An efficient method to identify, date and describe admixture events using haplotype information

Abstract

We present fastGLOBETROTTER, an efficient new haplotype-based technique to identify, date and describe admixture events using genome-wide autosomal data. With simulations, we demonstrate how fastGLOBETROTTER reduces computation time by 4-20 fold relative to the haplotype-based technique GLOBETROTTER without suffering loss of accuracy. We apply fastGLOBETROTTER to a cohort of >6000 Europeans from ten countries, revealing previously unreported admixture signals. In particular we infer multiple periods of admixture related to East Asian or Siberian-like sources, starting >2000 years ago, in people living in countries north of the Baltic Sea. In contrast, we infer admixture related to West Asian, North African and/or Southern European sources in populations south of the Baltic Sea, including admixture dated to {approx}300-700CE, overlapping the fall of the Roman Empire, in people from Belgium, France and parts of Germany. Our new approach scales to analysing hundreds to thousands of individuals from a putatively admixed populations and hence is applicable to emerging large-scale cohorts of genetically homogeneous populations.