ArticleGenetics2016
Testing for Ancient Selection Using Cross-population Allele Frequency Differentiation.
Article in Genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed, 112 citations in OpenAlex.
- Adaptation to seasonal drought in Arabis alpina is linked to the demographic history and climatic changes since the last glacial maximum.Molecular biology and evolution · 2026Article
- Haplotype-Based Models Improve Sweep Detection in Ancient Populations with Complex Demography.bioRxiv : the preprint server for biology · 2026Article
- Detecting Positive Selection by Modeling Structure Within Images of Genetic Variation.Genome biology and evolution · 2026Article
- Polymorphisms and Expression Characteristics of theAnimals : an open access journal from MDPI · 2026Article
- Hybridization Drives Trait Integration in Telomere-To-Telomere Apocynum Genomes.Plant biotechnology journal · 2025Article
- Positive selection on rare variants of IGF1R and BRD4 underlying the cold adaptation of wild boar.Genetics, selection, evolution : GSE · 2025Article
- Review
- Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes.Genome research · 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
- Population genomics advances in frontier ethnic minorities in China.Science China. Life sciences · 2025Review
- Efficient detection and characterization of targets of natural selection using transfer learning.bioRxiv : the preprint server for biology · 2025Article
- Whole-Genome Resequencing to Identify Selection Signatures Associated with High Fertility in Lüliang Black Goat.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
- Population genomics and epigenomics of Spirodela polyrhiza provide insights into the evolution of facultative asexuality.Communications biology · 2024Article
- More than a decade of genetic research on the Denisovans.Nature reviews. Genetics · 2024Review
- Tensor Decomposition-based Feature Extraction and Classification to Detect Natural Selection from Genomic Data.Molecular biology and evolution · 2023Article
- Versatile Detection of Diverse Selective Sweeps with Flex-Sweep.Molecular biology and evolution · 2023Article
- Archaic introgression contributed to the pre-agriculture adaptation of vitamin B1 metabolism in East Asia.iScience · 2022Article
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Authors and funding
1 author at 1 institution in 1 country.
Funding
Abstract
A powerful way to detect selection in a population is by modeling local allele frequency changes in a particular region of the genome under scenarios of selection and neutrality and finding which model is most compatible with the data. A previous method based on a cross-population composite likelihood ratio (XP-CLR) uses an outgroup population to detect departures from neutrality that could be compatible with hard or soft sweeps, at linked sites near a beneficial allele. However, this method is most sensitive to recent selection and may miss selective events that happened a long time ago. To overcome this, we developed an extension of XP-CLR that jointly models the behavior of a selected allele in a three-population tree. Our method - called "3-population composite likelihood ratio" (3P-CLR) - outperforms XP-CLR when testing for selection that occurred before two populations split from each other and can distinguish between those events and events that occurred specifically in each of the populations after the split. We applied our new test to population genomic data from the 1000 Genomes Project, to search for selective sweeps that occurred before the split of Yoruba and Eurasians, but after their split from Neanderthals, and that could have led to the spread of modern-human-specific phenotypes. We also searched for sweep events that occurred in East Asians, Europeans, and the ancestors of both populations, after their split from Yoruba. In both cases, we are able to confirm a number of regions identified by previous methods and find several new candidates for selection in recent and ancient times. For some of these, we also find suggestive functional mutations that may have driven the selective events.
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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.