Inference of population history using a likelihood approach.

Genetics
G Weiss, A von Haeseler

Abstract

We introduce an approach to revealing the likelihood of different population histories that utilizes an explicit model of sequence evolution for the DNA segment under study. Based on a phylogenetic tree reconstruction method we show that a Tamura-Nei model with heterogeneous mutation rates is a fair description of the evolutionary process of the hypervariable region I of the mitochondrial DNA from humans. Assuming this complex model still allows the estimation of population history parameters, we suggest a likelihood approach to conducting statistical inference within a class of expansion models. More precisely, the likelihood of the data is based on the mean pairwise differences between DNA sequences and the number of variable sites in a sample. The use of likelihood ratios enables comparison of different hypotheses about population history, such as constant population size during the past or an increase or decrease of population size starting at some point back in time. This method was applied to show that the population of the Basques has expanded, whereas that of the Biaka pygmies is most likely decreasing. The Nuu-Chah-Nulth data are consistent with a model of constant population.

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Citations

Aug 19, 2007·Bioinformatics·Heiko A SchmidtJutta Buschbom
Jun 11, 2004·Molecular Biology and Evolution·Giovanni Destro-BisolCristian Capelli
Oct 17, 2006·PLoS Genetics·Haipeng Li, Wolfgang Stephan
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May 17, 2006·Genetics·Rong JiangSimon Tavaré
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Dec 10, 2003·Proceedings of the National Academy of Sciences of the United States of America·Paul MarjoramSimon Tavare
Sep 7, 2005·Genetics·Scotland C LemanMarcy K Uyenoyama
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Jun 17, 2010·BMC Evolutionary Biology·Michael ReagonAna L Caicedo

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