Computational protocol: Light matters: testing the “Light Environment Hypothesis” under intra‐ and interspecific contexts

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Protocol publication

[…] I examined the evolution of color signals using the phylogeny of the clade by Derryberry et al. (), which was based on sequencing of three mitochondrial genes and one nuclear intron (Derryberry et al. ). To test whether plumage evolution is influenced by ambient light, I compared three models of evolution for each color descriptor: a Brownian motion model (BM), an Ornstein–Uhlenbeck model (OU) with a single optimum, and an OU model with three selective regimes based on the amount of ambient light available at each habitat (low, intermediate, high). I then compared the models using the AIC criterion corrected for small sample size (AICc). When ΔAICc < 4, I used a likelihood ratio test to test for significant differences with simpler models; however, this could not be carried out when the less‐complex model had the lower AICc. In cases when ΔAICc < 2, I considered the simpler model as the best model, because the additional parameters do not explain enough variation to be included in the model (Arnold ). Finally, I estimated the respective parameters for the best‐fit model of each descriptor from 10,000 bootstrap replicates.I performed all analyses in R (R Development Core Team ) using the Pavo (Maia et al. ), Ape (Paradis et al. ), Geiger (Harmon et al. ), and Ouch (King and Butler ) libraries. […]

Pipeline specifications

Software tools pavo, APE, GEIGER
Applications Miscellaneous, Phylogenetics
Organisms Homo sapiens