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      Age of the Association between Helicobacter pylori and Man

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          When modern humans left Africa ca. 60,000 years ago (60 kya), they were already infected with Helicobacter pylori, and these bacteria have subsequently diversified in parallel with their human hosts. But how long were humans infected by H. pylori prior to the out-of-Africa event? Did this co-evolution predate the emergence of modern humans, spanning the species divide? To answer these questions, we investigated the diversity of H. pylori in Africa, where both humans and H. pylori originated. Three distinct H. pylori populations are native to Africa: hpNEAfrica in Afro-Asiatic and Nilo-Saharan speakers, hpAfrica1 in Niger-Congo speakers and hpAfrica2 in South Africa. Rather than representing a sustained co-evolution over millions of years, we find that the coalescent for all H. pylori plus its closest relative H. acinonychis dates to 88–116 kya. At that time the phylogeny split into two primary super-lineages, one of which is associated with the former hunter-gatherers in southern Africa known as the San. H. acinonychis, which infects large felines, resulted from a later host jump from the San, 43–56 kya. These dating estimates, together with striking phylogenetic and quantitative human-bacterial similarities show that H. pylori is approximately as old as are anatomically modern humans. They also suggest that H. pylori may have been acquired via a single host jump from an unknown, non-human host. We also find evidence for a second Out of Africa migration in the last 52,000 years, because hpEurope is a hybrid population between hpAsia2 and hpNEAfrica, the latter of which arose in northeast Africa 36–52 kya, after the Out of Africa migrations around 60 kya.

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          We previously showed that the population history of H. pylori may be used as a marker for human migrations, including the demonstration that humans carried H. pylori out of Africa 60,000 years ago during their recent global expansions. But how long were humans infected by H. pylori prior to the out-of-Africa event? Here we showed that chimpanzees in Central-East Africa do not possess Helicobacter-like bacteria, as would have been expected for pathogen-host co-evolution over millions of years. Using H. pylori gene sequences isolated from San, a group of click-speaking hunter-gatherers, and numerous other sources, we calculated that humans have been infected with H. pylori for at least 88,000–116,000 years. Phylogenetic comparisons showed similar evolutionary histories for human and H. pylori lineages and suggest that this association stemmed from a single host jump. We showed that hpAfrica2, the most divergent H. pylori population, arose in the San and that their progenitors were the source of H. acinonychis which was acquired by large felines approximately 50,000 years ago. Furthermore, our data provided clear evidence for a recent second exodus Out of Africa in the last 52,000 years which was essential for the formation of the hybrid population that currently infects Europeans.

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          Most cited references 97

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          MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.

          We announce the release of the fourth version of MEGA software, which expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. Version 4 includes a unique facility to generate captions, written in figure legend format, in order to provide natural language descriptions of the models and methods used in the analyses. This facility aims to promote a better understanding of the underlying assumptions used in analyses, and of the results generated. Another new feature is the Maximum Composite Likelihood (MCL) method for estimating evolutionary distances between all pairs of sequences simultaneously, with and without incorporating rate variation among sites and substitution pattern heterogeneities among lineages. This MCL method also can be used to estimate transition/transversion bias and nucleotide substitution pattern without knowledge of the phylogenetic tree. This new version is a native 32-bit Windows application with multi-threading and multi-user supports, and it is also available to run in a Linux desktop environment (via the Wine compatibility layer) and on Intel-based Macintosh computers under the Parallels program. The current version of MEGA is available free of charge at (
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            Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies.

            We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci. The new model accounts for the correlations between linked loci that arise in admixed populations ("admixture linkage disequilibium"). This modification has several advantages, allowing (1) detection of admixture events farther back into the past, (2) inference of the population of origin of chromosomal regions, and (3) more accurate estimates of statistical uncertainty when linked loci are used. It is also of potential use for admixture mapping. In addition, we describe a new prior model for the allele frequencies within each population, which allows identification of subtle population subdivisions that were not detectable using the existing method. We present results applying the new methods to study admixture in African-Americans, recombination in Helicobacter pylori, and drift in populations of Drosophila melanogaster. The methods are implemented in a program, structure, version 2.0, which is available at
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              distruct: a program for the graphical display of population structure


                Author and article information

                Role: Editor
                PLoS Pathog
                PLoS Pathog
                PLoS Pathogens
                Public Library of Science (San Francisco, USA )
                May 2012
                May 2012
                10 May 2012
                : 8
                : 5
                [1 ]Max-Planck-Institut für Infektionsbiologie, Department of Molecular Biology, Berlin, Germany
                [2 ]Konrad Lorenz Institute for Ethology, Department of Integrative Biology and Evolution, University of Veterinary Medicine Vienna, Vienna, Austria
                [3 ]Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
                [4 ]Hepatology and GI-Research Laboratory, Department of Immunology, University of Pretoria, Pretoria, South Africa
                [5 ]Human Genomic Diversity and Disease Research Unit, Division of Human Genetics, School of Pathology, University of the Witwatersrand/National Health Laboratory Services, Johannesburg, South Africa
                [6 ]Environmental Research Institute and Department of Microbiology, University College Cork, Cork, Ireland
                [7 ]Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
                [8 ]Ngamba Island Chimpanzee Sanctuary, Entebbe, Uganda
                Yale University, United States of America
                Author notes

                Conceived and designed the experiments: SWVM MA SS BL YM HS LM. Performed the experiments: SB BL SWVM LM CMS JH SS MN RPB. Analyzed the data: YM BL CMS. Contributed reagents/materials/analysis tools: MA SWVM SS HS. Wrote the paper: YM MA BL.

                Moodley 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.
                Pages: 16
                Research Article
                Evolutionary Biology
                Evolutionary Genetics
                Bacterial Evolution
                Bacterial Pathogens
                Host-Pathogen Interaction

                Infectious disease & Microbiology


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