ArticleGenetics2013
Quantifying population genetic differentiation from next-generation sequencing data.
Article in Genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 99 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
99 citing papers in PubMed, 220 citations in OpenAlex.
- Identifying adaptive variation in spatially structured populations using low-coverage whole-genome sequencing data.Molecular biology and evolution · 2026Article
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- Genetic Diversity and Population Structure of the Black-Footed Cat: Insights intobioRxiv : the preprint server for biology · 2026Article
- How precise are mutation rate estimates? Comparison of different approaches to estimate de novo mutation rates.Heredity · 2026Article
- Chromosome-level genome assembly and population genomics analysis ofPlant diversity · 2026Article
- Machine learning improves SNP microarray performance in challenged samples.Bioinformatics advances · 2026Article
- Estimating allele frequencies, ancestry proportions and genotype likelihoods in the presence of mapping bias.G3 (Bethesda, Md.) · 2025Article
- Haploblocks contribute to parallel climate adaptation following global invasion of a cosmopolitan plant.Nature ecology & evolution · 2025Article
- Signatures of natural selection may indicate a genetic basis for the beneficial effects of oily fish intake in indigenous people from coastal Ecuador.G3 (Bethesda, Md.) · 2025Article
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- Assessing population allele frequency differences using low-depth sequencing data.Journal of the Royal Society of New Zealand · 2025Article
- Divergence in Regulatory Regions and Gene Duplications May Underlie Chronobiological Adaptation in Desert Tortoises.Molecular ecology · 2025Article
- Whole-Genome Resequencing Reveals Polygenic Signatures of Directional and Balancing Selection on Alternative Migratory Life Histories.Molecular ecology · 2024Article
- Sequential introgression of a carotenoid processing gene underlies sexual ornament diversity in a genus of manakins.Science advances · 2024Article
- Linked Selection and Gene Density Shape Genome-Wide Patterns of Diversification in Peatmosses.Evolutionary applications · 2024Article
- Genomic evidence for domestication selection in three hatchery populations of Chinook salmon,Evolutionary applications · 2024Article
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- Population genetics of the Ixodes affinis (Ixodida: Ixodidae) complex in America: new findings and a host-parasite review.Parasitology research · 2023Article
- SUP: a probabilistic framework to propagate genome sequence uncertainty, with applications.NAR genomics and bioinformatics · 2023Article
- Co-diversification of an intestinal Mycoplasma and its salmonid host.The ISME journal · 2023Article
39 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
Abstract
Over the past few years, new high-throughput DNA sequencing technologies have dramatically increased speed and reduced sequencing costs. However, the use of these sequencing technologies is often challenged by errors and biases associated with the bioinformatical methods used for analyzing the data. In particular, the use of naïve methods to identify polymorphic sites and infer genotypes can inflate downstream analyses. Recently, explicit modeling of genotype probability distributions has been proposed as a method for taking genotype call uncertainty into account. Based on this idea, we propose a novel method for quantifying population genetic differentiation from next-generation sequencing data. In addition, we present a strategy for investigating population structure via principal components analysis. Through extensive simulations, we compare the new method herein proposed to approaches based on genotype calling and demonstrate a marked improvement in estimation accuracy for a wide range of conditions. We apply the method to a large-scale genomic data set of domesticated and wild silkworms sequenced at low coverage. We find that we can infer the fine-scale genetic structure of the sampled individuals, suggesting that employing this new method is useful for investigating the genetic relationships of populations sampled at low coverage.
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What OpenQuestion holds
Registered trials
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.