Comparing likelihood and Bayesian coalescent estimation of population parameters

Genetics
Mary K Kuhner, Lucian P Smith

Abstract

We have developed a Bayesian version of our likelihood-based Markov chain Monte Carlo genealogy sampler LAMARC and compared the two versions for estimation of theta = 4N(e)mu, exponential growth rate, and recombination rate. We used simulated DNA data to assess accuracy of means and support or credibility intervals. In all cases the two methods had very similar results. Some parameter combinations led to overly narrow support or credibility intervals, excluding the truth more often than the desired percentage, for both methods. However, the Bayesian approach rejected the generative parameter values significantly less often than the likelihood approach, both in cases where the level of rejection was normal and in cases where it was too high.

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Citations

Jan 13, 2009·Molecular Biology and Evolution·Krystyna Nadachowska, Wieslaw Babik
Apr 23, 2010·Proceedings. Biological Sciences·B R Barber, J Klicka
Jul 10, 2008·PloS One·Leonardo de Oliveira MartinsHirohisa Kishino
Jun 18, 2016·Annals of Botany·Helena Augusta Viana E SouzaMaria Bernadete Lovato
Apr 20, 2014·PLoS Computational Biology·David A RasmussenKatia Koelle
Mar 17, 2007·Journal of Theoretical Biology·Martin O'Hely, Leesa Wockner
Apr 22, 2006·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Marcos Pérez-LosadaKeith A Crandall
Aug 19, 2009·Nature Reviews. Genetics·Kent E Holsinger, Bruce S Weir
Sep 29, 2009·Evolution; International Journal of Organic Evolution·Nathan D Jackson, Christopher C Austin
Jun 22, 2010·Molecular Ecology·Marco V G TorrianiSilvia Dorn
Jul 14, 2010·Molecular Ecology·Enrique P LessaUlyses F J Pardiñas
Jul 22, 2009·Evolution; International Journal of Organic Evolution·Luana S MarojaRichard G Harrison
Aug 19, 2014·Evolution; International Journal of Organic Evolution·Brook L FlukerPhillip M Harris
Sep 13, 2019·Genetics·Julia A PalaciosSohini Ramachandran
Aug 26, 2009·Evolution; International Journal of Organic Evolution·Juan Luis Parra
Dec 22, 2010·Molecular Biology and Evolution·Yosef E MaruvkaJohn Wakeley

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