and protein-and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.
                Bookmark

                Author and article information

                Journal
                101528555
                37539
                Nat Commun
                Nat Commun
                Nature communications
                2041-1723
                3 June 2014
                2014
                09 July 2014
                : 5
                : 3346
                Affiliations
                [1 ]Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
                [2 ]Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
                [3 ]Columbia University, New York, NY 10027, USA
                [4 ]Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
                [5 ]Unité Mixte Internationale 233 Institut de Recherche pour le Développement and University of Montpellier 1, 34394 Montpellier, France
                [6 ]Institut National de Recherche Biomedicale, Kinshasa, Democratic Republic of the Congo, Swedish University of Agricultural Sciences, Uppsala, Sweden
                [7 ]Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
                [8 ]Department of Ecology and Management of Plant and Animal Resources, Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
                [9 ]Sanaga-Yong Chimpanzee Rescue Center, IDA-Africa, Washington University, Saint Louis, MO 63130, USA
                [10 ]Department of Anthropology, Washington University, Saint Louis, MO 63130, USA
                [11 ]Wildlife Conservation Society, Congo Program, Brazzaville, Republic of the Congo, Chicago, IL 60614, USA
                [12 ]Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, Chicago, IL 60614, USA
                [13 ]Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
                [14 ]Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
                [15 ]Division of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
                [16 ]Department of Human Evolutionary Biology, Harvard University, Boston, MA 02115, USA
                [17 ]Department of Anthropology, University of New Mexico, Albuquerque, NM 87131, USA
                [18 ]Department of Anthropology, University of California, San Diego, CA 92093, USA
                [19 ]Department of Anthropology, University of Minnesota, Minneapolis, MN 55455, USA
                [20 ]Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
                [21 ]Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA
                [22 ]Infectious Disease Unit, Department of Medicine Solna, Karolinska Institute, Karolinska University Hospital, Stockholm SE-17176, Sweden
                [23 ]Public Health England Malaria Reference Laboratory, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, UK
                [24 ]Lukuru Wildlife Research Foundation, Tshuapa-Lomami-Lualaba Project, Kinshasa, Democratic Republic of the Congo, University of Cambridge, UK
                [25 ]Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, UK
                [26 ]Global Viral Forecasting Initiative, San Francisco CA 94104, USA
                [27 ]Ape Action Africa, BP 20072, Yaounde, Cameroon
                [28 ]Limbe Wildlife Centre, PO Box 878, Limbe, Cameroon
                [29 ]Institut de Recherches Médicales et d'Études des Plantes Médicinales Prévention du Sida au Cameroun, Centre de Recherche Médicale, BP 906, Yaoundé, République du Cameroun
                [30 ]Institute of Immunology and Infection Research and University of Edinburgh, Edinburgh EH9 3JT, UK
                [31 ]Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3JT, UK
                [32 ]Malaria Unit, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
                [33 ]Malaria Programme, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
                Author notes
                [* ]corresponding author: paul.sharp@ 123456ed.ac.uk
                [#]

                Current address: Institute for Mind and Biology, The University of Chicago, Chicago, IL 60637, USA

                Article
                NIHMS561763
                10.1038/ncomms4346
                4089193
                24557500
                131ae90a-4739-444d-aba9-320f1467e0b1
                History
                Categories
                Article

                Uncategorized
                Uncategorized

                Comments

                Comment on this article