Confidence Sets for Phylogenetic Trees

DOI10.1080/01621459.2017.1395342zbMATH Open1462.62693arXiv1607.08288OpenAlexW2962715551MaRDI QIDQ5229907FDOQ5229907

Authors: Amy Willis 

Publication date: 19 August 2019

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

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.

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

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

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)

Cites Work

• Geometry of the space of phylogenetic trees
• Polyhedral computational geometry for averaging metric phylogenetic trees
• Title not available (Why is that?)
• Statistical Inference of Phylogenies
• Title not available (Why is that?)
• Title not available (Why is that?)
• Computing medians and means in Hadamard spaces
• Sticky central limit theorems on open books
• Statistical approach to tests involving phylogenies
• Principal components analysis in the space of phylogenetic trees
• Statistics for phylogenetic trees
• Applied Multivariate Analysis
• A generalization of the Wishart distribution for the elliptical model and its moments for the multivariate t model
• Bootstrapping phylogenetic trees: theory and methods
• Consistency of a phylogenetic tree maximum likelihood estimator
• Limiting behaviour of Fréchet means in the space of phylogenetic trees
• Tree-oriented analysis of brain artery structure

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
• Maximum likelihood estimation of log-concave densities on tree space
• Shortest paths and convex hulls in 2D complexes with non-positive curvature
• Level sets of depth measures in abstract spaces

Uses Software

• Clustal X
• kdetrees

This page was built for publication: Confidence Sets for Phylogenetic Trees

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q5229907)