Phylogenetic effective sample size

TL;DR

This paper introduces a new way to measure the effective number of independent samples in phylogenetic studies, using concepts like regression and mutual information, to improve biodiversity analysis and model selection.

Contribution

It proposes novel definitions of phylogenetic effective sample size for Brownian motion and Ornstein-Uhlenbeck processes, and compares them with existing concepts.

Findings

AICc remains robust when corrected for effective sample size.

Mutual information can define effective sample size in non-normal processes.

The concept aids biodiversity quantification and phylogenetic correlation assessment.

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.