title: Estimating the age of retrotransposon subfamilies using maximum likelihood.
abstract: We present a maximum likelihood model to estimate the age of retrotransposon subfamilies. This method is designed around a master gene model which assumes a constant retrotransposition rate. The statistical properties of this model and an ad hoc estimation procedure are compared using two simulated data sets. We also test whether each estimation procedure is robust to violation of the master gene model. According to our results, both estimation procedures are accurate under the master gene model. While both methods tend to overestimate ages under the intermediate model, the maximum likelihood estimate is significantly less inflated than the ad hoc estimate. We estimate the ages of two subfamilies of human-specific LINE-I insertions using both estimation procedures. By calculating confidence intervals around the maximum likelihood estimate, our model can both provide an estimate of retrotransposon subfamily age and describe the range of subfamily ages consistent with the data.
authors.affiliation: Division of Medical Genetics, University of Washington, BOX 357720, Seattle, WA 98195, USA. em27@u.washington.edu
authors.forename: Elizabeth E
authors.initials: EE
authors.lastname: Marchani
authors.forename: Jinchuan
authors.initials: J
authors.lastname: Xing
authors.forename: David J
authors.initials: DJ
authors.lastname: Witherspoon
authors.forename: Lynn B
authors.initials: LB
authors.lastname: Jorde
authors.forename: Alan R
authors.initials: AR
authors.lastname: Rogers
mesh_terms: D019143:Evolution, Molecular; D006801:Humans; D016013:Likelihood Functions; D020084:Long Interspersed Nucleotide Elements; D008957:Models, Genetic; D018626:Retroelements / Q000235:genetics*
chemical_list: D018626:Retroelements