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 show how fastGLOBETROTTER reduces computation time by an order of magnitude relative to the related technique GLOBETROTTER without suffering loss of accuracy. We apply fastGLOBETROTTER to a cohort of more than 6000 Europeans from 10 countries, revealing previously unreported admixture signals. In particular, we infer multiple periods of admixture related to East Asian or Siberian-like sources, starting >2000 yr 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 ∼300–700 CE, overlapping the fall of the Roman Empire, in people from Belgium, France, and parts of Germany. Our new approach scales to analyzing hundreds to thousands of individuals from a putatively admixed population and, hence, is applicable to emerging large-scale cohorts of genetically homogeneous populations.

Reconstructing the formation of Hmong-Mien genetic fine-structure

“…Besides the variation of N e over time, admixture with external populations is another factor that can contribute to the genetic differentiation among the HM-speaking populations. To this end, we verified and inferred the temporal scenario of admixture events in HM population history using the haplotype-based fastGLOBETROTTER (Hellenthal et al ., 2014, Wangkumhang et al ., 2022). We used all three populations in the ‘Hmong’ cluster defined by fineSTRUCTURE (i.e., Hmong, Hmong Daw, and Hmong Njua, Figure 3, referred to as ‘Hmong_all’) to surrogate the shared ancestry by HM speakers, along with 120 ancient and modern global populations to surrogate other ancestries potentially contributing to present-day HM speakers genetically (SI Table 2).…”

“…It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 24, 2022. ; https://doi.org/10. 1101/2022 For SOURCEFIND (Chacón-Duque et al, 2018) and fastGLOBETROTTER (Hellenthal et al, 2014, Wangkumhang et al, 2022 analyses, we used all the three populations in the 'Hmong' cluster defined by fineSTRUCTURE (i.e., Hmong, Hmong Daw, and Hmong Njua, Figure 3, referred as 'Hmong_all') to surrogate the shared ancestry by HM speakers, along with 120 ancient and modern global populations to surrogate other ancestries potentially contributing to present-day HM speakers genetically (SI Table 2). In addition to the other 14 HM-speaking populations, we also included 10 non-HM populations who likely received recent HM-related gene flow (SI Table 2) with the HM-related component > 5% in ADMIXTURE when K = 10 (SI Figure 1).…”

“…In addition to the other 14 HM-speaking populations, we also included 10 non-HM populations who likely received recent HM-related gene flow (SI Table 2) with the HM-related component > 5% in ADMIXTURE when K = 10 (SI Figure 1). We generated the copying-vector profiles for both analyses following the suggestions by Wangkumhang et al (2022). All the other parameters of both methods were kept by default.…”

Reconstructing the genetic history of Kra-Dai speakers from Thailand

“…We phased a world-wide dataset of 3,945 individuals (compiled from published sources) using SHAPEIT v.2 (r900) 27 with 1000 Genomes Phase 3 genetic maps 28 . We then ran ChromoPainter v.2 11,24 to generate inputs for SOURCEFIND v.2 18 and fastGLOBETROTTER 29 . We selected 75 surrogates and 20 target populations (14 Kra-Dai-speaking groups from Thailand for whom the data were reported by Kutanan et al.…”

“…2 11,24 to generate inputs for SOURCEFIND v . 2 18 and fastGLOBETROTTER 29 . We selected 75 surrogates and 20 target populations (14 Kra-Dai-speaking groups from Thailand for whom the data were reported by Kutanan et al .…”