Estimating allele age and selection coefficient from time-serial data

• Published in: Genetics (Austin) Vol. 192; no. 2; pp. 599 - 607
• Main Authors: Malaspinas, Anna-Sapfo, Malaspinas, Orestis, Evans, Steven N, Slatkin, Montgomery
• Format: Journal Article
• Language: English
• Published: United States Genetics Society of America 01-10-2012
• Subjects: Age Factors; Alleles; Animals; Animals, Domestic; Color; Evolution, Molecular; Gene Frequency; Genetics, Population - methods; Genomics; Horses - genetics; Investigations; Models, Genetic; Models, Theoretical; Mutagenesis; Mutation; Pigments, Biological - genetics; Polymorphism; Polymorphism, Single Nucleotide; Population genetics; Selection, Genetic; Time series
• ISSN: 1943-2631; 0016-6731; 1943-2631
• DOI: 10.1534/genetics.112.140939

Recent advances in sequencing technologies have made available an ever-increasing amount of ancient genomic data. In particular, it is now possible to target specific single nucleotide polymorphisms in several samples at different time points. Such time-series data are also available in the context of experimental or viral evolution. Time-series data should allow for a more precise inference of population genetic parameters and to test hypotheses about the recent action of natural selection. In this manuscript, we develop a likelihood method to jointly estimate the selection coefficient and the age of an allele from time-serial data. Our method can be used for allele frequencies sampled from a single diallelic locus. The transition probabilities are calculated by approximating the standard diffusion equation of the Wright-Fisher model with a one-step process. We show that our method produces unbiased estimates. The accuracy of the method is tested via simulations. Finally, the utility of the method is illustrated with an application to several loci encoding coat color in horses, a pattern that has previously been linked with domestication. Importantly, given our ability to estimate the age of the allele, it is possible to gain traction on the important problem of distinguishing selection on new mutations from selection on standing variation. In this coat color example for instance, we estimate the age of this allele, which is found to predate domestication.