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Estimation of Natural Selection and Allele Age from Time Series Allele Frequency Data Using a Novel Likelihood-Based Approach
- Source :
- Genetics
- Publication Year :
- 2020
- Publisher :
- Oxford University Press (OUP), 2020.
-
Abstract
- Temporally spaced genetic data allow for more accurate inference of population genetic parameters and hypothesis testing on the recent action of natural selection. In this work, we develop a novel likelihood-based method for jointly estimating selection coefficient and allele age from time series data of allele frequencies. Our approach is based on a hidden Markov model where the underlying process is a Wright-Fisher diffusion conditioned to survive until the time of the most recent sample. This formulation circumvents the assumption required in existing methods that the allele is created by mutation at a certain low frequency. We calculate the likelihood by numerically solving the resulting Kolmogorov backward equation backward in time while reweighting the solution with the emission probabilities of the observation at each sampling time point. This procedure reduces the two-dimensional numerical search for the maximum of the likelihood surface, for both the selection coefficient and the allele age, to a one-dimensional search over the selection coefficient only. We illustrate through extensive simulations that our method can produce accurate estimates of the selection coefficient and the allele age under both constant and nonconstant demographic histories. We apply our approach to reanalyze ancient DNA data associated with horse base coat colors. We find that ignoring demographic histories or grouping raw samples can significantly bias the inference results.
- Subjects :
- Population
Inference
Investigations
Biology
Gene Frequency
Statistics
Genetics
Animals
Humans
Quantitative Biology::Populations and Evolution
DNA, Ancient
Selection, Genetic
Time series
Hidden Markov model
education
Allele frequency
Statistical hypothesis testing
Likelihood Functions
education.field_of_study
Natural selection
Models, Genetic
Quantitative Biology::Genomics
Diploidy
Markov Chains
Mutation (genetic algorithm)
Subjects
Details
- ISSN :
- 19432631
- Volume :
- 216
- Database :
- OpenAIRE
- Journal :
- Genetics
- Accession number :
- edsair.doi.dedup.....959240232b4dc7b805c6e4b5d01b1058