Estimating the age of retrotransposon subfamilies using maximum likelihood

Elizabeth E. Marchani, Jinchuan Xing, David J. Witherspoon, Lynn B. Jorde, Alan R. Rogers

Research output: Contribution to journalArticlepeer-review

8 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)78-82
Number of pages5
JournalGenomics
Volume94
Issue number1
DOIs
StatePublished - Jul 2009
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Genetics

Keywords

  • LINE-1
  • Maximum likelihood
  • Retrotransposon
  • Subfamily age

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