title: The detection of shared and ancestral polymorphisms.
abstract: There is increasing evidence that closely related species contain many polymorphisms that were present in their common ancestral species. Use of a more distant relative as an outgroup increases the ability to detect such ancestral polymorphisms. We describe a method for further improving estimates of the fraction of polymorphisms that are ancestral, and illustrate this with reference to data on Drosophila pseudoobscura and D. miranda. We also derive formulae for the proportion of fixations arising from ancestral polymorphisms and new mutations, respectively. The results should be useful for tests of selection based on the levels of expected and observed ancestral polymorphisms.
authors.affiliation: Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, King's Buildings, UK. Brian.Charlesworth@ed.ac.uk
authors.forename: Brian
authors.initials: B
authors.lastname: Charlesworth
authors.forename: Carolina
authors.initials: C
authors.lastname: Bartolomé
authors.forename: Véronique
authors.initials: V
authors.lastname: Noël
mesh_terms: D000483:Alleles; D000818:Animals; D005075:Biological Evolution; D004330:Drosophila / Q000235:genetics*; D019143:Evolution, Molecular; D005787:Gene Frequency; D017344:Genes, Insect; D014644:Genetic Variation; D005828:Genetics, Population; D008957:Models, Genetic; D015233:Models, Statistical; D011110:Polymorphism, Genetic; D015203:Reproducibility of Results; D012641:Selection, Genetic; D013045:Species Specificity