A unified method for detecting phylogenetic signals in continuous traits, discrete traits, and multi-trait combinations (Yao and Yuan 2024 submitted to Ecology Letters)
Study Overview
Phylogenetic signals are widely used in the ecological and evolutionary research area. Trait data used to detect phylogenetic signals can be continuous or discrete. Existing indices are either designed for continuous variables or for discrete variables, but not both. Moreover, most existing methods could only perform phylogenetic detection for each trait separately. Here, we developed a method, called M statistic, to detect the phylogenetic signals in continuous traits, discrete traits, and combinations of multiple traits. We compared the performance of our new approach with existing commonly used indices using simulated continuous data. The results showed that our method is not inferior to the existing methods. It also performed well in handling discrete variables and multi-variable combinations. Then we used the trait data of turtles (Testudines) to demonstrate the utility of our new method. We provided an R package called “phylosignalDB” to facilitate all calculations.
Description of the Data and Code File
"README.txt" - The summary file.
Plot Figure 1-4
"Plot.R" - R code for ploting figure 1-4.
Case Study for Turtles
"ecological trait dataset for turtles.xlsx" - ecological trait dataset for turtles.
"turtle_signals.R" - R code for detecting phylogenetic signals in ecological traits of turtles.
Simulation Study
"Simulation.R" - R code for simulation study.
"sim_signals.rds" - result dataset of simulation study.
Notes
The code for the M statistics has been written as the R package phylosignalDB. The package is available on GitHub: https://github.com/Dylan-Yao/phylosignalDB.
We used the maximum clade credibility tree with 288 tips provided in Thomson et al. (2021) for the phylogeny of turtles. The phylogeny file "bd.mcc.median_heights.tre" can be obtained from Thomson et al. (2021).
Thomson, R.C., Spinks, P.Q. & Shaffer, H.B. (2021) A global phylogeny of turtles reveals a burst of climate-associated diversification on continental margins. Proceedings of the National Academy of Sciences, 118(7): e2012215118.
