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Seeing the wood for the trees: philosophical aspects of classical, Bayesian and likelihood approaches in statistical inference and some implications for phylogenetic analysis

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Abstract

The three main approaches in statistical inference—classical statistics, Bayesian and likelihood—are in current use in phylogeny research. The three approaches are discussed and compared, with particular emphasis on theoretical properties illustrated by simple thought-experiments. The methods are problematic on axiomatic grounds (classical statistics), extra-mathematical grounds relating to the use of a prior (Bayesian inference) or practical grounds (likelihood). This essay aims to increase understanding of these limits among those with an interest in phylogeny.

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Acknowledgments

I thank Maria Dornelas, Heleen Plaisier and Graeme Ruxton for their comments on an earlier version of the manuscript. Discussions at the University of St Andrews, particularly at the Harold Mitchell Building’s Lab Chat series organised by Mike Ritchie’s group and the Centre for Biological Diversity’s Quantitative Biology Discussion Group organised by Mike Morrisey, have also been helpful. I further thank Heleen Plaisier for pointing out the truth about librarians and farmers.

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  1. Sir Harold Mitchell Building, School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK

    Daniel Barker

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Barker, D. Seeing the wood for the trees: philosophical aspects of classical, Bayesian and likelihood approaches in statistical inference and some implications for phylogenetic analysis. Biol Philos 30, 505–525 (2015). https://doi.org/10.1007/s10539-014-9455-x

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