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description Publicationkeyboard_double_arrow_right Article , Preprint 2017 Ireland, Portugal, SwitzerlandPublisher:Cold Spring Harbor Laboratory Publicly fundedFunded by:WT, IRC, EC | BEANWT ,IRC ,EC| BEANRui Martiniano; Lara M. Cassidy; Ros Ó’Maoldúin; Russell L. McLaughlin; Nuno Silva; Licínio Manco; Daniel Fidalgo; Tania Pereira; Maria J. Coelho; Miguel Serra; Joachim Burger; Rui Parreira; Elena Morán; António Carlos Valera; Eduardo Porfirio; Rui Boaventura; Ana Margarida Dias da Silva; Daniel G. Bradley;We analyse new genomic data (0.05-2.95x) from 14 ancient individuals from Portugal distributed from the Middle Neolithic (4200-3500 BC) to the Middle Bronze Age (1740-1430 BC) and impute genomewide diploid genotypes in these together with published ancient Eurasians. While discontinuity is evident in the transition to agriculture across the region, sensitive haplotype-based analyses suggest a significant degree of local hunter-gatherer contribution to later Iberian Neolithic populations. A more subtle genetic influx is also apparent in the Bronze Age, detectable from analyses including haplotype sharing with both ancient and modern genomes, D-statistics and Y-chromosome lineages. However, the limited nature of this introgression contrasts with the major Steppe migration turnovers within third Millennium northern Europe and echoes the survival of non-Indo-European language in Iberia. Changes in genomic estimates of individual height across Europe are also associated with these major cultural transitions, and ancestral components continue to correlate with modern differences in stature. BEAN project of the Marie Curie Initial Training Network [289966]; Irish Research Council Government of Ireland Scholarship Scheme [GOIPG/2013/1219] info:eu-repo/semantics/publishedVersion
bioRxiv arrow_drop_down bioRxivPreprint . 2017Europe PubMed CentralArticle . 2017Full-Text: http://europepmc.org/articles/PMC5531429Data sources: PubMed CentralSapientia Repositório da Universidade do AlgarveArticle . 2018Data sources: Sapientia Repositório da Universidade do AlgarveTrinity's Access to Research ArchiveArticle . 2017 . Peer-reviewedData sources: Trinity's Access to Research Archiveadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/134254&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 110 citations 110 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!visibility 223visibility views 223 download downloads 308 Powered bymore_vert bioRxiv arrow_drop_down bioRxivPreprint . 2017Europe PubMed CentralArticle . 2017Full-Text: http://europepmc.org/articles/PMC5531429Data sources: PubMed CentralSapientia Repositório da Universidade do AlgarveArticle . 2018Data sources: Sapientia Repositório da Universidade do AlgarveTrinity's Access to Research ArchiveArticle . 2017 . Peer-reviewedData sources: Trinity's Access to Research Archiveadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/134254&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2013 Ireland, AustriaPublisher:Public Library of Science (PLoS) Publicly fundedFunded by:WTWTSandra Nell; Daniel Eibach; Valeria Montano; Ayas Maady; Armand Nkwescheu; Jose Siri; Wael F Elamin; Daniel Falush; Bodo Linz; Mark Achtman; Yoshan Moodley; Sebastian Suerbaum;Both anatomically modern humans and the gastric pathogen Helicobacter pylori originated in Africa, and both species have been associated for at least 100,000 years. Seven geographically distinct H. pylori populations exist, three of which are indigenous to Africa: hpAfrica1, hpAfrica2, and hpNEAfrica. The oldest and most divergent population, hpAfrica2, evolved within San hunter-gatherers, who represent one of the deepest branches of the human population tree. Anticipating the presence of ancient H. pylori lineages within all hunter-gatherer populations, we investigated the prevalence and population structure of H. pylori within Baka Pygmies in Cameroon. Gastric biopsies were obtained by esophagogastroduodenoscopy from 77 Baka from two geographically separated populations, and from 101 non-Baka individuals from neighboring agriculturalist populations, and subsequently cultured for H. pylori. Unexpectedly, Baka Pygmies showed a significantly lower H. pylori infection rate (20.8%) than non-Baka (80.2%). We generated multilocus haplotypes for each H. pylori isolate by DNA sequencing, but were not able to identify Baka-specific lineages, and most isolates in our sample were assigned to hpNEAfrica or hpAfrica1. The population hpNEAfrica, a marker for the expansion of the Nilo-Saharan language family, was divided into East African and Central West African subpopulations. Similarly, a new hpAfrica1 subpopulation, identified mainly among Cameroonians, supports eastern and western expansions of Bantu languages. An age-structured transmission model shows that the low H. pylori prevalence among Baka Pygmies is achievable within the timeframe of a few hundred years and suggests that demographic factors such as small population size and unusually low life expectancy can lead to the eradication of H. pylori from individual human populations. The Baka were thus either H. pylori-free or lost their ancient lineages during past demographic fluctuations. Using coalescent simulations and phylogenetic inference, we show that Baka almost certainly acquired their extant H. pylori through secondary contact with their agriculturalist neighbors. Author Summary Genetic analyses of Helicobacter pylori have illuminated human migrations and the history of human infection by these bacteria. Both humans and H. pylori originated in Africa, and have been intimately associated for at least 100,000 years. We hypothesized that communities who still live in relative isolation might provide further details about the evolutionary history of H. pylori in Africa. We therefore investigated H. pylori within Baka Pygmies of southeast Cameroon, who live as hunter-gatherers in the tropical rainforest, and compared those bacteria to H. pylori from neighboring farming populations of non-Baka ethnicities. Unexpectedly, Baka Pygmies were much less commonly infected (20.8%) than the non-Baka (80.2%). H. pylori from hunter-gatherers and agriculturalists were genetically very similar and ancient H. pylori lineages were not identified in Baka. We used an epidemiological model to show that demographic factors including small population size and low life expectancy can account for the low infection rate among Baka Pygmies, and that this low rate could have been attained within a few hundred years of secondary contact with their neighbors. We also suggest that the ancestors of the Baka Pygmies were initially H. pylori-free or that their ancestral bacteria have been lost through past demographic fluctuations.
CORE (RIOXX-UK Aggre... arrow_drop_down Europe PubMed CentralArticle . 2013Full-Text: http://europepmc.org/articles/PMC3777998Data sources: PubMed CentralCork Open Research Archive (CORA)Article . 2013License: CC BYData sources: Cork Open Research Archive (CORA)add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1371/journal.pgen.1003775&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 34 citations 34 popularity Top 10% influence Average impulse Top 10% Powered by BIP!visibility 10visibility views 10 download downloads 53 Powered bymore_vert CORE (RIOXX-UK Aggre... arrow_drop_down Europe PubMed CentralArticle . 2013Full-Text: http://europepmc.org/articles/PMC3777998Data sources: PubMed CentralCork Open Research Archive (CORA)Article . 2013License: CC BYData sources: Cork Open Research Archive (CORA)add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1371/journal.pgen.1003775&type=result"></script>'); --> </script>
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description Publicationkeyboard_double_arrow_right Article , Preprint 2017 Ireland, Portugal, SwitzerlandPublisher:Cold Spring Harbor Laboratory Publicly fundedFunded by:WT, IRC, EC | BEANWT ,IRC ,EC| BEANRui Martiniano; Lara M. Cassidy; Ros Ó’Maoldúin; Russell L. McLaughlin; Nuno Silva; Licínio Manco; Daniel Fidalgo; Tania Pereira; Maria J. Coelho; Miguel Serra; Joachim Burger; Rui Parreira; Elena Morán; António Carlos Valera; Eduardo Porfirio; Rui Boaventura; Ana Margarida Dias da Silva; Daniel G. Bradley;We analyse new genomic data (0.05-2.95x) from 14 ancient individuals from Portugal distributed from the Middle Neolithic (4200-3500 BC) to the Middle Bronze Age (1740-1430 BC) and impute genomewide diploid genotypes in these together with published ancient Eurasians. While discontinuity is evident in the transition to agriculture across the region, sensitive haplotype-based analyses suggest a significant degree of local hunter-gatherer contribution to later Iberian Neolithic populations. A more subtle genetic influx is also apparent in the Bronze Age, detectable from analyses including haplotype sharing with both ancient and modern genomes, D-statistics and Y-chromosome lineages. However, the limited nature of this introgression contrasts with the major Steppe migration turnovers within third Millennium northern Europe and echoes the survival of non-Indo-European language in Iberia. Changes in genomic estimates of individual height across Europe are also associated with these major cultural transitions, and ancestral components continue to correlate with modern differences in stature. BEAN project of the Marie Curie Initial Training Network [289966]; Irish Research Council Government of Ireland Scholarship Scheme [GOIPG/2013/1219] info:eu-repo/semantics/publishedVersion
bioRxiv arrow_drop_down bioRxivPreprint . 2017Europe PubMed CentralArticle . 2017Full-Text: http://europepmc.org/articles/PMC5531429Data sources: PubMed CentralSapientia Repositório da Universidade do AlgarveArticle . 2018Data sources: Sapientia Repositório da Universidade do AlgarveTrinity's Access to Research ArchiveArticle . 2017 . Peer-reviewedData sources: Trinity's Access to Research Archiveadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/134254&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 110 citations 110 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!visibility 223visibility views 223 download downloads 308 Powered bymore_vert bioRxiv arrow_drop_down bioRxivPreprint . 2017Europe PubMed CentralArticle . 2017Full-Text: http://europepmc.org/articles/PMC5531429Data sources: PubMed CentralSapientia Repositório da Universidade do AlgarveArticle . 2018Data sources: Sapientia Repositório da Universidade do AlgarveTrinity's Access to Research ArchiveArticle . 2017 . Peer-reviewedData sources: Trinity's Access to Research Archiveadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/134254&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2013 Ireland, AustriaPublisher:Public Library of Science (PLoS) Publicly fundedFunded by:WTWTSandra Nell; Daniel Eibach; Valeria Montano; Ayas Maady; Armand Nkwescheu; Jose Siri; Wael F Elamin; Daniel Falush; Bodo Linz; Mark Achtman; Yoshan Moodley; Sebastian Suerbaum;Both anatomically modern humans and the gastric pathogen Helicobacter pylori originated in Africa, and both species have been associated for at least 100,000 years. Seven geographically distinct H. pylori populations exist, three of which are indigenous to Africa: hpAfrica1, hpAfrica2, and hpNEAfrica. The oldest and most divergent population, hpAfrica2, evolved within San hunter-gatherers, who represent one of the deepest branches of the human population tree. Anticipating the presence of ancient H. pylori lineages within all hunter-gatherer populations, we investigated the prevalence and population structure of H. pylori within Baka Pygmies in Cameroon. Gastric biopsies were obtained by esophagogastroduodenoscopy from 77 Baka from two geographically separated populations, and from 101 non-Baka individuals from neighboring agriculturalist populations, and subsequently cultured for H. pylori. Unexpectedly, Baka Pygmies showed a significantly lower H. pylori infection rate (20.8%) than non-Baka (80.2%). We generated multilocus haplotypes for each H. pylori isolate by DNA sequencing, but were not able to identify Baka-specific lineages, and most isolates in our sample were assigned to hpNEAfrica or hpAfrica1. The population hpNEAfrica, a marker for the expansion of the Nilo-Saharan language family, was divided into East African and Central West African subpopulations. Similarly, a new hpAfrica1 subpopulation, identified mainly among Cameroonians, supports eastern and western expansions of Bantu languages. An age-structured transmission model shows that the low H. pylori prevalence among Baka Pygmies is achievable within the timeframe of a few hundred years and suggests that demographic factors such as small population size and unusually low life expectancy can lead to the eradication of H. pylori from individual human populations. The Baka were thus either H. pylori-free or lost their ancient lineages during past demographic fluctuations. Using coalescent simulations and phylogenetic inference, we show that Baka almost certainly acquired their extant H. pylori through secondary contact with their agriculturalist neighbors. Author Summary Genetic analyses of Helicobacter pylori have illuminated human migrations and the history of human infection by these bacteria. Both humans and H. pylori originated in Africa, and have been intimately associated for at least 100,000 years. We hypothesized that communities who still live in relative isolation might provide further details about the evolutionary history of H. pylori in Africa. We therefore investigated H. pylori within Baka Pygmies of southeast Cameroon, who live as hunter-gatherers in the tropical rainforest, and compared those bacteria to H. pylori from neighboring farming populations of non-Baka ethnicities. Unexpectedly, Baka Pygmies were much less commonly infected (20.8%) than the non-Baka (80.2%). H. pylori from hunter-gatherers and agriculturalists were genetically very similar and ancient H. pylori lineages were not identified in Baka. We used an epidemiological model to show that demographic factors including small population size and low life expectancy can account for the low infection rate among Baka Pygmies, and that this low rate could have been attained within a few hundred years of secondary contact with their neighbors. We also suggest that the ancestors of the Baka Pygmies were initially H. pylori-free or that their ancestral bacteria have been lost through past demographic fluctuations.
CORE (RIOXX-UK Aggre... arrow_drop_down Europe PubMed CentralArticle . 2013Full-Text: http://europepmc.org/articles/PMC3777998Data sources: PubMed CentralCork Open Research Archive (CORA)Article . 2013License: CC BYData sources: Cork Open Research Archive (CORA)add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1371/journal.pgen.1003775&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 34 citations 34 popularity Top 10% influence Average impulse Top 10% Powered by BIP!visibility 10visibility views 10 download downloads 53 Powered bymore_vert CORE (RIOXX-UK Aggre... arrow_drop_down Europe PubMed CentralArticle . 2013Full-Text: http://europepmc.org/articles/PMC3777998Data sources: PubMed CentralCork Open Research Archive (CORA)Article . 2013License: CC BYData sources: Cork Open Research Archive (CORA)add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1371/journal.pgen.1003775&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu