DOI: 10.5061/dryad.96qr7n2
title: Data from: Non-uniform evolutionary response of gecko eye size to changes in diel activity patterns

description: Geckos feature a large range of eye sizes, but what drives this phenotypic
 diversity is currently unknown. Earlier studies point towards diel
 activity patterns (DAP) and locomotory mode, but phylogenetic comparative
 studies in support of the proposed adaptive mode of eye evolution are
 lacking. Here we test the hypothesis of DAP as the driver of eye size
 evolution with a dataset on 99 species of gecko. Results from phylogenetic
 generalized least square analysis (PGLS) and multivariate model-fitting
 reveal smaller eyes in diurnal geckos consistent with different phenotypic
 optima. However, Bayesian analyses of selective regime shifts demonstrate
 that only 2 of 9 transitions from nocturnal to diurnal activity are
 coupled with decreases in eye size, and 2 other regime shifts are not
 associated with DAP transitions. This non-uniform evolutionary response
 suggests that eye size is not the only functionally relevant variable.
 Evolutionary adaptations may therefore include different combinations of
 several traits (e.g., photoreceptors), all with the same functional
 outcome. Our results further demonstrate that DAP only partially explains
 eye size diversity in geckos. As open habitats favor the evolution of
 large eyes while obstructed habitats favor small eyes, the degree of
 habitat clutter emerges as another potential axis of eye diversification.
description: README
 FIRSTImportant information
 about required packages and directory structure. Must read before
 downloading other files and executing R script._README.txtR scripts for phylogenetic comparative analysisThis R file contains the complete set of scripts to repeat all analyses that we performed and re-create all figures, plus some additional diagnostic and exploratory plots mentioned in the text. Please consult the README file before executing the script, and be aware that the bayou and mvMORPH anlyses will run for several hours.geckoEyes.RTime-calibrated phylogeny of geckos require for comparative analysisThis Newick tree file is from the following source: Zheng Y, Wiens JJ. 2016 Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species. Molecular Phylogenetics and Evolution 94, 537–547. (doi:10.1016/j.ympev.2015.10.009)wiens.time.treData on gecko body size, eye size, and diel activity patternThis csv file contains data for 99 species of gecko, specifically: 1) snout-vent length in mm as proxy for body size, 2) antero-posterior diameter of the eye in mm as proxy for eyeball diameter, and 3) discretized information on diel activity pattern (grouped into three categories (cathemeral/crepuscular, diurnal, nocturnal). Please make sure to preserve the file extension when saving the file.tableS1.csvExtensive dataset on diel activity patterns of geckosThis csv file contains data on diel activity pattern for 254 species of gecko. We combined our own data with information from Gamble T, Greenbaum E, Jackman TR, Bauer AM. 2015 Into the light: diurnality has evolved multiple times in geckos. Biological Journal of the Linnean Society 115, 896–910. (doi:10.1111/bij.12536). Please make sure to preserve the file extension when saving the file.tableS2.csv