Computational protocol: The Influence of Photoreceptor Size and Distribution on Optical Sensitivity in the Eyes of Lanternfishes (Myctophidae)

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Protocol publication

[…] The phylogenetic signal for continuous and discrete traits was estimated with Pagel's lambda (λ) using the package GEIGER in R . Pagel's λ is a measure of the degree of phylogenetic dependence in the data , meaning to which degree closely related species are more similar to each other than what is expected by random evolutionary processes. Pagel's λ varies from 0 to 1, with λ value of 1 indicating that traits gradually accumulate changes over time in a Brownian motion process (i.e. random change in any direction) and λ values of 0 indicating that no phylogenetic signal is present and that traits have evolved in response to selective processes. The observed λ value for each trait was compared to λ values of zero and one using likelihood ratio tests with df = 1. [...] The relationships between each of the morphological traits (eye size, photoreceptor size) and the relationships between the morphological and ecological traits (luminous organs, depth distribution) were all assessed using phylogenetic generalised least squares regressions (PGLS, ) with the package APE in R . PGLS regressions estimate a phylogenetic scaling parameter, λ, using maximum likelihood methods to determine the degree of covariance in the residuals of the model, while controlling for phylogenetic effects. This approach also examines whether the scaling parameter λ significantly differs from 0 or 1 using likelihood ratio tests, where λ = 0 indicates no phylogenetic dependence in the data and λ = 1 indicates strong phylogenetic association in the data , . PGLS models were first used to assess relationships between eye size and photoreceptor traits (rod diameter, outer and inner segment length). Since eye diameter is strongly correlated with standard length within the family , standard length was added as a covariate in all analyses. Finally, phylogenetically controlled multiple regression models were used to assess if photoreceptor length and diameter were related with various ecological parameters when correcting for the effect of eye size and standard length. Since all PGLS results were similar between phylogenies, only the results obtained with phylogeny A are presented throughout. […]

Pipeline specifications

Software tools PHYSIG, GEIGER, APE
Application Phylogenetics
Organisms Neoscopelus microchir, Ilex paraguariensis