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Journal of Theoretical Biology
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Journal of Theoretical Biology
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Journal of Theoretical Biology
Article . 2016
License: CC BY
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https://dx.doi.org/10.48550/ar...
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The space of ultrametric phylogenetic trees

Authors: Alexei J. Drummond; Alex Gavryushkin;

The space of ultrametric phylogenetic trees

Abstract

The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data. Hence the question of statistical consistency of such methods is equivalent to the consistency of the summary of the sample. More generally, statistical consistency is ensured by the tree space used to analyse the sample. In this paper, we consider two standard parameterisations of phylogenetic time-trees used in evolutionary models: inter-coalescent interval lengths and absolute times of divergence events. For each of these parameterisations we introduce a natural metric space on ultrametric phylogenetic trees. We compare the introduced spaces with existing models of tree space and formulate several formal requirements that a metric space on phylogenetic trees must possess in order to be a satisfactory space for statistical analysis, and justify them. We show that only a few known constructions of the space of phylogenetic trees satisfy these requirements. However, our results suggest that these basic requirements are not enough to distinguish between the two metric spaces we introduce and that the choice between metric spaces requires additional properties to be considered. Particularly, that the summary tree minimising the square distance to the trees from the sample might be different for different parameterisations. This suggests that further fundamental insight is needed into the problem of statistical consistency of phylogenetic inference methods.

Minor changes. This version has been published in JTB. 27 pages, 9 figures

Keywords

Statistics and Probability, Time-tree, Mathematics - Statistics Theory, Statistics Theory (math.ST), CAT(0), Mathematics - Metric Geometry, Modelling and Simulation, Immunology and Microbiology(all), FOS: Mathematics, Simplicial complex, Phylogeny, Medicine(all), Curvature, Agricultural and Biological Sciences(all), Biochemistry, Genetics and Molecular Biology(all), Applied Mathematics, Metric Geometry (math.MG), Posterior distribution summary, Models, Theoretical, Geodesic, Ultrametric tree, Phylogenetic inference, Phylogenetic tree

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    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
32
Top 10%
Top 10%
Top 10%
Green
hybrid