Estimating the age of retrotransposon subfamilies using maximum likelihood

TY - JOUR

T1 - Estimating the age of retrotransposon subfamilies using maximum likelihood

AU - Marchani, Elizabeth E.

AU - Xing, Jinchuan

AU - Witherspoon, David J.

AU - Jorde, Lynn B.

AU - Rogers, Alan R.

N1 - Funding Information: We thank Henry Harpending for his helpful comments during the preparation of this manuscript. This research was supported by NIH grant GM-59290 and NSF grant BCS-0218370.

PY - 2009/7

Y1 - 2009/7

N2 - 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.

AB - 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.

KW - LINE-1

KW - Maximum likelihood

KW - Retrotransposon

KW - Subfamily age

UR - https://www.scopus.com/pages/publications/67349183958

UR - https://www.scopus.com/pages/publications/67349183958#tab=citedBy

U2 - 10.1016/j.ygeno.2009.04.002

DO - 10.1016/j.ygeno.2009.04.002

M3 - Article

C2 - 19379804

SN - 0888-7543

VL - 94

SP - 78

EP - 82

JO - Genomics

JF - Genomics

IS - 1

ER -