A comparison of metrics for estimating phylogenetic signal under alternative evolutionary models

Thiago Fernando Rangel,Thiago Santos,José Alexandre F Diniz-Filho,Luis Mauricio Bini

doi:10.1590/s1415-47572012005000053

Thiago Fernando Rangel, Thiago Santos + Show 2 more

Open Access

https://doi.org/10.1590/s1415-47572012005000053

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Abstract

Several metrics have been developed for estimating phylogenetic signal in comparative data. These may be important both in guiding future studies on correlated evolution and for inferring broad-scale evolutionary and ecological processes (e.g., phylogenetic niche conservatism). Notwithstanding, the validity of some of these metrics is under debate, especially after the development of more sophisticated model-based approaches that estimate departure from particular evolutionary models (i.e., Brownian motion). Here, two of these model-based metrics (Blomberg’s K-statistics and Pagel’s λ) are compared with three statistical approaches [Moran’s I autocorrelation coefficient, coefficients of determination from the autoregressive method (ARM), and phylogenetic eigenvector regression (PVR)]. Based on simulations of a trait evolving under Brownian motion for a phylogeny with 209 species, we showed that all metrics are strongly, although non-linearly, correlated to each other. Our analyses revealed that statistical approaches provide valid results and may be still particularly useful when detailed phylogenies are unavailable or when trait variation among species is difficult to describe by more standard Brownian or O-U evolutionary models.

Highlights

Phylogenetic signal was defined by Blomberg and Garland (2002) “...as a tendency for related species to resemble each other more than they resemble species drawn at random from a tree”
Pagel’s l was equal to 1.0 in 97% of the simulations performed, revealing high statistical power and ability to correctly detect Brownian motion. This metric was not sensitive to stochastic variation in species values generated under Brownian motion and disturbing the magnitude of phylogenetic signals, being not correlated with the other metrics
Our analyses show that all metrics for estimating phylogenetic signal in quantitative traits are strongly, albeit among estimates of phylogenetic signals, when using different metrics, such as R2 from phylogenetic eigenvector regression (PVR) and autoregressive method (ARM), Moran’s I autocorrelation coefficient, Moran’s I for the first distance class (MORAN(1) and Blomberg’s K statistics, at log-scale

Summary

Introduction

Phylogenetic signal was defined by Blomberg and Garland (2002) “...as a tendency for related species to resemble each other more than they resemble species drawn at random from a tree”. One initial motivation for estimating phylogenetic signal was to establish which (in any) correction must be made to take the phylogenetic relationships among species into account (see Martins and Garland 1991; Martins et al, 2002). In addition to this methodological issue, there has been a growing interest on how phylogenetic signal can be used to infer broad-scale evolutionary and ecological processes (Martins, 2000; Diniz-Filho, 2001; Cooper et al.2010; Hof et al, 2010; and see Revell et al, 2008; Losos, 2008). Negative phylogenetic autocorrelations (i.e., when close relatives are more different in a given trait than randomly chosen pairs of taxa), not so common, may arise due to recent events of evolutionary divergence induced by character displacement

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