Strong positive selection biases identity-by-descent-based inferences of recent demography and population structure in Plasmodium falciparum

Bibliographic Details
Main Author: Guo, Bing
Publication Date: 2024
Other Authors: Borda, Victor, Laboulaye, Roland, Spring, Michele D., Wojnarski, Mariusz, Vesely, Brian A., Silva, Joana C., Waters, Norman C., O’Connor, Timothy D., Takala-Harrison, Shannon
Format: Article
Language: eng
Source: Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
Download full: http://hdl.handle.net/10362/172879
Summary: Funding Information: We would like to thank the participants in studies contributing clinical samples from which the parasite WGS data were generated, as well as the clinical investigators at the Armed Forces Research Institute of Medical Sciences who conducted the studies contributing parasite isolates to our in-house data set. This publication uses data from the MalariaGEN Consortium and Plasmodium falciparum Community Project as described in “An open data set of Plasmodium falciparum genome variation in 7000 worldwide samples. MalariaGEN et al., Wellcome Open Research 2021642 DOI: 10.12688/wellcomeopenres.16168.1.” This work was supported by NIH 1R01AI145852 granted to ST-H and TDO by the U.S. National Institutes of Health. Publisher Copyright: © The Author(s) 2024.
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spelling Strong positive selection biases identity-by-descent-based inferences of recent demography and population structure in Plasmodium falciparumChemistry(all)Biochemistry, Genetics and Molecular Biology(all)Physics and Astronomy(all)SDG 3 - Good Health and Well-beingFunding Information: We would like to thank the participants in studies contributing clinical samples from which the parasite WGS data were generated, as well as the clinical investigators at the Armed Forces Research Institute of Medical Sciences who conducted the studies contributing parasite isolates to our in-house data set. This publication uses data from the MalariaGEN Consortium and Plasmodium falciparum Community Project as described in “An open data set of Plasmodium falciparum genome variation in 7000 worldwide samples. MalariaGEN et al., Wellcome Open Research 2021642 DOI: 10.12688/wellcomeopenres.16168.1.” This work was supported by NIH 1R01AI145852 granted to ST-H and TDO by the U.S. National Institutes of Health. Publisher Copyright: © The Author(s) 2024.Malaria genomic surveillance often estimates parasite genetic relatedness using metrics such as Identity-By-Decent (IBD), yet strong positive selection stemming from antimalarial drug resistance or other interventions may bias IBD-based estimates. In this study, we use simulations, a true IBD inference algorithm, and empirical data sets from different malaria transmission settings to investigate the extent of this bias and explore potential correction strategies. We analyze whole genome sequence data generated from 640 new and 3089 publicly available Plasmodium falciparum clinical isolates. We demonstrate that positive selection distorts IBD distributions, leading to underestimated effective population size and blurred population structure. Additionally, we discover that the removal of IBD peak regions partially restores the accuracy of IBD-based inferences, with this effect contingent on the population’s background genetic relatedness and extent of inbreeding. Consequently, we advocate for selection correction for parasite populations undergoing strong, recent positive selection, particularly in high malaria transmission settings.Instituto de Higiene e Medicina Tropical (IHMT)Global Health and Tropical Medicine (GHTM)RUNGuo, BingBorda, VictorLaboulaye, RolandSpring, Michele D.Wojnarski, MariuszVesely, Brian A.Silva, Joana C.Waters, Norman C.O’Connor, Timothy D.Takala-Harrison, Shannon2024-10-02T22:23:29Z2024-122024-12-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10362/172879eng2041-1723PURE: 100538774https://doi.org/10.1038/s41467-024-46659-0info:eu-repo/semantics/openAccessreponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiainstacron:RCAAP2024-10-07T01:40:45Zoai:run.unl.pt:10362/172879Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireinfo@rcaap.ptopendoar:https://opendoar.ac.uk/repository/71602025-05-28T18:55:25.969907Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiafalse
dc.title.none.fl_str_mv Strong positive selection biases identity-by-descent-based inferences of recent demography and population structure in Plasmodium falciparum
title Strong positive selection biases identity-by-descent-based inferences of recent demography and population structure in Plasmodium falciparum
spellingShingle Strong positive selection biases identity-by-descent-based inferences of recent demography and population structure in Plasmodium falciparum
Guo, Bing
Chemistry(all)
Biochemistry, Genetics and Molecular Biology(all)
Physics and Astronomy(all)
SDG 3 - Good Health and Well-being
title_short Strong positive selection biases identity-by-descent-based inferences of recent demography and population structure in Plasmodium falciparum
title_full Strong positive selection biases identity-by-descent-based inferences of recent demography and population structure in Plasmodium falciparum
title_fullStr Strong positive selection biases identity-by-descent-based inferences of recent demography and population structure in Plasmodium falciparum
title_full_unstemmed Strong positive selection biases identity-by-descent-based inferences of recent demography and population structure in Plasmodium falciparum
title_sort Strong positive selection biases identity-by-descent-based inferences of recent demography and population structure in Plasmodium falciparum
author Guo, Bing
author_facet Guo, Bing
Borda, Victor
Laboulaye, Roland
Spring, Michele D.
Wojnarski, Mariusz
Vesely, Brian A.
Silva, Joana C.
Waters, Norman C.
O’Connor, Timothy D.
Takala-Harrison, Shannon
author_role author
author2 Borda, Victor
Laboulaye, Roland
Spring, Michele D.
Wojnarski, Mariusz
Vesely, Brian A.
Silva, Joana C.
Waters, Norman C.
O’Connor, Timothy D.
Takala-Harrison, Shannon
author2_role author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Instituto de Higiene e Medicina Tropical (IHMT)
Global Health and Tropical Medicine (GHTM)
RUN
dc.contributor.author.fl_str_mv Guo, Bing
Borda, Victor
Laboulaye, Roland
Spring, Michele D.
Wojnarski, Mariusz
Vesely, Brian A.
Silva, Joana C.
Waters, Norman C.
O’Connor, Timothy D.
Takala-Harrison, Shannon
dc.subject.por.fl_str_mv Chemistry(all)
Biochemistry, Genetics and Molecular Biology(all)
Physics and Astronomy(all)
SDG 3 - Good Health and Well-being
topic Chemistry(all)
Biochemistry, Genetics and Molecular Biology(all)
Physics and Astronomy(all)
SDG 3 - Good Health and Well-being
description Funding Information: We would like to thank the participants in studies contributing clinical samples from which the parasite WGS data were generated, as well as the clinical investigators at the Armed Forces Research Institute of Medical Sciences who conducted the studies contributing parasite isolates to our in-house data set. This publication uses data from the MalariaGEN Consortium and Plasmodium falciparum Community Project as described in “An open data set of Plasmodium falciparum genome variation in 7000 worldwide samples. MalariaGEN et al., Wellcome Open Research 2021642 DOI: 10.12688/wellcomeopenres.16168.1.” This work was supported by NIH 1R01AI145852 granted to ST-H and TDO by the U.S. National Institutes of Health. Publisher Copyright: © The Author(s) 2024.
publishDate 2024
dc.date.none.fl_str_mv 2024-10-02T22:23:29Z
2024-12
2024-12-01T00:00:00Z
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dc.language.iso.fl_str_mv eng
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PURE: 100538774
https://doi.org/10.1038/s41467-024-46659-0
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