ArticlePLoS genetics2015
Predicting Carriers of Ongoing Selective Sweeps without Knowledge of the Favored Allele.
Article in PLoS genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 15 papers.
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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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Who cites it
15 citing papers in PubMed.
- Article
- Pervasive findings of directional selection realize the promise of ancient DNA to elucidate human adaptation.bioRxiv : the preprint server for biology · 2024Article
- A Novel Approach Utilizing Domain Adversarial Neural Networks for the Detection and Classification of Selective Sweeps.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Versatile Detection of Diverse Selective Sweeps with Flex-Sweep.Molecular biology and evolution · 2023Article
- Admixture has obscured signals of historical hard sweeps in humans.Nature ecology & evolution · 2022Article
- Assessing Bos taurus introgression in the UOA Bos indicus assembly.Genetics, selection, evolution : GSE · 2021Article
- Integration of population and functional genomics to understand mechanisms of artemisinin resistance in Plasmodium falciparum.International journal for parasitology. Drugs and drug resistance · 2021Article
- Article
- Detection and Classification of Hard and Soft Sweeps from Unphased Genotypes by Multilocus Genotype Identity.Genetics · 2018Article
- Identifying the favored mutation in a positive selective sweep.Nature methods · 2018Article
- Detecting Recent Positive Selection with a Single Locus Test Bipartitioning the Coalescent Tree.Genetics · 2018Article
- New Insights into the Genetic Basis of Monge's Disease and Adaptation to High-Altitude.Molecular biology and evolution · 2017Article
- Senp1 drives hypoxia-induced polycythemia via GATA1 and Bcl-xL in subjects with Monge's disease.The Journal of experimental medicine · 2016Article
- Correction: Predicting Carriers of Ongoing Selective Sweeps without Knowledge of the Favored Allele.PLoS genetics · 2016Article
- Selection on the gametophyte: Modeling alternation of generations in plants.Applications in plant sciencesArticle
Corrections and comments
- Erratum issued
Authors and funding
6 authors.
Funding
Abstract
Methods for detecting the genomic signatures of natural selection have been heavily studied, and they have been successful in identifying many selective sweeps. For most of these sweeps, the favored allele remains unknown, making it difficult to distinguish carriers of the sweep from non-carriers. In an ongoing selective sweep, carriers of the favored allele are likely to contain a future most recent common ancestor. Therefore, identifying them may prove useful in predicting the evolutionary trajectory--for example, in contexts involving drug-resistant pathogen strains or cancer subclones. The main contribution of this paper is the development and analysis of a new statistic, the Haplotype Allele Frequency (HAF) score. The HAF score, assigned to individual haplotypes in a sample, naturally captures many of the properties shared by haplotypes carrying a favored allele. We provide a theoretical framework for computing expected HAF scores under different evolutionary scenarios, and we validate the theoretical predictions with simulations. As an application of HAF score computations, we develop an algorithm (PreCIOSS: Predicting Carriers of Ongoing Selective Sweeps) to identify carriers of the favored allele in selective sweeps, and we demonstrate its power on simulations of both hard and soft sweeps, as well as on data from well-known sweeps in human populations.
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