Journal
THEORETICAL POPULATION BIOLOGY
Volume 74, Issue 1, Pages 56-67Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.tpb.2008.04.006
Keywords
longitudinal sample; coalescent theory; summary statistics; measurably evolving population
Funding
- NIGMS NIH HHS [R01 GM060777-01A2, R01 GM060777, GM60777, R29 GM050428, GM50428, R01 GM050428, R01 GM050428-09] Funding Source: Medline
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Longitudinal samples of DNA sequences are the DNA sequences sampled from the same population at different time points. For fast evolving organisms, e.g. RNA virus, these kind of samples have increasingly been used to study the evolutionary process in action. Longitudinal samples provide some interesting new summary statistics of genetic variation, such as the frequency of mutation of size i in one sample and sizej in another, the average number of mutations accumulated since the common ancestor of two sequences each from a different sample, and number of private, shared and fixed mutations within samples. To make the results more applicable, we used in this study a general two-sample model, which assumes two longitudinal samples were taken from the same measurably evolving population. Inspired by the HIV study, we also studied a two-sample-two-stage model, which is a special case of two-sample model and assumes a treatment after the first sampling instantaneously changes the population size. We derived the formulas for calculating statistical properties, e.g. expectations, variances and covariances, of these new summary statistics under the two models. Potential applications of these results were discussed. Published by Elsevier Inc.
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