Sanderson, J., Sudoyo, H., Karafet, T.M. et al. (2 more authors) (2015) Reconstructing past admixture processes from local genomic ancestry using wavelet transformation. Genetics, 200 (2). 469 - 481. ISSN 0016-6731
Abstract
Admixture between long-separated populations is a defining feature of the genomes of many species. The mosaic block structure of admixed genomes can provide information about past contact events, including the time and extent of admixture. Here, we describe an improved wavelet-based technique that better characterizes ancestry block structure from observed genomic patterns. principal components analysis is first applied to genomic data to identify the primary population structure, followed by wavelet decomposition to develop a new characterization of local ancestry information along the chromosomes. For testing purposes, this method is applied to human genome-wide genotype data from Indonesia, as well as virtual genetic data generated using genome-scale sequential coalescent simulations under a wide range of admixture scenarios. Time of admixture is inferred using an approximate Bayesian computation framework, providing robust estimates of both admixture times and their associated levels of uncertainty. Crucially, we demonstrate that this revised wavelet approach, which we have released as the R package adwave, provides improved statistical power over existing wavelet-based techniques and can be used to address a broad range of admixture questions.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2015.Sanderson J, Sudoyo H, Karafet TM, Hammer MF, Cox MP. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial Licence (http://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. You may not use the material for commercial purposes. |
Keywords: | admixture; dating; local ancestry; principal component analysis (PCA); wavelets |
Dates: |
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Institution: | The University of Sheffield |
Academic Units: | The University of Sheffield > Faculty of Medicine, Dentistry and Health (Sheffield) > School of Health and Related Research (Sheffield) > ScHARR - Sheffield Centre for Health and Related Research |
Depositing User: | Symplectic Sheffield |
Date Deposited: | 17 Jul 2015 08:18 |
Last Modified: | 17 Jul 2015 08:18 |
Published Version: | http://dx.doi.org/10.1534/genetics.115.176842 |
Status: | Published |
Publisher: | Genetics Society of America |
Refereed: | Yes |
Identification Number: | 10.1534/genetics.115.176842 |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:87861 |