ArticleGenetics2018
Inferring Population Structure and Admixture Proportions in Low-Depth NGS Data.
Article in Genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 348 papers.
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348 citing papers in PubMed.
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- Genomic Signatures of Selection Are Enriched in Differentially Expressed Genes in Sticklebacks Adapting to Contrasting Environments.Genome biology and evolution · 2026Article
- Admixture and Selection Driven by El Niño-Southern Oscillation Events Shape the Genetic Structure ofEcology and evolution · 2026Article
- Low-Coverage Whole-Genome Resequencing in Livestock and Poultry: Statistical Foundations, Applications and Future Directions.Biology · 2026Review
- A complete genome for the common marmoset.Cell · 2026Article
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- On the Causes of Correlated Genomic Ancestry Across Contrasting Hybridization Histories in a Monkeyflower Species Pair.Molecular ecology · 2026Article
- Natural and Anthropogenic Drivers of Genomic Diversity in the California Towhee: Conservation Implications for Peripheral Populations.Evolutionary applications · 2026Article
- Maintenance of phenotypic divergence in two sympatric monkeyflowers with weak reproductive isolation.bioRxiv : the preprint server for biology · 2026Article
- Multiple Eurasian Origins and Admixture Shaped the Genomic Legacy of the House Mouse Invasion in Africa.Molecular ecology · 2026Article
- Targeted chromosomal sequencing of wild bonobos identifies a genetically distinct subpopulation east of the Lomami river.Genome biology · 2026Article
- Adaptation across an extreme elevational gradient in Andean leaf-eared mice, the world's highest-dwelling mammal.Science (New York, N.Y.) · 2026Article
- An Assessment of Allelic and SNP Bias in a Genome-Wide SNP Enrichment Kit for Killer Whales.Ecology and evolution · 2026Article
- Identification of two genomic cryptotypes of Plasmodium malariae in Africa.PLoS neglected tropical diseases · 2026Article
- Stepwise emergence of recombination suppression precedes fissiparous asexuality in the planarian Schmidtea mediterranea.Nature communications · 2026Article
- Long-term isolation and archaic introgression shape functional genetic variation in Near Oceania.Science (New York, N.Y.) · 2026Article
- Long-term small effective population size, inbreeding, and a recessive lethal haplotype drive premature death in the endangered Devils Hole pupfish (bioRxiv : the preprint server for biology · 2026Article
288 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We here present two methods for inferring population structure and admixture proportions in low-depth next-generation sequencing (NGS) data. Inference of population structure is essential in both population genetics and association studies, and is often performed using principal component analysis (PCA) or clustering-based approaches. NGS methods provide large amounts of genetic data but are associated with statistical uncertainty, especially for low-depth sequencing data. Models can account for this uncertainty by working directly on genotype likelihoods of the unobserved genotypes. We propose a method for inferring population structure through PCA in an iterative heuristic approach of estimating individual allele frequencies, where we demonstrate improved accuracy in samples with low and variable sequencing depth for both simulated and real datasets. We also use the estimated individual allele frequencies in a fast non-negative matrix factorization method to estimate admixture proportions. Both methods have been implemented in the PCAngsd framework available at http://www.popgen.dk/software/.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.