FAST INFERENCE OF INDIVIDUAL ADMIXTURE COEFFICIENTS USING GEOGRAPHIC DATA

• 成果类型: Article
• 署名作者: Caye, Kevin; Jay, Flora; Michel, Olivier; Francois, Olivier
• 署名单位: Centre National de la Recherche Scientifique (CNRS); CNRS - Institute for Engineering & Systems Sciences (INSIS); Communaute Universite Grenoble Alpes; Institut National Polytechnique de Grenoble; Universite Grenoble Alpes (UGA); Centre National de la Recherche Scientifique (CNRS); CNRS - Institute of Ecology & Environment (INEE); Universite Paris Saclay; Communaute Universite Grenoble Alpes; Institut National Polytechnique de Grenoble; Universite Grenoble Alpes (UGA); Centre National de la Recherche Scientifique (CNRS); CNRS - Institute for Information Sciences & Technologies (INS2I)
• 刊物名称: ANNALS OF APPLIED STATISTICS
• ISSN/ISSBN: 1932-6157
• DOI: 10.1214/17-AOAS1106
• 发表日期: 2018
• 页码: 586-608
• 关键词: spatial population-structure; genome scans; ancestry; localization; adaptation; components; samples; models; CHOICE; number

摘要

Accurately evaluating the distribution of genetic ancestry across geographic space is one of the main questions addressed by evolutionary biologists. This question has been commonly addressed through the application of Bayesian estimation programs allowing their users to estimate individual admixture proportions and allele frequencies among putative ancestral populations. Following the explosion of high-throughput sequencing technologies, several algorithms have been proposed to cope with computational burden generated by the massive data in those studies. In this context, incorporating geographic proximity in ancestry estimation algorithms is an open statistical and computational challenge. In this study, we introduce new algorithms that use geographic information to estimate ancestry proportions and ancestral genotype frequencies from population genetic data. Our algorithms combine matrix factorization methods and spatial statistics to provide estimates of ancestry matrices based on least-squares approximation. We demonstrate the benefit of using spatial algorithms through extensive computer simulations, and we provide an example of application of our new algorithms to a set of spatially referenced samples for the plant species Arabidopsis thaliana. Without loss of statistical accuracy, the new algorithms exhibit runtimes that are much shorter than those observed for previously developed spatial methods. Our algorithms are implemented in the R package, tess3r.