title: Reconstructing Past Admixture Processes from Local Genomic Ancestry Using Wavelet Transformation.
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.
authors: Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand.
authors: Jean
authors: J
authors: Sanderson
authors: Eijkman Institute for Molecular Biology, Jakarta, Indonesia.
authors: Herawati
authors: H
authors: Sudoyo
authors: Division of Biotechnology, Arizona Research Laboratories, University of Arizona, Tucson, Arizona 85721.
authors: Tatiana M
authors: TM
authors: Karafet
authors: Division of Biotechnology, Arizona Research Laboratories, University of Arizona, Tucson, Arizona 85721 Department of Anthropology, University of Arizona, Tucson, Arizona 85721.
authors: Michael F
authors: MF
authors: Hammer
authors: Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand m.p.cox@massey.ac.nz.
authors: Murray P
authors: MP
authors: Cox
mesh_terms: D000465:Algorithms; D005828:Genetics, Population; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods; D006801:Humans; D007214:Indonesia; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D058067:Wavelet Analysis
keywords: admixture; dating; local ancestry; principal component analysis (PCA); wavelets