ArticleGenetics2015
A Composite-Likelihood Method for Detecting Incomplete Selective Sweep from Population Genomic Data.
Article in Genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed, 54 citations in OpenAlex.
- Severe bottleneck of ancient Homo populations: insights from computational modeling and relevant fossil evidence.Molecular biology and evolution · 2026Article
- Detecting Positive Selection by Modeling Structure Within Images of Genetic Variation.Genome biology and evolution · 2026Article
- Pleiotropy and Facilitation of Local Adaptation in the Silverleaf Sunflower Helianthus argophyllus.Genome biology and evolution · 2026Article
- Whole-genome selective sweep analysis of Danish Large White and Chinese indigenous pig populations.Animal biotechnology · 2025Article
- Integrated multi-omics analysis and functional validation uncovers RPL26 roles in regulating growth traits of Asian water buffaloes (Bubalus bubalis).BMC genomics · 2025Article
- Efficient Detection and Characterization of Targets of Natural Selection Using Transfer Learning.Molecular biology and evolution · 2025Article
- Efficient detection and characterization of targets of natural selection using transfer learning.bioRxiv : the preprint server for biology · 2025Article
- Genome-Wide Scans for Selection Signatures in Ningxia Angus Cattle Reveal Genetic Variants Associated with Economic and Adaptive Traits.Animals : an open access journal from MDPI · 2024Article
- Computational Genomics and Its Applications to Anthropological Questions.American journal of biological anthropology · 2024Review
- Population Genomic Scans for Natural Selection and Demography.Annual review of genetics · 2024Review
- Article
- Tensor Decomposition-based Feature Extraction and Classification to Detect Natural Selection from Genomic Data.Molecular biology and evolution · 2023Article
- Timesweeper: accurately identifying selective sweeps using population genomic time series.Genetics · 2023Article
- A spatially aware likelihood test to detect sweeps from haplotype distributions.PLoS genetics · 2022Article
- Whole Genome Sequencing Provides New Insights Into the Genetic Diversity and Coat Color of Asiatic Wild Ass and Its Hybrids.Frontiers in genetics · 2022Article
- Article
- Benchmarking the performance of Pool-seq SNP callers using simulated and real sequencing data.Molecular ecology resources · 2021Article
- Article
- A Likelihood Approach for Uncovering Selective Sweep Signatures from Haplotype Data.Molecular biology and evolution · 2020Article
- VolcanoFinder: Genomic scans for adaptive introgression.PLoS genetics · 2020Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Adaptive evolution occurs as beneficial mutations arise and then increase in frequency by positive natural selection. How, when, and where in the genome such evolutionary events occur is a fundamental question in evolutionary biology. It is possible to detect ongoing positive selection or an incomplete selective sweep in species with sexual reproduction because, when a beneficial mutation is on the way to fixation, homologous chromosomes in the population are divided into two groups: one carrying the beneficial allele with very low polymorphism at nearby linked loci and the other carrying the ancestral allele with a normal pattern of sequence variation. Previous studies developed long-range haplotype tests to capture this difference between two groups as the signal of an incomplete selective sweep. In this study, we propose a composite-likelihood-ratio (CLR) test for detecting incomplete selective sweeps based on the joint sampling probabilities for allele frequencies of two groups as a function of strength of selection and recombination rate. Tested against simulated data, this method yielded statistical power and accuracy in parameter estimation that are higher than the iHS test and comparable to the more recently developed nSL test. This procedure was also applied to African Drosophila melanogaster population genomic data to detect candidate genes under ongoing positive selection. Upon visual inspection of sequence polymorphism, candidates detected by our CLR method exhibited clear haplotype structures predicted under incomplete selective sweeps. Our results suggest that different methods capture different aspects of genetic information regarding incomplete sweeps and thus are partially complementary to each other.
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