Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations
Autor(a) principal: | |
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Data de Publicação: | 2022 |
Outros Autores: | , , , , , , , , , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10451/59116 |
Resumo: | Helicobacter pylori lives in the human stomach and has a population structure resembling that of its host. However, H. pylori from Europe and the Middle East trace substantially more ancestry from modern African populations than the humans that carry them. Here, we use a collection of Afro-Eurasian H. pylori genomes to show that this African ancestry is due to at least three distinct admixture events. H. pylori from East Asia, which have undergone little admixture, have accumulated many more non-synonymous mutations than African strains. European and Middle Eastern bacteria have elevated African ancestry at the sites of these mutations, implying selection to remove them during admixture. Simulations show that population fitness can be restored after bottlenecks by migration and subsequent admixture of small numbers of bacteria from non-bottlenecked populations. We conclude that recent spread of African DNA has been driven by deleterious mutations accumulated during the original out-of-Africa bottleneck. |
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Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutationsHelicobacter pylori lives in the human stomach and has a population structure resembling that of its host. However, H. pylori from Europe and the Middle East trace substantially more ancestry from modern African populations than the humans that carry them. Here, we use a collection of Afro-Eurasian H. pylori genomes to show that this African ancestry is due to at least three distinct admixture events. H. pylori from East Asia, which have undergone little admixture, have accumulated many more non-synonymous mutations than African strains. European and Middle Eastern bacteria have elevated African ancestry at the sites of these mutations, implying selection to remove them during admixture. Simulations show that population fitness can be restored after bottlenecks by migration and subsequent admixture of small numbers of bacteria from non-bottlenecked populations. We conclude that recent spread of African DNA has been driven by deleterious mutations accumulated during the original out-of-Africa bottleneck.The authors thank Sabrina Woltemate for technical assistance. This work was supported by Sequencing Grants-in-aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of Japan (221S0002, 18KK0266, 19H03473, 21H00346 and 22H02871) to Y.Y. F.F.V. is financed by FCT through Assistant Researcher grant CEECIND/03023/2017 and a project grant PTDC/BTM-TEC/3238/2020. I.K. studentship was funded by the National Strategic Reference Framework Operational Program “Competitiveness, Entrepreneurship and Innovation” (NSRF 2014-2020, project No. MIS5002486) and sequencing of strains was supported by the InfeNeutra Project (NSRF 2007-2013, project no. MIS450598) of the Ministry of Culture and Education, Greece. K.T. and the sequencing of KI isolates was supported by Erik Philip-Sörensen Foundation grant G2016-08, and Swedish Society for Medical research (SSMF). All primary bioinformatics and parts of the comparative genomics were performed on resources provided by Swedish National Infrastructure for Computing (SNIC) through Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) under projects snic2018-8-24 and uppstore2017270, and those provided by the National Institute of Genetics and the Human Genome Center at the Institute of Medical Science (University of Tokyo). Work by S.S. was supported by the German Research Foundation (DFG, project number 158 989 968–SFB 900/A1) and by the Bavarian Ministry of Science and the Arts in the framework of the Bavarian Research Network “New Strategies Against Multi-Resistant Pathogens by Means of Digital Networking—bayresq.net”. D.F. was supported by Shanghai Municipal Science and Technology Major Project No. 2019SHZDZX02.Springer NatureRepositório da Universidade de LisboaThorpe, Harry ATourrette, EliseYahara, KojiVale, Filipa F.Liu, SiqiOleastro, MónicaAlarcon, TeresaPerets, Tsachi-TsadokLatifi-Navid, SaeidYamaoka, YoshioMartinez-Gonzalez, BeatrizKarayiannis, IoannisKaramitros, TimokratisSgouras, Dionyssios N.Elamin, WaelPascoe, BenSheppard, Samuel K.Ronkainen, JukkaAro, PerttiEngstrand, LarsAgreus, LarsSuerbaum, SebastianThorell, KaisaFalush, Daniel2023-09-01T11:10:22Z2022-11-112023-03-07T14:42:48Z2022-11-11T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10451/59116engThorpe HA, Tourrette E, Yahara K, Vale FF, Liu S, Oleastro M, et al. Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations. Nat Commun [Internet]. 11 de novembro de 2022;13(1):6842. Disponível em: https://www.nature.com/articles/s41467-022-34475-3cv-prod-315871510.1038/s41467-022-34475-3info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-11-08T17:04:15Zoai:repositorio.ul.pt:10451/59116Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T22:07:06.405113Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations |
title |
Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations |
spellingShingle |
Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations Thorpe, Harry A |
title_short |
Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations |
title_full |
Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations |
title_fullStr |
Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations |
title_full_unstemmed |
Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations |
title_sort |
Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations |
author |
Thorpe, Harry A |
author_facet |
Thorpe, Harry A Tourrette, Elise Yahara, Koji Vale, Filipa F. Liu, Siqi Oleastro, Mónica Alarcon, Teresa Perets, Tsachi-Tsadok Latifi-Navid, Saeid Yamaoka, Yoshio Martinez-Gonzalez, Beatriz Karayiannis, Ioannis Karamitros, Timokratis Sgouras, Dionyssios N. Elamin, Wael Pascoe, Ben Sheppard, Samuel K. Ronkainen, Jukka Aro, Pertti Engstrand, Lars Agreus, Lars Suerbaum, Sebastian Thorell, Kaisa Falush, Daniel |
author_role |
author |
author2 |
Tourrette, Elise Yahara, Koji Vale, Filipa F. Liu, Siqi Oleastro, Mónica Alarcon, Teresa Perets, Tsachi-Tsadok Latifi-Navid, Saeid Yamaoka, Yoshio Martinez-Gonzalez, Beatriz Karayiannis, Ioannis Karamitros, Timokratis Sgouras, Dionyssios N. Elamin, Wael Pascoe, Ben Sheppard, Samuel K. Ronkainen, Jukka Aro, Pertti Engstrand, Lars Agreus, Lars Suerbaum, Sebastian Thorell, Kaisa Falush, Daniel |
author2_role |
author author author author author author author author author author author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Repositório da Universidade de Lisboa |
dc.contributor.author.fl_str_mv |
Thorpe, Harry A Tourrette, Elise Yahara, Koji Vale, Filipa F. Liu, Siqi Oleastro, Mónica Alarcon, Teresa Perets, Tsachi-Tsadok Latifi-Navid, Saeid Yamaoka, Yoshio Martinez-Gonzalez, Beatriz Karayiannis, Ioannis Karamitros, Timokratis Sgouras, Dionyssios N. Elamin, Wael Pascoe, Ben Sheppard, Samuel K. Ronkainen, Jukka Aro, Pertti Engstrand, Lars Agreus, Lars Suerbaum, Sebastian Thorell, Kaisa Falush, Daniel |
description |
Helicobacter pylori lives in the human stomach and has a population structure resembling that of its host. However, H. pylori from Europe and the Middle East trace substantially more ancestry from modern African populations than the humans that carry them. Here, we use a collection of Afro-Eurasian H. pylori genomes to show that this African ancestry is due to at least three distinct admixture events. H. pylori from East Asia, which have undergone little admixture, have accumulated many more non-synonymous mutations than African strains. European and Middle Eastern bacteria have elevated African ancestry at the sites of these mutations, implying selection to remove them during admixture. Simulations show that population fitness can be restored after bottlenecks by migration and subsequent admixture of small numbers of bacteria from non-bottlenecked populations. We conclude that recent spread of African DNA has been driven by deleterious mutations accumulated during the original out-of-Africa bottleneck. |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022-11-11 2022-11-11T00:00:00Z 2023-09-01T11:10:22Z 2023-03-07T14:42:48Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10451/59116 |
url |
http://hdl.handle.net/10451/59116 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Thorpe HA, Tourrette E, Yahara K, Vale FF, Liu S, Oleastro M, et al. Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations. Nat Commun [Internet]. 11 de novembro de 2022;13(1):6842. Disponível em: https://www.nature.com/articles/s41467-022-34475-3 cv-prod-3158715 10.1038/s41467-022-34475-3 |
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info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Springer Nature |
publisher.none.fl_str_mv |
Springer Nature |
dc.source.none.fl_str_mv |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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