ArticleGenetics2016
Bayesian Inference of Natural Selection from Allele Frequency Time Series.
Article in Genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers, 1 of them a synthesis that pooled it.
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Who cites it
65 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The practice and promise of temporal genomics for measuring evolutionary responses to global change.Molecular ecology resources · 2025Pooled it
- Optimal control and the dynamics of ancestral lineages.Genetics · 2026Article
- Direct estimation of genotype fitness from time series.bioRxiv : the preprint server for biology · 2026Article
- Summary statistics and approximate bayesian computation are comparable to convolutional neural networks for inferring times to fixation.bioRxiv : the preprint server for biology · 2026Article
- Assessing Ancient DNA Sampling Strategies for Natural Selection Inference in Humans Using Allele Frequency Time Series Data.Genome biology and evolution · 2026Article
- Linkage-aware inference of fitness from short-read time-series genomic data.bioRxiv : the preprint server for biology · 2026Article
- Linkage-aware inference of fitness from short-read time-series genomic data.Virus evolution · 2026Article
- Selection Estimation from Genetic Time-Series Data: Effects of Limited Sampling and Genetic Drift.Molecular biology and evolution · 2025Article
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- A novel expectation-maximization approach to infer general diploid selection from time-series genetic data.PLoS genetics · 2025Article
- Inferring fitness seascapes from evolutionary histories.bioRxiv : the preprint server for biology · 2025Article
- A novel expectation-maximization approach to infer general diploid selection from time-series genetic data.bioRxiv : the preprint server for biology · 2025Article
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- A binary trait model reveals the fitness effects of HIV-1 escape from T cell responses.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
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- Computational Genomics and Its Applications to Anthropological Questions.American journal of biological anthropology · 2024Review
- A binary trait model reveals the fitness effects of HIV-1 escape from T cell responses.bioRxiv : the preprint server for biology · 2024Article
- Conditional frequency spectra as a tool for studying selection on complex traits in biobanks.bioRxiv : the preprint server for biology · 2024Article
5 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
The advent of accessible ancient DNA technology now allows the direct ascertainment of allele frequencies in ancestral populations, thereby enabling the use of allele frequency time series to detect and estimate natural selection. Such direct observations of allele frequency dynamics are expected to be more powerful than inferences made using patterns of linked neutral variation obtained from modern individuals. We developed a Bayesian method to make use of allele frequency time series data and infer the parameters of general diploid selection, along with allele age, in nonequilibrium populations. We introduce a novel path augmentation approach, in which we use Markov chain Monte Carlo to integrate over the space of allele frequency trajectories consistent with the observed data. Using simulations, we show that this approach has good power to estimate selection coefficients and allele age. Moreover, when applying our approach to data on horse coat color, we find that ignoring a relevant demographic history can significantly bias the results of inference. Our approach is made available in a C++ software package.
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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.