Age of the Association between Helicobacter pylori and Man
Publication Date
May 10, 2012
Journal
PLOS Pathogens
Authors
Yoshan Moodley, Bodo Linz, Robert P. Bond, Martin Nieuwoudt, et al
Volume
8
Issue
5
Pages
e1002693
DOI
https://dx.plos.org/10.1371/journal.ppat.1002693
Publisher URL
http://journals.plos.org/plospathogens/article?id=10.1371%2Fjournal.ppat.1002693
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/22589724
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3349757
Europe PMC
http://europepmc.org/abstract/MED/22589724
Web of Science
000305322900027
Scopus
84863692086
Mendeley
http://www.mendeley.com/research/age-association-between-helicobacter-pylori-man
Events
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Mendeley | Further Information

{"title"=>"Age of the association between Helicobacter pylori and man", "type"=>"journal", "authors"=>[{"first_name"=>"Yoshan", "last_name"=>"Moodley", "scopus_author_id"=>"55882861700"}, {"first_name"=>"Bodo", "last_name"=>"Linz", "scopus_author_id"=>"6603195490"}, {"first_name"=>"Robert P.", "last_name"=>"Bond", "scopus_author_id"=>"12241680300"}, {"first_name"=>"Martin", "last_name"=>"Nieuwoudt", "scopus_author_id"=>"6507958597"}, {"first_name"=>"Himla", "last_name"=>"Soodyall", "scopus_author_id"=>"57195051521"}, {"first_name"=>"Carina M.", "last_name"=>"Schlebusch", "scopus_author_id"=>"35316211000"}, {"first_name"=>"Steffi", "last_name"=>"Bernhöft", "scopus_author_id"=>"26022936300"}, {"first_name"=>"James", "last_name"=>"Hale", "scopus_author_id"=>"46961053300"}, {"first_name"=>"Sebastian", "last_name"=>"Suerbaum", "scopus_author_id"=>"7005430657"}, {"first_name"=>"Lawrence", "last_name"=>"Mugisha", "scopus_author_id"=>"35107723300"}, {"first_name"=>"Schalk W.", "last_name"=>"van der Merwe", "scopus_author_id"=>"7003839470"}, {"first_name"=>"Mark", "last_name"=>"Achtman", "scopus_author_id"=>"7006051116"}], "year"=>2012, "source"=>"PLoS Pathogens", "identifiers"=>{"scopus"=>"2-s2.0-84863692086", "sgr"=>"84863692086", "issn"=>"15537366", "doi"=>"10.1371/journal.ppat.1002693", "pmid"=>"22589724", "isbn"=>"1553-7366", "pui"=>"365220878"}, "id"=>"5740c044-321f-3bf7-be39-53475662abc8", "abstract"=>"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.", "link"=>"http://www.mendeley.com/research/age-association-between-helicobacter-pylori-man", "reader_count"=>145, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>5, "Researcher"=>32, "Student > Doctoral Student"=>12, "Student > Ph. D. 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CrossRef

Scopus | Further Information

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  • {"files"=>["https://ndownloader.figshare.com/files/330418", "https://ndownloader.figshare.com/files/330438", "https://ndownloader.figshare.com/files/330454", "https://ndownloader.figshare.com/files/330476", "https://ndownloader.figshare.com/files/330505"], "description"=>"<div><p>When modern humans left Africa ca. 60,000 years ago (60 kya), they were already infected with <em>Helicobacter pylori</em>, and these bacteria have subsequently diversified in parallel with their human hosts. But how long were humans infected by <em>H. pylori</em> 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 <em>H. pylori</em> in Africa, where both humans and <em>H. pylori</em> originated. Three distinct <em>H. pylori</em> 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 <em>H. pylori</em> plus its closest relative <em>H. acinonychis</em> 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. <em>H. acinonychis</em>, 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 <em>H. pylori</em> is approximately as old as are anatomically modern humans. They also suggest that <em>H. pylori</em> may have been acquired <em>via</em> 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.</p> </div>", "links"=>[], "tags"=>[], "article_id"=>125250, "categories"=>["Microbiology", "Evolutionary Biology"], "users"=>["Yoshan Moodley", "Bodo Linz", "Robert P. Bond", "Martin Nieuwoudt", "Himla Soodyall", "Carina M. Schlebusch", "Steffi Bernhöft", "James Hale", "Sebastian Suerbaum", "Lawrence Mugisha", "Schalk W. van der Merwe", "Mark Achtman"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1002693.s001", "https://dx.doi.org/10.1371/journal.ppat.1002693.s002", "https://dx.doi.org/10.1371/journal.ppat.1002693.s003", "https://dx.doi.org/10.1371/journal.ppat.1002693.s004", "https://dx.doi.org/10.1371/journal.ppat.1002693.s005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Age_of_the_Association_between_Helicobacter_pylori_and_Man/125250", "title"=>"Age of the Association between <em>Helicobacter pylori</em> and Man", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-05-10 01:27:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/640641"], "description"=>"<p>Circle diameters are proportional to the within-population genetic diversity (π). Angles of filled arcs are proportional to the number of isolates. Data are from <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat.1002693-Schwarz1\" target=\"_blank\">[2]</a>, <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat.1002693-Falush2\" target=\"_blank\">[6]</a>–<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat.1002693-Moodley1\" target=\"_blank\">[8]</a> and the figure is modified from Figure 1 in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat.1002693-Falush2\" target=\"_blank\">[6]</a>.</p>", "links"=>[], "tags"=>["extant", "populations"], "article_id"=>311124, "categories"=>["Microbiology", "Evolutionary Biology"], "users"=>["Yoshan Moodley", "Bodo Linz", "Robert P. Bond", "Martin Nieuwoudt", "Himla Soodyall", "Carina M. Schlebusch", "Steffi Bernhöft", "James Hale", "Sebastian Suerbaum", "Lawrence Mugisha", "Schalk W. van der Merwe", "Mark Achtman"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1002693.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Neighbor_joining_population_tree_of_extant_populations_of_H_pylori_/311124", "title"=>"Neighbor-joining population tree of extant populations of <i>H. pylori</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-10 00:18:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/640780"], "description"=>"<p>Sequences from gastric Helicobacters (open circles) such as <i>H. pylori</i>, <i>H. cetorum</i> or <i>H. suis</i> form a cluster separate from enterohepatic Helicobacter species (filled circles) such as <i>H. cinaedi</i> or <i>H. macacae</i>. The tree was rooted with the 16SrRNA sequences of the epsilon-proteobacteria <i>Wolinella succinogenes</i> and <i>Campylobacter jejuni</i> (squares). 16SrRNA sequences were obtained from Genbank, accession numbers are provided in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#s4\" target=\"_blank\">Materials and Methods</a>.</p>", "links"=>[], "tags"=>["16srrna", "sequences", "gastric", "enterohepatic", "helicobacter"], "article_id"=>311258, "categories"=>["Microbiology", "Evolutionary Biology"], "users"=>["Yoshan Moodley", "Bodo Linz", "Robert P. Bond", "Martin Nieuwoudt", "Himla Soodyall", "Carina M. Schlebusch", "Steffi Bernhöft", "James Hale", "Sebastian Suerbaum", "Lawrence Mugisha", "Schalk W. van der Merwe", "Mark Achtman"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1002693.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Neighbor_joining_tree_of_16SrRNA_sequences_from_gastric_and_enterohepatic_Helicobacter_species_/311258", "title"=>"Neighbor-joining tree of 16SrRNA sequences from gastric and enterohepatic Helicobacter species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-10 00:20:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/640862"], "description"=>"<p>(A) The proportions of haplotypes at each sampling location (numbers; <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat-1002693-t002\" target=\"_blank\">Table 2</a>, <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat.1002693.s001\" target=\"_blank\">Table S1</a>) from different bacterial populations are displayed as pie charts whose sizes indicate the numbers of haplotypes. (B) The distribution of the three major subgroups of the San language family in south-central Africa (adapted from <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat.1002693-Guldemann1\" target=\"_blank\">[21]</a>). s: Southern Khoisan was spoken on much of the South African plateau and the central Kalahari in Botswana; c: Central Khoisan was distributed in southern and western South Africa, most of Namibia and most of northern Botswana; and n: Northern Khoisan (Ju), was spoken in southern Angola, north-eastern Namibia and north-western Botswana (<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat-1002693-t001\" target=\"_blank\">Table 1</a>). The position of the letters indicates the geographical origin of Northern San (n; !Xun from Angola), Central San (c; Khwe from Namibia) and Southern San (s; Khomani from South Africa). (C) Phylogenetic relationships among hpAfrica2 strains (80% consensus of 100 ClonalFrame analyses). The tree was rooted with <i>H. pylori</i> strains from other populations.</p>", "links"=>[], "tags"=>["populations"], "article_id"=>311340, "categories"=>["Microbiology", "Evolutionary Biology"], "users"=>["Yoshan Moodley", "Bodo Linz", "Robert P. Bond", "Martin Nieuwoudt", "Himla Soodyall", "Carina M. Schlebusch", "Steffi Bernhöft", "James Hale", "Sebastian Suerbaum", "Lawrence Mugisha", "Schalk W. van der Merwe", "Mark Achtman"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1002693.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_distribution_of_H_pylori_populations_in_Africa_/311340", "title"=>"The distribution of <i>H. pylori</i> populations in Africa.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-10 00:22:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/640934"], "description"=>"<p>(A) Distruct plot of the assignment of <i>H. pylori</i> haplotypes from Africa, the Middle East and southern Europe as determined by the no admixture model. Each isolate is represented by a thin line that is color coded according to the population assignment. (B) Distruct plot of the proportions of ancestral nucleotides as determined by the linkage model. A thin line for each isolate indicates the estimated amount of ancestry from each of the four ancestral populations as four colored segments. (C) Distruct plot of the population assignment (no admixture model) of <i>H. pylori</i> hpAfrica1 and hpAfrica2 haplotypes from southern Africa and <i>H. acinonychis</i> (Hac).</p>", "links"=>[], "tags"=>["assignments"], "article_id"=>311416, "categories"=>["Microbiology", "Evolutionary Biology"], "users"=>["Yoshan Moodley", "Bodo Linz", "Robert P. Bond", "Martin Nieuwoudt", "Himla Soodyall", "Carina M. Schlebusch", "Steffi Bernhöft", "James Hale", "Sebastian Suerbaum", "Lawrence Mugisha", "Schalk W. van der Merwe", "Mark Achtman"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1002693.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bayesian_population_assignments_using_S_tructure_V2_0_/311416", "title"=>"Bayesian population assignments using Structure V2.0.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-10 00:23:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/641049"], "description"=>"<p>Circles in red show ClonalFrame estimates and those in blue are IMa values. Closed circles denote median values for calibration times used for the regression (<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat-1002693-t003\" target=\"_blank\">Table 3</a>). Open circles show inferred times for the four African pair-wise comparisons (<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat-1002693-t004\" target=\"_blank\">Table 4</a>) after calibration with rate-smoothing.</p>", "links"=>[], "tags"=>["relationships", "calibration", "dates", "posterior", "parameters", "node"], "article_id"=>311522, "categories"=>["Microbiology", "Evolutionary Biology"], "users"=>["Yoshan Moodley", "Bodo Linz", "Robert P. Bond", "Martin Nieuwoudt", "Himla Soodyall", "Carina M. Schlebusch", "Steffi Bernhöft", "James Hale", "Sebastian Suerbaum", "Lawrence Mugisha", "Schalk W. van der Merwe", "Mark Achtman"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1002693.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Linear_relationships_between_known_calibration_dates_and_posterior_parameters_node_height_C_lonal_F_rame_and_t_IM_a_/311522", "title"=>"Linear relationships between known calibration dates and posterior parameters node height (ClonalFrame) and <i>t</i> (IMa).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-10 00:25:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/641173"], "description"=>"<p>(A) Global phylogeny of <i>H. pylori</i> displayed as the strict consensus of 100 ClonalFrame analyses. After outgroup-rooting with <i>H. cetorum</i>, the time of the basal <i>H. pylori</i> divergence between hpAfrica2 and all other populations was estimated to 102 kya (95% confidence limit, 88–116 kya). Divergence of the other African <i>H. pylori</i> populations, hpAfrica1 and hpNEAfrica, began between 36 and 52 kya. (B) Simplified human mtDNA phylogeny adapted from Behar <i>et al.</i>, 2008 <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat.1002693-Eppinger1\" target=\"_blank\">[14]</a> with the permission of <i>AJHG</i>. African lineages are shown on a green background whereas the background for lineages outside Africa is light blue. San clades are purple, non-San clades are orange and <i>H. acinonychis</i> is yellow. San mtDNA lineages in our sample are shown as white lines.</p>", "links"=>[], "tags"=>["mtdna"], "article_id"=>311653, "categories"=>["Microbiology", "Evolutionary Biology"], "users"=>["Yoshan Moodley", "Bodo Linz", "Robert P. Bond", "Martin Nieuwoudt", "Himla Soodyall", "Carina M. Schlebusch", "Steffi Bernhöft", "James Hale", "Sebastian Suerbaum", "Lawrence Mugisha", "Schalk W. van der Merwe", "Mark Achtman"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1002693.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_comparison_of_global_H_pylori_and_human_mtDNA_phylogenies_/311653", "title"=>"A comparison of global <i>H. pylori</i> and human mtDNA phylogenies.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-10 00:27:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/641244"], "description"=>"<p>A Mantel regression (<i>R</i><sup>2</sup> = 0.62, P<0.0001) showed that 62% of the pair-wise genetic distances between <i>H. pylori</i> sequences can be accounted for by the pair-wise genetic distances between human mtDNA sequences from analogous geographic locations.</p>", "links"=>[], "tags"=>["patterns", "pair-wise", "distances", "mtdna"], "article_id"=>311724, "categories"=>["Microbiology", "Evolutionary Biology"], "users"=>["Yoshan Moodley", "Bodo Linz", "Robert P. Bond", "Martin Nieuwoudt", "Himla Soodyall", "Carina M. Schlebusch", "Steffi Bernhöft", "James Hale", "Sebastian Suerbaum", "Lawrence Mugisha", "Schalk W. van der Merwe", "Mark Achtman"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1002693.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Parallel_patterns_of_pair_wise_genetic_distances_between_human_mtDNA_and_H_pylori_gene_sequences_/311724", "title"=>"Parallel patterns of pair-wise genetic distances between human mtDNA and <i>H. pylori</i> gene sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-10 00:28:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/641315"], "description"=>"<p>Black lines indicate undifferentiated populations and all other lines are color-coded according to population as in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat-1002693-g001\" target=\"_blank\">Figs. 1</a>, <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat-1002693-g003\" target=\"_blank\">3A</a>, <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat-1002693-g004\" target=\"_blank\">4A</a>, <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat-1002693-g006\" target=\"_blank\">6A</a>. The sequence of events is as follows: 1) Initial acquisition of <i>H. pylori</i> by a human ancestor; 2) Divergence of <i>H. pylori</i> into two super-lineages; 3) First successful migration of modern humans Out of Africa <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat.1002693-Linz1\" target=\"_blank\">[7]</a>, <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat.1002693-Liu2\" target=\"_blank\">[42]</a> via the southern route <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat.1002693-Macaulay1\" target=\"_blank\">[57]</a>; 4) <i>H. pylori</i> divergence into hpAfrica1 and hpNEAfrica with migration eastwards (hpNEAfrica) and westwards (hpAfrica1); 5) Divergence of <i>H. pylori</i> out of Africa into hpSahul <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat.1002693-Moodley1\" target=\"_blank\">[8]</a> and 6) hpAsia2 and hpEastAsia; 7) Host jump from San to large felines giving rise to <i>H. acinonychis</i>. 8) Southward migration of San <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat.1002693-Behar1\" target=\"_blank\">[16]</a> carrying the ancestor of hpAfrica2; 9) Second successful migration Out of Africa via the Levant; 10) Hybridization of AE1 from central and south-west Asia and AE2 from north-east Africa <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat.1002693-Linz1\" target=\"_blank\">[7]</a> in the Middle East or western Asia resulting in hpEurope; 11) Spread of hpEurope bacteria to Europe; 12) Back migration from the Middle East <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat.1002693-Olivieri1\" target=\"_blank\">[75]</a>, <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat.1002693-Henn2\" target=\"_blank\">[76]</a> and Spain <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat.1002693-Ottoni1\" target=\"_blank\">[74]</a> spreading hpEurope into North Africa. Dates in italics represent estimates obtained from sources other than <i>H. pylori</i>.</p>", "links"=>[], "tags"=>["reconstruction", "events", "occurring"], "article_id"=>311793, "categories"=>["Microbiology", "Evolutionary Biology"], "users"=>["Yoshan Moodley", "Bodo Linz", "Robert P. Bond", "Martin Nieuwoudt", "Himla Soodyall", "Carina M. Schlebusch", "Steffi Bernhöft", "James Hale", "Sebastian Suerbaum", "Lawrence Mugisha", "Schalk W. van der Merwe", "Mark Achtman"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1002693.g008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Chronological_reconstruction_of_the_major_population_events_occurring_during_the_intimate_human_H_pylori_association_/311793", "title"=>"Chronological reconstruction of the major population events occurring during the intimate human-<i>H. pylori</i> association.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-10 00:29:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/641402"], "description"=>"<p>gen, generation.</p><p>CL 95, 95% confidence limit.</p><p>n, number of haplotypes used in pair-wise IMa simulations.</p><p>kya, kilo years ago.</p><p>hp, <i>Helicobacter</i> population.</p><p>hsp, <i>Helicobacter</i> sub-population.</p><p>hpAfrica2 Southern Group, derived subclade of hpAfrica2, isolated mainly in San and Bantu-speakers of South Africa.</p><p>hpAfrica2 Northern Group, subgroup of hpAfrica2, isolated in San inhabitants of Namibia and Angola.</p><p>TMRCA, time to the most recent common ancestor.</p>", "links"=>[], "tags"=>["parameters", "simulated", "clonalframe", "african"], "article_id"=>311886, "categories"=>["Microbiology", "Evolutionary Biology"], "users"=>["Yoshan Moodley", "Bodo Linz", "Robert P. Bond", "Martin Nieuwoudt", "Himla Soodyall", "Carina M. Schlebusch", "Steffi Bernhöft", "James Hale", "Sebastian Suerbaum", "Lawrence Mugisha", "Schalk W. van der Merwe", "Mark Achtman"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1002693.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Posterior_population_parameters_simulated_using_an_isolation_with_migration_model_IMa_and_ClonalFrame_for_African_H_pylori_populations_/311886", "title"=>"Posterior population parameters simulated using an isolation with migration model (IMa) and ClonalFrame for African <i>H. pylori</i> populations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-10 00:31:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/641449"], "description"=>"1<p>mtDNA haplogroups were not determined for samples 1 to 17.</p>", "links"=>[], "tags"=>["haplotypes", "mtdna", "haplogroups"], "article_id"=>311927, "categories"=>["Microbiology", "Evolutionary Biology"], "users"=>["Yoshan Moodley", "Bodo Linz", "Robert P. Bond", "Martin Nieuwoudt", "Himla Soodyall", "Carina M. Schlebusch", "Steffi Bernhöft", "James Hale", "Sebastian Suerbaum", "Lawrence Mugisha", "Schalk W. van der Merwe", "Mark Achtman"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1002693.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Population_assignment_of_unique_H_pylori_haplotypes_from_Africa_Mediterranean_and_human_mtDNA_haplogroups_from_Southern_Africa_/311927", "title"=>"Population assignment of unique <i>H. pylori</i> haplotypes from Africa/Mediterranean and human mtDNA haplogroups from Southern Africa.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-10 00:32:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/641496"], "description"=>"<p>n, number of haplotypes used in pair-wise IMa simulations.</p><p>kya, kilo years ago.</p><p>hp, <i>Helicobacter</i> population.</p><p>hsp, <i>Helicobacter</i> sub-population.</p><p>hspAmerind South America, South American subclade within hspAmerind.</p><p>hspAmerind North America, North American subclade within hspAmerind.</p><p>hspMaori Taiwan, the subgroup of hspMaori isolated in aboriginal people of Taiwan.</p><p>hspMaori Pacific, a derived subclade within hspMaori consisting of isolates from the Philippines, Melanesia, Polynesia and New Zealand.</p>", "links"=>[], "tags"=>["events", "inferred", "archaeological", "molecular", "studies", "calibrate", "dating"], "article_id"=>311970, "categories"=>["Microbiology", "Evolutionary Biology"], "users"=>["Yoshan Moodley", "Bodo Linz", "Robert P. Bond", "Martin Nieuwoudt", "Himla Soodyall", "Carina M. Schlebusch", "Steffi Bernhöft", "James Hale", "Sebastian Suerbaum", "Lawrence Mugisha", "Schalk W. van der Merwe", "Mark Achtman"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1002693.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Known_human_population_events_inferred_from_either_archaeological_or_molecular_studies_and_used_to_calibrate_dating_analyses_/311970", "title"=>"Known human population events inferred from either archaeological or molecular studies and used to calibrate dating analyses.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-10 00:32:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/641550"], "description"=>"<p>The individuals from the Khwe and !Xun communities in this study had recently migrated to South Africa.</p>", "links"=>[], "tags"=>["san"], "article_id"=>312033, "categories"=>["Microbiology", "Evolutionary Biology"], "users"=>["Yoshan Moodley", "Bodo Linz", "Robert P. Bond", "Martin Nieuwoudt", "Himla Soodyall", "Carina M. Schlebusch", "Steffi Bernhöft", "James Hale", "Sebastian Suerbaum", "Lawrence Mugisha", "Schalk W. van der Merwe", "Mark Achtman"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1002693.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Origin_of_the_San_samples_/312033", "title"=>"Origin of the San samples.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-10 00:33:53"}

PMC Usage Stats | Further Information

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Relative Metric

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