Inferring Human Demographic Histories of Non-African Populations from Patterns of Allele Sharing

Wall, Jeffrey D.

doi:10.1016/j.ajhg.2017.04.002

Cited by 25 publications

(19 citation statements)

References 31 publications

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“…We accessed publicly available high-coverage, whole-genome FASTQ files from previous studies of human genetic variation [52][53][54][55] and combined these with 1,267 high-coverage genomes generated as part of this project. Full details on the samples chosen for sequencing and the informed consent processes for these samples can be found in Supplementary Information 1.…”

Section: Methodsmentioning

confidence: 99%

The GenomeAsia 100K Project enables genetic discoveries across Asia

Wall¹,

Stawiski²,

Ratan³

et al. 2019

Nature

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The underrepresentation of non-Europeans in human genetic studies so far has limited the diversity of individuals in genomic datasets and led to reduced medical relevance for a large proportion of the world's population. Population-specific reference genome datasets as well as genome-wide association studies in diverse populations are needed to address this issue. Here we describe the pilot phase of the GenomeAsia 100K Project. This includes a whole-genome sequencing reference dataset from 1,739 individuals of 219 population groups and 64 countries across Asia. We catalogue genetic variation, population structure, disease associations and founder effects. We also explore the use of this dataset in imputation, to facilitate genetic studies in populations across Asia and worldwide.

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Section: Methodsmentioning

confidence: 99%

The GenomeAsia 100K Project enables genetic discoveries across Asia

Wall¹,

Stawiski²,

Ratan³

et al. 2019

Nature

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270

197

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“…Nevertheless, it is commonly accepted that Southeast Asia was initially populated by the Austro‐Melanesians (Barker et al., ; Détroit et al., ; Matsumura & Pookajorn, ). Subsequent Neolithic dispersals from mainland Southeast Asia or Taiwan left traces of genetic admixture in the extant populations in Southeast Asia (The HUGO Pan‐Asian SNP Consortium, ; Delfin et al., ; Rasmussen et al., ; Lipson et al., ; Matsumura & Oxenham, ; Brandāo et al., ; Soares et al., ; Corny et al., ; Wall, ).…”

Section: Introductionmentioning

confidence: 99%

Genetic relatedness of indigenous ethnic groups in northern Borneo to neighboring populations from Southeast Asia, as inferred from genome‐wide SNP data

Yew

Hoque

Pugh-Kitingan

et al. 2018

Annals of Human Genetics

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The region of northern Borneo is home to the current state of Sabah, Malaysia. It is located closest to the southern Philippine islands and may have served as a viaduct for ancient human migration onto or off of Borneo Island. In this study, five indigenous ethnic groups from Sabah were subjected to genome-wide SNP genotyping. These individuals represent the "North Borneo"-speaking group of the great Austronesian family. They have traditionally resided in the inland region of Sabah. The dataset was merged with public datasets, and the genetic relatedness of these groups to neighboring populations from the islands of Southeast Asia, mainland Southeast Asia and southern China was inferred. Genetic structure analysis revealed that these groups formed a genetic cluster that was independent of the clusters of neighboring populations. Additionally, these groups exhibited near-absolute proportions of a genetic component that is also common among Austronesians from Taiwan and the Philippines. They showed no genetic admixture with Austro-Melanesian populations. Furthermore, phylogenetic analysis showed that they are closely related to non-Austro-Melansian Filipinos as well as to Taiwan natives but are distantly related to populations from mainland Southeast Asia. Relatively lower heterozygosity and higher pairwise genetic differentiation index (F ) values than those of nearby populations indicate that these groups might have experienced genetic drift in the past, resulting in their differentiation from other Austronesians. Subsequent formal testing suggested that these populations have received no gene flow from neighboring populations. Taken together, these results imply that the indigenous ethnic groups of northern Borneo shared a common ancestor with Taiwan natives and non-Austro-Melanesian Filipinos and then isolated themselves on the inland of Sabah. This isolation presumably led to no admixture with other populations, and these individuals therefore underwent strong genetic differentiation. This report contributes to addressing the paucity of genetic data on representatives from this strategic region of ancient human migration event(s).

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“…We used our method to investigate the pattern of population splits between Australians, East Asians, Europeans, and Papuans. There has been some debate about the relative ordering of population splits; specifically, there has been competing evidence about whether East Asians and Europeans split most recently (e.g., [26]) or whether Australo-Papuans and East Asians split most recently (e.g., [27]). To date these splits, we used Australian, French, Han, and Papuan individuals from the SGDP [20] and fit models for each of the six possible pairs of these populations, allowing for recent population size changes and pulse admixture.…”

Section: Application To Simons Genome Diversity Project (Sgdp) Datamentioning

confidence: 99%

“…We applied our method to data from the Simons Genome Diversity Project (SGDP) [20] to investigate the population history of Australians, East Asians, Europeans, and Papuans. There has been some debate whether the population ancestral to Australians and Papuans (which we call Australo-Papuans following [26]) split off prior to the divergence of East Asians and Europeans (e.g., [26]), or whether East Asians and Australo-Papuans first split from Europeans (e.g., [27]). We find substantial evidence in favor of the former hypothesis, but that there has been pervasive gene flow between all of these populations since their divergence.…”

Section: Introductionmentioning

confidence: 99%

Inference of complex population histories using whole-genome sequences from multiple populations

Steinrücken

Kamm

Song

2015

Preprint

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There has been much interest in analyzing genome-scale DNA sequence data to infer population histories, but inference methods developed hitherto are limited in model complexity and computational scalability. Here we present an efficient, flexible statistical method, diCal2, that can utilize wholegenome sequence data from multiple populations to infer complex demographic models involving population size changes, population splits, admixture, and migration. Applying our method to data from Australian, East Asian, European, and Papuan populations, we find that the population ancestral to Australians and Papuans started separating from East Asians and Europeans about 100,000 years ago, and that the separation of East Asians and Europeans started about 50,000 years ago, with pervasive gene flow between all pairs of populations.1. An arbitrary number of populations specified by the user.2. An arbitrary pattern of population splits and mergers. 3. More general population size changes (e.g., piecewise-exponential). 4. Arbitrary migration patterns with time-varying continuous migration rates or pulse admixture events. 5. An arbitrary poly-allelic mutation model at each site (including di-or tetra-allelic).

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Inferring Human Demographic Histories of Non-African Populations from Patterns of Allele Sharing

Cited by 25 publications

References 31 publications

The GenomeAsia 100K Project enables genetic discoveries across Asia

The GenomeAsia 100K Project enables genetic discoveries across Asia

Genetic relatedness of indigenous ethnic groups in northern Borneo to neighboring populations from Southeast Asia, as inferred from genome‐wide SNP data

Inference of complex population histories using whole-genome sequences from multiple populations

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