Phylogenetic effective sample size

DOI10.1016/J.JTBI.2016.06.026zbMATH Open1344.92115arXiv1507.07113OpenAlexW1779341151WikidataQ36061518 ScholiaQ36061518MaRDI QIDQ309246FDOQ309246

Authors: Krzysztof Bartoszek 

Publication date: 7 September 2016

Published in: Journal of Theoretical Biology (Search for Journal in Brave)

Abstract: In this paper I address the question - how large is a phylogenetic sample I propose a definition of a phylogenetic effective sample size for Brownian motion and Ornstein-Uhlenbeck processes - the regression effective sample size. I discuss how mutual information can be used to define an effective sample size in the non-normal process case and compare these two definitions to an already present concept of effective sample size (the mean effective sample size). Through a simulation study I find that the AICc is robust if one corrects for the number of species or effective number of species. Lastly I discuss how the concept of the phylogenetic effective sample size can be useful for biodiversity quantification, identification of interesting clades and deciding on the importance of phylogenetic correlations.

Full work available at URL: https://arxiv.org/abs/1507.07113

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zbMATH Keywords

measurement errorbiodiversityOrnstein-Uhlenbeck processeffective sample sizephylogenetic comparative methodsquantitative trait evolution

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) General biostatistics (92B15) Problems related to evolution (92D15)

Cites Work

• A phylogenetic comparative method for studying multivariate adaptation
• Estimating the dimension of a model
• Regression and time series model selection in small samples
• A new look at the statistical model identification
• On incomplete sampling under birth-death models and connections to the sampling-based coalescent
• The conditioned reconstructed process
• Quantifying the effects of anagenetic and cladogenetic evolution
• Interspecies correlation for neutrally evolving traits
• Distribution of branch lengths and phylogenetic diversity under homogeneous speciation models
• New analytic results for speciation times in neutral models
• Analysis of comparative data with hierarchical autocorrelation
• On the distribution of interspecies correlation for Markov models of character evolution on Yule trees
• CLT for Ornstein-Uhlenbeck branching particle system
• Measuring diversity from dissimilarities with Rao's quadratic entropy: are any dissimilarities suitable?
• Phylogenetic confidence intervals for the optimal trait value
• A consistent estimator of the evolutionary rate
• Analysis of phylogenetics and evolution with R
• Information conversion, effective samples, and parameter size
• Title not available (Why is that?)
• \(U\)-statistics of Ornstein-Uhlenbeck branching particle system
• The effective sample size and an alternative small-sample degrees-of-freedom method
• Analysis of Multivariate and High-Dimensional Data

Cited In (3)

• Interspecies correlation for neutrally evolving traits
• The phylogenetic effective sample size and jumps
• Analysis of comparative data with hierarchical autocorrelation

Uses Software

• R
• ade4
• mvMORPH

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