ArticleGenetics2008
Bayesian variable selection for detecting adaptive genomic differences among populations.
Article in Genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
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Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A Meta-Assembly of Selection Signatures in Cattle.PloS one · 2016Pooled it
- Computational Genomics and Its Applications to Anthropological Questions.American journal of biological anthropology · 2024Review
- Selective Sweeps Uncovering the Genetic Basis of Horn and Adaptability Traits on Fine-Wool Sheep in China.Frontiers in genetics · 2021Article
- Detecting Selection from Linked Sites Using anGenetics · 2020Article
- Environmental variation shapes genetic variation inEcology and evolution · 2019Article
- Selective Sweeps.Genetics · 2019Review
- Article
- Detecting Genomic Signatures of Natural Selection with Principal Component Analysis: Application to the 1000 Genomes Data.Molecular biology and evolution · 2016Article
- Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates.Genetics · 2015Article
- Detection of Selection Signatures on the X Chromosome in Three Sheep Breeds.International journal of molecular sciences · 2015Article
- Article
- Combined QTL and selective sweep mappings with coding SNP annotation and cis-eQTL analysis revealed PARK2 and JAG2 as new candidate genes for adiposity regulation.G3 (Bethesda, Md.) · 2015Article
- Genetic relatedness among indigenous rice varieties in the Eastern Himalayan region based on nucleotide sequences of the Waxy gene.BMC research notes · 2014Article
- Genome scans for detecting footprints of local adaptation using a Bayesian factor model.Molecular biology and evolution · 2014Article
- Fine-mapping and selective sweep analysis of QTL for cold tolerance in Drosophila melanogaster.G3 (Bethesda, Md.) · 2014Article
- Detecting and measuring selection from gene frequency data.Genetics · 2014Article
- Article
- Assessing the spatial dependence of adaptive loci in 43 European and Western Asian goat breeds using AFLP markers.PloS one · 2014Article
- Article
- Detecting signatures of selection through haplotype differentiation among hierarchically structured populations.Genetics · 2013Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We extend an F(st)-based Bayesian hierarchical model, implemented via Markov chain Monte Carlo, for the detection of loci that might be subject to positive selection. This model divides the F(st)-influencing factors into locus-specific effects, population-specific effects, and effects that are specific for the locus in combination with the population. We introduce a Bayesian auxiliary variable for each locus effect to automatically select nonneutral locus effects. As a by-product, the efficiency of the original approach is improved by using a reparameterization of the model. The statistical power of the extended algorithm is assessed with simulated data sets from a Wright-Fisher model with migration. We find that the inclusion of model selection suggests a clear improvement in discrimination as measured by the area under the receiver operating characteristic (ROC) curve. Additionally, we illustrate and discuss the quality of the newly developed method on the basis of an allozyme data set of the fruit fly Drosophila melanogaster and a sequence data set of the wild tomato Solanum chilense. For data sets with small sample sizes, high mutation rates, and/or long sequences, however, methods based on nucleotide statistics should be preferred.
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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.