ArticleMolecular ecology2016
Detecting recent selective sweeps while controlling for mutation rate and background selection.
Article in Molecular ecology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers, 1 of them a synthesis that pooled it.
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Who cites it
83 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection.Nature genetics · 2018Pooled it
- Enhancing detection of polygenic adaptation: a comparative study of machine learning and statistical approaches using simulated evolve-and-resequence data.BMC genomics · 2026Article
- Detecting Positive Selection by Modeling Structure Within Images of Genetic Variation.Genome biology and evolution · 2026Article
- ThebioRxiv : the preprint server for biology · 2026Article
- Selection scans and downstream analysis with selscan.Human population genetics and genomics · 2026Article
- Selection scans and downstream analysis with selscan.bioRxiv : the preprint server for biology · 2025Article
- Urban Life Shapes Genetic Diversity in the Green Anole, Anolis carolinensis.Molecular ecology · 2025Article
- Evolution of Functional Genomic Diversity During a Bottleneck.Genome biology and evolution · 2025Article
- Efficient Detection and Characterization of Targets of Natural Selection Using Transfer Learning.Molecular biology and evolution · 2025Article
- The Precision and Power of Population Branch Statistics in Identifying the Genomic Signatures of Local Adaptation.Genome biology and evolution · 2025Article
- Inferring demographic and selective histories from population genomic data using a 2-step approach in species with coding-sparse genomes: an application to human data.G3 (Bethesda, Md.) · 2025Article
- Efficient detection and characterization of targets of natural selection using transfer learning.bioRxiv : the preprint server for biology · 2025Article
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- Inversions contribute disproportionately to parallel genomic divergence in dune sunflowers.Nature ecology & evolution · 2025Article
- Repeated global adaptation across plant species.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Digital Image Processing to Detect Adaptive Evolution.Molecular biology and evolution · 2024Article
- Computational Genomics and Its Applications to Anthropological Questions.American journal of biological anthropology · 2024Review
- Inferring demographic and selective histories from population genomic data using a two-step approach in species with coding-sparse genomes: an application to human data.bioRxiv : the preprint server for biology · 2024Article
- Signals of selection and ancestry in independently feral Gallus gallus populations.Molecular ecology · 2024Article
- Comparative mitochondrial genomics in Nematoda reveal astonishing variation in compositional biases and substitution rates indicative of multi-level selection.BMC genomics · 2024Article
23 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
A composite likelihood ratio test implemented in the program sweepfinder is a commonly used method for scanning a genome for recent selective sweeps. sweepfinder uses information on the spatial pattern (along the chromosome) of the site frequency spectrum around the selected locus. To avoid confounding effects of background selection and variation in the mutation process along the genome, the method is typically applied only to sites that are variable within species. However, the power to detect and localize selective sweeps can be greatly improved if invariable sites are also included in the analysis. In the spirit of a Hudson-Kreitman-Aguadé test, we suggest adding fixed differences relative to an out-group to account for variation in mutation rate, thereby facilitating more robust and powerful analyses. We also develop a method for including background selection, modelled as a local reduction in the effective population size. Using simulations, we show that these advances lead to a gain in power while maintaining robustness to mutation rate variation. Furthermore, the new method also provides more precise localization of the causative mutation than methods using the spatial pattern of segregating sites alone.
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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.