Estimating the time since admixture from phased and unphased molecular data

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• dc.contributor.author Janzen, Thijs
• dc.contributor.author Miró Pina, Verónica
• dc.date.accessioned 2022-01-25T11:46:41Z
• dc.date.available 2022-01-25T11:46:41Z
• dc.date.issued 2022
• dc.description.abstract After admixture, recombination breaks down genomic blocks of contiguous ancestry. The breakdown of these blocks forms a new "molecular clock" that ticks at a much faster rate than the mutation clock, enabling accurate dating of admixture events in the recent past. However, existing theory on the breakdown of these blocks, or the accumulation of delineations between blocks, so-called "junctions", has mostly been limited to using regularly spaced markers on phased data. Here, we present an extension to the theory of junctions using the ancestral recombination graph that describes the expected number of junctions for any distribution of markers along the genome. Furthermore, we provide a new framework to infer the time since admixture using unphased data. We demonstrate both the phased and unphased methods on simulated data and show that our new extensions have improved accuracy with respect to previous methods, especially for smaller population sizes and more ancient admixture times. Lastly, we demonstrate the applicability of our method on three empirical data sets, including labcrosses of yeast (Saccharomyces cerevisae) and two case studies of hybridization in swordtail fish and Populus trees.
• dc.description.sponsorship Funding information: Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México, Grant/Award Number: 2018
• dc.format.mimetype application/pdf
• dc.identifier.citation Thijs J, Miró Pina V. Estimating the time since admixture from phased and unphased molecular data. Mol Ecol Resour. 2022;22(3):908-26. DOI: 10.1111/1755-0998.13519
• dc.identifier.doi http://dx.doi.org/10.1111/1755-0998.13519
• dc.identifier.issn 1755-0998
• dc.identifier.uri http://hdl.handle.net/10230/52316
• dc.language.iso eng
• dc.publisher Wiley
• dc.relation.ispartof Molecular Ecology Resources. 2022;22(3):908-26.
• dc.rights © 2021 Thijs Janzen and Verónica Miró Pina. Molecular Ecology Resources published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri https://creativecommons.org/licenses/by-nc/4.0/
• dc.subject.other Genòmica
• dc.subject.other Molècules
• dc.title Estimating the time since admixture from phased and unphased molecular data
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion