ArticleTheoretical population biology2015
A hidden Markov model for investigating recent positive selection through haplotype structure.
Article in Theoretical population biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
27 citing papers in PubMed, 58 citations in OpenAlex.
- Detecting Positive Selection by Modeling Structure Within Images of Genetic Variation.Genome biology and evolution · 2026Article
- HaploSweep: Detecting and Distinguishing Recent Soft and Hard Selective Sweeps through Haplotype Structure.Molecular biology and evolution · 2024Article
- Harnessing deep learning for population genetic inference.Nature reviews. Genetics · 2024Review
- HaploBlocks: Efficient Detection of Positive Selection in Large Population Genomic Datasets.Molecular biology and evolution · 2023Article
- Demographic history differences between Hispanics and Brazilians imprint haplotype features.G3 (Bethesda, Md.) · 2022Article
- Article
- Article
- High frequency of an otherwise rare phenotype in a small and isolated tiger population.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- The distribution of runs of homozygosity in the genome of river and swamp buffaloes reveals a history of adaptation, migration and crossbred events.Genetics, selection, evolution : GSE · 2021Article
- Population genetic variation ofJournal of genetics · 2021Article
- Ancient familial Mediterranean fever mutations in human pyrin and resistance to Yersinia pestis.Nature immunology · 2020Article
- The Evolutionary History of Human Skin Pigmentation.Journal of molecular evolution · 2020Review
- Article
- Finding all maximal perfect haplotype blocks in linear time.Algorithms for molecular biology : AMB · 2020Article
- Searching for Sympatric Speciation in the Genomic Era.BioEssays : news and reviews in molecular, cellular and developmental biology · 2019Review
- Detection and Classification of Hard and Soft Sweeps from Unphased Genotypes by Multilocus Genotype Identity.Genetics · 2018Article
- Estimating Time to the Common Ancestor for a Beneficial Allele.Molecular biology and evolution · 2018Article
- Loci associated with skin pigmentation identified in African populations.Science (New York, N.Y.) · 2017Article
- Human Demographic History Impacts Genetic Risk Prediction across Diverse Populations.American journal of human genetics · 2017Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Recent positive selection can increase the frequency of an advantageous mutant rapidly enough that a relatively long ancestral haplotype will be remained intact around it. We present a hidden Markov model (HMM) to identify such haplotype structures. With HMM identified haplotype structures, a population genetic model for the extent of ancestral haplotypes is then adopted for parameter inference of the selection intensity and the allele age. Simulations show that this method can detect selection under a wide range of conditions and has higher power than the existing frequency spectrum-based method. In addition, it provides good estimate of the selection coefficients and allele ages for strong selection. The method analyzes large data sets in a reasonable amount of running time. This method is applied to HapMap III data for a genome scan, and identifies a list of candidate regions putatively under recent positive selection. It is also applied to several genes known to be under recent positive selection, including the LCT, KITLG and TYRP1 genes in Northern Europeans, and OCA2 in East Asians, to estimate their allele ages and selection coefficients.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.