Reconstructing past admixture processes from local genomic ancestry using wavelet transformation

Jean Sanderson, Herawati Sudoyo, Tatiana Karafet, Michael F Hammer, Murray P. Cox

Research output: Contribution to journalArticle

10 Citations (Scopus)

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 genomescale 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.

Original languageEnglish (US)
Pages (from-to)469-481
Number of pages13
JournalGenetics
Volume200
Issue number2
DOIs
StatePublished - 2015

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Genome
Indonesia
Human Genome
Principal Component Analysis
Population
Uncertainty
Chromosomes
Genotype

Keywords

  • Admixture
  • Dating
  • Local ancestry
  • Principal component analysis (PCA)
  • Wavelets

ASJC Scopus subject areas

  • Genetics

Cite this

Reconstructing past admixture processes from local genomic ancestry using wavelet transformation. / Sanderson, Jean; Sudoyo, Herawati; Karafet, Tatiana; Hammer, Michael F; Cox, Murray P.

In: Genetics, Vol. 200, No. 2, 2015, p. 469-481.

Research output: Contribution to journalArticle

Sanderson, Jean ; Sudoyo, Herawati ; Karafet, Tatiana ; Hammer, Michael F ; Cox, Murray P. / Reconstructing past admixture processes from local genomic ancestry using wavelet transformation. In: Genetics. 2015 ; Vol. 200, No. 2. pp. 469-481.
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