title: Estimating allele age.
abstract: The age of an allele can be estimated both from genetic variation among different copies (intra-allelic variation) and from its frequency. Estimates based on intra-allelic variation follow from the exponential decay of linkage disequilibrium because of recombination and mutation. The confidence interval depends both on the uncertainty in recombination and mutation rates and on randomness of the genealogy of chromosomes that carry the allele (the intra-allelic genealogy). Several approximate methods to account for variation in the intra-allelic genealogy have been derived. Allele frequency alone also provides an estimate of age. Estimates based on frequency and on intra-allelic variability can be combined to provide a more accurate estimate or can be contrasted to show that an allele has been subject to natural selection. These methods have been applied to numerous cases, including alleles associated with cystic fibrosis, idiopathic torsion dystonia, and resistance to infection by HIV. We emphasize that estimates of allele age depend on assumptions about demographic history and natural selection.
authors.affiliation: Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA. slatkin@socrates.berkeley.edu
authors.forename: M
authors.initials: M
authors.lastname: Slatkin
authors.forename: B
authors.initials: B
authors.lastname: Rannala
mesh_terms: D000163:Acquired Immunodeficiency Syndrome / Q000235:genetics; D000483:Alleles; D001943:Breast Neoplasms / Q000235:genetics; D003550:Cystic Fibrosis / Q000235:genetics; D004422:Dystonia Musculorum Deformans / Q000235:genetics; D005172:Factor XI / Q000235:genetics; D005260:Female; D019398:Genes, BRCA1; D024522:Genes, BRCA2; D005819:Genetic Markers; D014644:Genetic Variation; D005828:Genetics, Population; D006801:Humans; D015810:Linkage Disequilibrium; D008297:Male; D011158:Population Growth; D019713:Receptors, CCR5 / Q000235:genetics; D012641:Selection, Genetic; D013997:Time Factors
chemical_list: D005819:Genetic Markers; D019713:Receptors, CCR5; D005172:Factor XI