Testing the existence of an unadmixed ancestor from a specific population t generations ago
Editor(es): Chaubey, Gyaneshwer
Resumen:
The ancestry of each locus of the genome can be estimated (local ancestry) based on sequencing or genotyping information together with reference panels of ancestral source populations. The length of those ancestry-specific genomic segments are commonly used to understand migration waves and admixture events. In short time scales, it is often of interest to determine the existence of the most recent unadmixed ancestor from a specific population t generations ago. We built a hypothesis test to determine if an individual has an ancestor belonging to a target ancestral population t generations ago based on these lengths of the ancestry-specific segments at an individual level. We applied this test on a data set that includes 20 Uruguayan admixed individuals to estimate for each one how many generations ago the most recent indigenous ancestor lived. As this method tests each individual separately, it is particularly suited to small sample sizes, such as our study or ancient genome samples.
| 2022 | |
| Inglés | |
| Universidad de la República | |
| COLIBRI | |
| https://hdl.handle.net/20.500.12008/39130 | |
| Acceso abierto | |
| Licencia Creative Commons Atribución - No Comercial - Sin Derivadas (CC - By-NC-ND 4.0) |
| _version_ | 1807522798553268224 |
|---|---|
| author | Illanes, Gabriel |
| author2 | Fariello Rico, María Inés Spangenberg, Lucía Mordecki, Ernesto Naya Monteverde, Hugo Mario |
| author2_role | author author author author |
| author_facet | Illanes, Gabriel Fariello Rico, María Inés Spangenberg, Lucía Mordecki, Ernesto Naya Monteverde, Hugo Mario |
| author_role | author |
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| collection | COLIBRI |
| dc.contributor.filiacion.none.fl_str_mv | Illanes Gabriel, Universidad de la República (Uruguay). Facultad de Ciencias. Centro de Matemática. Fariello Rico María Inés, Universidad de la República (Uruguay). Facultad de Ingeniería. Spangenberg Lucía, Universidad de la República (Uruguay). Facultad de Ingeniería. Mordecki Pupko Ernesto, Universidad de la República (Uruguay). Facultad de Ciencias. Centro de Matemática. Naya Monteverde Hugo Mario, Instituto Pasteur (Montevideo) |
| dc.creator.editor.none.fl_str_mv | Chaubey, Gyaneshwer |
| dc.creator.none.fl_str_mv | Illanes, Gabriel Fariello Rico, María Inés Spangenberg, Lucía Mordecki, Ernesto Naya Monteverde, Hugo Mario |
| dc.date.accessioned.none.fl_str_mv | 2023-08-09T14:57:09Z |
| dc.date.available.none.fl_str_mv | 2023-08-09T14:57:09Z |
| dc.date.issued.none.fl_str_mv | 2022 |
| dc.description.abstract.none.fl_txt_mv | The ancestry of each locus of the genome can be estimated (local ancestry) based on sequencing or genotyping information together with reference panels of ancestral source populations. The length of those ancestry-specific genomic segments are commonly used to understand migration waves and admixture events. In short time scales, it is often of interest to determine the existence of the most recent unadmixed ancestor from a specific population t generations ago. We built a hypothesis test to determine if an individual has an ancestor belonging to a target ancestral population t generations ago based on these lengths of the ancestry-specific segments at an individual level. We applied this test on a data set that includes 20 Uruguayan admixed individuals to estimate for each one how many generations ago the most recent indigenous ancestor lived. As this method tests each individual separately, it is particularly suited to small sample sizes, such as our study or ancient genome samples. |
| dc.description.es.fl_txt_mv | Datos y códigos en: https://figshare.com/articles/dataset/Testing_the_existence_of_an_unadmixed_ancestor_from_a_specific_population_t_ |
| dc.format.extent.es.fl_str_mv | 13 h. |
| dc.format.mimetype.es.fl_str_mv | application/pdf |
| dc.identifier.citation.es.fl_str_mv | Illanes, G, Rico, M, Spangenberg, L. [y otros autores]. "Testing the existence of an unadmixed ancestor from a specific population t generations agoTesting the existence of an unadmixed ancestor from a specific population t generations ago". PLoS ONE. [en línea]. 2022 17(8): e0271097. DOI: 10.1371/journal.pone.0271097 |
| dc.identifier.doi.none.fl_str_mv | 10.1371/journal.pone.0271097 |
| dc.identifier.issn.none.fl_str_mv | 1932-6203 |
| dc.identifier.uri.none.fl_str_mv | https://hdl.handle.net/20.500.12008/39130 |
| dc.language.iso.none.fl_str_mv | en eng |
| dc.publisher.es.fl_str_mv | PLoS |
| dc.relation.ispartof.es.fl_str_mv | PLoS ONE, 2022, 17(8): e0271097 |
| dc.rights.license.none.fl_str_mv | Licencia Creative Commons Atribución - No Comercial - Sin Derivadas (CC - By-NC-ND 4.0) |
| dc.rights.none.fl_str_mv | info:eu-repo/semantics/openAccess |
| dc.source.none.fl_str_mv | reponame:COLIBRI instname:Universidad de la República instacron:Universidad de la República |
| dc.title.none.fl_str_mv | Testing the existence of an unadmixed ancestor from a specific population t generations ago |
| dc.type.es.fl_str_mv | Artículo |
| dc.type.none.fl_str_mv | info:eu-repo/semantics/article |
| dc.type.version.none.fl_str_mv | info:eu-repo/semantics/publishedVersion |
| description | Datos y códigos en: https://figshare.com/articles/dataset/Testing_the_existence_of_an_unadmixed_ancestor_from_a_specific_population_t_ |
| eu_rights_str_mv | openAccess |
| format | article |
| id | COLIBRI_19139d191629c5052821bcb305c4b8d6 |
| identifier_str_mv | Illanes, G, Rico, M, Spangenberg, L. [y otros autores]. "Testing the existence of an unadmixed ancestor from a specific population t generations agoTesting the existence of an unadmixed ancestor from a specific population t generations ago". PLoS ONE. [en línea]. 2022 17(8): e0271097. DOI: 10.1371/journal.pone.0271097 1932-6203 10.1371/journal.pone.0271097 |
| instacron_str | Universidad de la República |
| institution | Universidad de la República |
| instname_str | Universidad de la República |
| language | eng |
| language_invalid_str_mv | en |
| network_acronym_str | COLIBRI |
| network_name_str | COLIBRI |
| oai_identifier_str | oai:colibri.udelar.edu.uy:20.500.12008/39130 |
| publishDate | 2022 |
| reponame_str | COLIBRI |
| repository.mail.fl_str_mv | mabel.seroubian@seciu.edu.uy |
| repository.name.fl_str_mv | COLIBRI - Universidad de la República |
| repository_id_str | 4771 |
| rights_invalid_str_mv | Licencia Creative Commons Atribución - No Comercial - Sin Derivadas (CC - By-NC-ND 4.0) |
| spelling | Illanes Gabriel, Universidad de la República (Uruguay). Facultad de Ciencias. Centro de Matemática.Fariello Rico María Inés, Universidad de la República (Uruguay). Facultad de Ingeniería.Spangenberg Lucía, Universidad de la República (Uruguay). Facultad de Ingeniería.Mordecki Pupko Ernesto, Universidad de la República (Uruguay). Facultad de Ciencias. Centro de Matemática.Naya Monteverde Hugo Mario, Instituto Pasteur (Montevideo)2023-08-09T14:57:09Z2023-08-09T14:57:09Z2022Illanes, G, Rico, M, Spangenberg, L. [y otros autores]. "Testing the existence of an unadmixed ancestor from a specific population t generations agoTesting the existence of an unadmixed ancestor from a specific population t generations ago". PLoS ONE. [en línea]. 2022 17(8): e0271097. DOI: 10.1371/journal.pone.02710971932-6203https://hdl.handle.net/20.500.12008/3913010.1371/journal.pone.0271097Datos y códigos en: https://figshare.com/articles/dataset/Testing_the_existence_of_an_unadmixed_ancestor_from_a_specific_population_t_The ancestry of each locus of the genome can be estimated (local ancestry) based on sequencing or genotyping information together with reference panels of ancestral source populations. The length of those ancestry-specific genomic segments are commonly used to understand migration waves and admixture events. In short time scales, it is often of interest to determine the existence of the most recent unadmixed ancestor from a specific population t generations ago. We built a hypothesis test to determine if an individual has an ancestor belonging to a target ancestral population t generations ago based on these lengths of the ancestry-specific segments at an individual level. We applied this test on a data set that includes 20 Uruguayan admixed individuals to estimate for each one how many generations ago the most recent indigenous ancestor lived. As this method tests each individual separately, it is particularly suited to small sample sizes, such as our study or ancient genome samples.Submitted by Egaña Florencia (florega@gmail.com) on 2023-08-09T14:26:24Z No. of bitstreams: 2 license_rdf: 23149 bytes, checksum: 1996b8461bc290aef6a27d78c67b6b52 (MD5) journal.pone.0271097.pdf: 952705 bytes, checksum: cf5d52ab7f313663c612b84e6b541874 (MD5)Approved for entry into archive by Faget Cecilia (lfaget@fcien.edu.uy) on 2023-08-09T14:56:54Z (GMT) No. of bitstreams: 2 license_rdf: 23149 bytes, checksum: 1996b8461bc290aef6a27d78c67b6b52 (MD5) journal.pone.0271097.pdf: 952705 bytes, checksum: cf5d52ab7f313663c612b84e6b541874 (MD5)Made available in DSpace by Luna Fabiana (fabiana.luna@seciu.edu.uy) on 2023-08-09T14:57:09Z (GMT). No. of bitstreams: 2 license_rdf: 23149 bytes, checksum: 1996b8461bc290aef6a27d78c67b6b52 (MD5) journal.pone.0271097.pdf: 952705 bytes, checksum: cf5d52ab7f313663c612b84e6b541874 (MD5) Previous issue date: 202213 h.application/pdfenengPLoSPLoS ONE, 2022, 17(8): e0271097Las obras depositadas en el Repositorio se rigen por la Ordenanza de los Derechos de la Propiedad Intelectual de la Universidad de la República.(Res. Nº 91 de C.D.C. de 8/III/1994 – D.O. 7/IV/1994) y por la Ordenanza del Repositorio Abierto de la Universidad de la República (Res. Nº 16 de C.D.C. de 07/10/2014)info:eu-repo/semantics/openAccessLicencia Creative Commons Atribución - No Comercial - Sin Derivadas (CC - By-NC-ND 4.0)Testing the existence of an unadmixed ancestor from a specific population t generations agoArtículoinfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionreponame:COLIBRIinstname:Universidad de la Repúblicainstacron:Universidad de la RepúblicaIllanes, GabrielFariello Rico, María InésSpangenberg, LucíaMordecki, ErnestoNaya Monteverde, Hugo MarioChaubey, GyaneshwerLICENSElicense.txtlicense.txttext/plain; charset=utf-84267http://localhost:8080/xmlui/bitstream/20.500.12008/39130/5/license.txt6429389a7df7277b72b7924fdc7d47a9MD55CC-LICENSElicense_urllicense_urltext/plain; charset=utf-850http://localhost:8080/xmlui/bitstream/20.500.12008/39130/2/license_urla006180e3f5b2ad0b88185d14284c0e0MD52license_textlicense_texttext/html; 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| spellingShingle | Testing the existence of an unadmixed ancestor from a specific population t generations ago Illanes, Gabriel |
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| title_full | Testing the existence of an unadmixed ancestor from a specific population t generations ago |
| title_fullStr | Testing the existence of an unadmixed ancestor from a specific population t generations ago |
| title_full_unstemmed | Testing the existence of an unadmixed ancestor from a specific population t generations ago |
| title_short | Testing the existence of an unadmixed ancestor from a specific population t generations ago |
| title_sort | Testing the existence of an unadmixed ancestor from a specific population t generations ago |
| url | https://hdl.handle.net/20.500.12008/39130 |
