ArticlePLoS genetics2013
Robust demographic inference from genomic and SNP data.
Article in PLoS genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 617 papers.
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Who cites it
617 citing papers in PubMed.
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- Contrasting Patterns of Genetic Isolation Among Diadromous, Landlocked, and Non-Migratory Gobiid Fish Populations.Molecular ecology · 2026Article
- Targeted population genomics uncovers demographic history and genetic divergence in north American wild cranberry.Horticulture research · 2026Article
- Inferring the demographic history of Chinese and Indian rhesus macaque (Macaca mulatta) populations from PacBio HiFi long-read sequencing data.Molecular biology and evolution · 2026Article
- Genomic evidence for widespread hybridization and demographic history in invasive saltcedar.Heredity · 2026Article
- Faster inference of complex demographic models from large allele frequency spectra.Bioinformatics (Oxford, England) · 2026Article
- How Did a Size-Divergent Water Strider Species Group Exhibiting an East Asia-Eastern North America Disjunction Originate and Diversify?Molecular ecology · 2026Article
- Genes Related to Sperm Motility Are Under Recent Ongoing Selection in Two Shorebird Species With a Polygynous Mating System and Frequent Multiple Paternity.Molecular ecology · 2026Article
- Population history rather than tree age contributes to the evolutionary importance of ancient trees in an endangered conifer.Nature plants · 2026Article
- Phylogeographic history of the ring distribution inZoological research · 2026Article
- Severe bottleneck of ancient Homo populations: insights from computational modeling and relevant fossil evidence.Molecular biology and evolution · 2026Article
- Local adaptation sustains genetic differentiation between two varieties of Chinese walnut (Plant diversity · 2026Article
- Large-Scale Genomics Reveals Three-Source Ancestry and Layered Adaptation to High Altitude in Tibetan Chickens.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Vegetative Propagation Preserves Genomic Diversity and Informs Translocation Strategies in a Rare Clonal Plant.Evolutionary applications · 2026Article
- FRAME: Fine-Resolution Asymmetric Migration Estimation.Nature communications · 2026Article
- Pervasive cryptic selection in the human noncoding genome.bioRxiv : the preprint server for biology · 2026Article
- High-resolution analysis of recent population structure using rare variants.G3 (Bethesda, Md.) · 2026Article
- Methods to estimate marine functional connectivity: A primer.Ecological applications : a publication of the Ecological Society of America · 2026Review
557 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
We introduce a flexible and robust simulation-based framework to infer demographic parameters from the site frequency spectrum (SFS) computed on large genomic datasets. We show that our composite-likelihood approach allows one to study evolutionary models of arbitrary complexity, which cannot be tackled by other current likelihood-based methods. For simple scenarios, our approach compares favorably in terms of accuracy and speed with ∂a∂i, the current reference in the field, while showing better convergence properties for complex models. We first apply our methodology to non-coding genomic SNP data from four human populations. To infer their demographic history, we compare neutral evolutionary models of increasing complexity, including unsampled populations. We further show the versatility of our framework by extending it to the inference of demographic parameters from SNP chips with known ascertainment, such as that recently released by Affymetrix to study human origins. Whereas previous ways of handling ascertained SNPs were either restricted to a single population or only allowed the inference of divergence time between a pair of populations, our framework can correctly infer parameters of more complex models including the divergence of several populations, bottlenecks and migration. We apply this approach to the reconstruction of African demography using two distinct ascertained human SNP panels studied under two evolutionary models. The two SNP panels lead to globally very similar estimates and confidence intervals, and suggest an ancient divergence (>110 Ky) between Yoruba and San populations. Our methodology appears well suited to the study of complex scenarios from large genomic data sets.
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