Approximate Likelihood Estimation of Divergence Time Range Using a Coalescent-based Model. (January 2013)

• Record Type: Journal Article
• Authors: RoyChoudhury, Arindam
• Is Part Of: Evolutionary bioinformatics online. Volume 9(2013)
• Publication Date: 2013-01
• Subjects: divergence time -- range -- confidence interval -- maximum likelihood -- coalescent; Bioinformatics -- Periodicals; Evolutionary computation -- Periodicals; Genetic programming (Computer science) -- Periodicals; Computational Biology; Evolution, Molecular; Bioinformatics; Electronic journals; Periodicals; Fulltext; Internet Resources; Periodicals; Periodicals; 576.8
• DOI: 10.4137/EBO.S13080
• Languages: English
• ISSNs: 1176-9343

Abstract

We present an estimation of divergence time-range based on a coalescent model. This model sum the probability of coalescent trees, taking into account the effect of incomplete lineage sorting. Maximum likelihood estimate based on this model has been computed previously; however, a formula for divergence time-range estimate or confidence interval has never been presented for this model as the expression of the likelihood makes this estimation difficult to compute. Our formula for the divergence time-range estimate can be readily coded into a program. We did not use a simulation or resampling-based approach and therefore our method is fast and less computationally intensive. We demonstrate that our method is much faster and as accurate a simulation-based approach.