Confidence Sets for Phylogenetic Trees

DOI10.1080/01621459.2017.1395342MaRDI QIDQ5229907zbMATH OpenOpenAlexFDO

Authors Amy Willis

Publication date 19 August 2019

Published in Journal of the American Statistical Association (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1607.08288

zbMATH Keywords

simultaneous testingstatistical inferencephylogeniesnon-Euclidean

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Nonparametric tolerance and confidence regions (62G15) Estimation in multivariate analysis (62H12)

Abstract: Inferring evolutionary histories (phylogenetic trees) has important applications in biology, criminology and public health. However, phylogenetic trees are complex mathematical objects that reside in a non-Euclidean space, which complicates their analysis. While our mathematical, algorithmic, and probabilistic understanding of phylogenies in their metric space is mature, rigorous inferential infrastructure is as yet undeveloped. In this manuscript we unify recent computational and probabilistic advances to construct tree--valued confidence sets. The procedure accounts for both centre and multiple directions of tree--valued variability. We draw on block replicates to improve testing, identifying the best supported most recent ancestor of the Zika virus, and formally testing the hypothesis that a Floridian dentist with AIDS infected two of his patients with HIV. The method illustrates connections between variability in Euclidean and tree space, opening phylogenetic tree analysis to techniques available in the multivariate Euclidean setting.

Recommendations

• Statistics for phylogenetic trees
• The space of ultrametric phylogenetic trees
• Bootstrap confidence levels for phylogenetic trees
• Some statistical methods for phylogenetic trees with application to HIV disease

Cites work

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Cited in

(13)

• Random walks and Brownian motion on cubical complexes
• Information geometry for phylogenetic trees
• Lagged couplings diagnose Markov chain Monte Carlo phylogenetic inference
• Old and new challenges in Hadamard spaces
• Exact Confidence Regions for Species Assignment Based on DNA Markers
• The space of equidistant phylogenetic cactuses
• Representations of partial leaf sets in phylogenetic tree space
• The isometry group of phylogenetic tree space is $S_n$
• Limiting behaviour of Fréchet means in the space of phylogenetic trees
• Uncertainty in Phylogenetic Tree Estimates
• Shortest paths and convex hulls in 2D complexes with non-positive curvature
• Maximum likelihood estimation of log-concave densities on tree space
• Level sets of depth measures in abstract spaces

Describes a project that uses

Uses Software

• kdetrees
• Clustal X

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