ArticleGenome research2008
Confounding between recombination and selection, and the Ped/Pop method for detecting selection.
Article in Genome research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers, 1 of them a synthesis that pooled it.
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Who cites it
56 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A Meta-Assembly of Selection Signatures in Cattle.PloS one · 2016Pooled it
- Genomic insights on conservation priorities for North Sea houting and European lake whitefish (Coregonus spp.).Molecular ecology · 2025Article
- Multiple-testing corrections in selection scans using identity-by-descent segments.American journal of human genetics · 2025Article
- Identity by descent and local ancestry mapping of HCV spontaneous clearance in populations of diverse ancestries.BMC genomics · 2025Article
- Multiple-testing corrections in selection scans using identity-by-descent segments.bioRxiv : the preprint server for biology · 2025Article
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- Striking Departures from Polygenic Architecture in the Tails of Complex Traits.bioRxiv : the preprint server for biology · 2024Article
- Diversity in Recombination Hotspot Characteristics and Gene Structure Shape Fine-Scale Recombination Patterns in Plant Genomes.Molecular biology and evolution · 2024Article
- Assessing the Presence of Recent Adaptation in the Human Genome With Mixture Density Regression.Genome biology and evolution · 2023Article
- Versatile Detection of Diverse Selective Sweeps with Flex-Sweep.Molecular biology and evolution · 2023Article
- An estimator for the recombination rate from a continuously observed diffusion of haplotype frequencies.Journal of mathematical biology · 2023Article
- The effect of mutation subtypes on the allele frequency spectrum and population genetics inference.G3 (Bethesda, Md.) · 2023Article
- A chromosome-level reference genome and pangenome for barn swallow population genomics.Cell reports · 2023Article
- The Impact of Genetic Surfing on Neutral Genomic Diversity.Molecular biology and evolution · 2022Article
- Evidence of hard-selective sweeps suggests independent adaptation to insecticides in Colorado potato beetle (Coleoptera: Chrysomelidae) populations.Evolutionary applications · 2022Article
- Multiple Sources of Introduction of North American Arabidopsis thaliana from across Eurasia.Molecular biology and evolution · 2021Article
- Article
- Human-modified canids in human-modified landscapes: The evolutionary consequences of hybridization for grey wolves and free-ranging domestic dogs.Evolutionary applications · 2021Article
- Application of a novel haplotype-based scan for local adaptation to study high-altitude adaptation in rhesus macaques.Evolution letters · 2021Article
- Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data.PLoS genetics · 2021Article
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3 authors.
Funding
Abstract
In recent years, there have been major developments of population genetics methods to estimate both rates of recombination and levels of natural selection. However, genomic variants subject to positive selection are likely to have arisen recently and, consequently, had less opportunity to be affected by recombination. Thus, the two processes have an intimately related impact on genetic variation, and inference of either may be vulnerable to confounding by the other. We illustrate here that even modest levels of positive selection can substantially reduce population-based recombination rate estimates. We also show that genome-wide scans to detect loci under recent selection in humans have tended to highlight loci in regions of low recombination, suggesting that confounding by recombination rate may have reduced the power of these studies. Motivated by these findings, we introduce a new genome-wide approach for detecting selection, based on the ratio of pedigree-based to population-based estimates of recombination rate. Simulations suggest that our "Ped/Pop" method, which is designed to capture completed sweeps, has good power to discriminate between neutral and adaptive evolution. Unusually for a multimarker method, our approach performs well in regions of high recombination and also has good power for many generations after the fixation of an advantageous variant. We apply the method to human HapMap and Perlegen data sets, finding confirmation of reported candidates as well as identifying new loci that may have undergone recent intense selection.
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