ArticleGenetics2009
Methods for human demographic inference using haplotype patterns from genomewide single-nucleotide polymorphism data.
Article in Genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Genomic evidence for shared common ancestry of East African hunting-gathering populations and insights into local adaptation.Proceedings of the National Academy of Sciences of the United States of America · 2019Trial
- The Breeding Sex Ratio Interacts With Demographic History to Shape Comparative Patterns of Variation on the X Chromosome and the Autosomes.Genome biology and evolution · 2025Article
- Comparative Patterns of Variation on the X Chromosome and Autosomes: The Role of the Breeding Sex Ratio.bioRxiv : the preprint server for biology · 2025Article
- Hunter-gatherer genetics research: Importance and avenues.Evolutionary human sciences · 2024Article
- Inference of Chromosome-Length Haplotypes Using Genomic Data of Three or a Few More Single Gametes.Molecular biology and evolution · 2020Article
- Flexible Mixture Model Approaches That Accommodate Footprint Size Variability for Robust Detection of Balancing Selection.Molecular biology and evolution · 2020Article
- A Likelihood Approach for Uncovering Selective Sweep Signatures from Haplotype Data.Molecular biology and evolution · 2020Article
- Detection of Shared Balancing Selection in the Absence of Trans-Species Polymorphism.Molecular biology and evolution · 2019Article
- Detection and Classification of Hard and Soft Sweeps from Unphased Genotypes by Multilocus Genotype Identity.Genetics · 2018Article
- Comparison of Single Genome and Allele Frequency Data Reveals Discordant Demographic Histories.G3 (Bethesda, Md.) · 2017Article
- Inferring Demographic History Using Two-Locus Statistics.Genetics · 2017Article
- Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences.Nature genetics · 2016Review
- A multivariate Bernoulli model to predict DNaseI hypersensitivity status from haplotype data.Bioinformatics (Oxford, England) · 2015Article
- A spatial haplotype copying model with applications to genotype imputation.Journal of computational biology : a journal of computational molecular cell biology · 2015Article
- Article
- A model-based approach for identifying signatures of ancient balancing selection in genetic data.PLoS genetics · 2014Article
- Demographic history of a recent invasion of house mice on the isolated Island of Gough.Molecular ecology · 2014Article
- The impact of population demography and selection on the genetic architecture of complex traits.PLoS genetics · 2014Article
- Natural selection reduced diversity on human y chromosomes.PLoS genetics · 2014Article
- Genomic inference accurately predicts the timing and severity of a recent bottleneck in a nonmodel insect population.Molecular ecology · 2014Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
We propose a novel approximate-likelihood method to fit demographic models to human genomewide single-nucleotide polymorphism (SNP) data. We divide the genome into windows of constant genetic map width and then tabulate the number of distinct haplotypes and the frequency of the most common haplotype for each window. We summarize the data by the genomewide joint distribution of these two statistics-termed the HCN statistic. Coalescent simulations are used to generate the expected HCN statistic for different demographic parameters. The HCN statistic provides additional information for disentangling complex demography beyond statistics based on single-SNP frequencies. Application of our method to simulated data shows it can reliably infer parameters from growth and bottleneck models, even in the presence of recombination hotspots when properly modeled. We also examined how practical problems with genomewide data sets, such as errors in the genetic map, haplotype phase uncertainty, and SNP ascertainment bias, affect our method. Several modifications of our method served to make it robust to these problems. We have applied our method to data collected by Perlegen Sciences and find evidence for a severe population size reduction in northwestern Europe starting 32,500-47,500 years ago.
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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.