Estimating divergence times

DOI10.1016/0040-5809(88)90026-3MaRDI QIDQ1109710zbMATH OpenOpenAlexFDO

Authors Septiadi Padmadisastra

Publication date 1988

Published in Theoretical Population Biology (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/0040-5809(88)90026-3

zbMATH Keywords

estimating genetic divergence timesestimating population splitting timesmaximum likelihood methodmethod of momentsphylogenetic treesimulation studiestree topology

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Genetics and epigenetics (92D10)

Review text

A statistical method of estimating population splitting times is developed. We consider three populations, with an assumed known tree topology for their phylogenetic tree. From simulation studies, we find that the method of moments performs very well, in particular for both large number of loci and divergence times, in estimating genetic divergence times. The bias decreases as the number of loci increases. The maximum likelihood method proves to be a good method for constructing an unknown phylogenetic tree, in particular for large divergence times.

Recommendations

• Maximum likelihood estimation of population divergence times and population phylogenies under the infinite sites model
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Cites work

• Comparison of phylogenetic trees
• Exact sampling distributions from the infinite neutral alleles model
• Lines of descent and the coalescent
• Lines of descent in the diffusion approximation of neutral Wright-Fisher models
• Partition structures, Polya urns, the Ewens sampling formula, and the ages of alleles
• Pólya-like urns and the Ewens' sampling formula
• The genetic divergence of three populations
• The genetic divergence of two populations
• The transient behaviour of the Moran model in population genetics

Cited in

(10)

• Maximum likelihood estimation of population divergence times and population phylogenies under the infinite sites model
• Divergence time and population size in the lineage leading to modern humans
• A Bayesian method for estimating evolutionary history
• Bayesian estimation of the phylogeography of African gorillas with genome-differentiated population trees
• Using rare mutations to estimate population divergence times: A maximum likelihood approach
• Understanding the tripartite approach to Bayesian divergence time estimation
• Estimating primate divergence times by using conditioned birth-and-death processes
• Genealogy of neutral genes in two partially isolated populations
• The exact distribution of divergence times
• Logarithmic bounds on the posterior divergence time of two sequences

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