Towards Improvements in the Estimation of the Coalescent: Implications for the Most Effective Use of Y Chromosome Short Tandem Repeat Mutation Rates

Date

2012-10-31

Authors

Bird, Steven

Journal Title

Journal ISSN

Volume Title

Publisher

Public Library of Science

Abstract

Over the past two decades, many short tandem repeat (STR) microsatellite loci on the human Y chromosome have been identified together with mutation rate estimates for the individual loci. These have been used to estimate the coalescent age, or the time to the most recent common ancestor (TMRCA) expressed in generations, in conjunction with the average square difference measure (ASD), an unbiased point estimator of TMRCA based upon the average within-locus allele variance between haplotypes. The ASD estimator, in turn, depends on accurate mutation rate estimates to be able to produce good approximations of the coalescent age of a sample. Here, a comparison is made between three published sets of per locus mutation rate estimates as they are applied to the calculation of the coalescent age for real and simulated population samples. A novel evaluation method is developed for estimating the degree of conformity of any Y chromosome STR locus of interest to the strict stepwise mutation model and specific recommendations are made regarding the suitability of thirty-two commonly used Y-STR loci for the purpose of estimating the coalescent. The use of the geometric mean for averaging ASD and μ^ across loci is shown to improve the consistency of the resulting estimates, with decreased sensitivity to outliers and to the number of STR loci compared or the particular set of mutation rates selected.

Description

Keywords

genetic loci, arithmetic, haplotypes, y chromosomes, mutation, haplogroups, normal distribution, point mutation, Biology

Citation

Bird, S. (2012). Towards Improvements in the Estimation of the Coalescent: Implications for the most effective use of Y chromosome short tandem repeat mutation rates. PLoS One, 7(10): e48638.

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© 2012 Steven C. Bird.

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This work is licensed under a Creative Commons Attribution 4.0 International License.

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