DOI: 10.5061/dryad.m5ct8
title: Data from: Keeping an eye on coloration: ecological correlates of the evolution of pitcher traits in the genus Nepenthes (Caryophyllales)

description: Nepenthes is a genus of carnivorous pitcher plants with high intra- and
 interspecific morphological diversity. Many species produce dimorphic
 pitchers, and the relative production rate of the two morphs varies
 interspecifically. Despite their likely ecological importance to the
 plants, little is known about the selective context under which various
 pitcher traits have evolved. This is especially true of color-related
 traits, which have not been examined in a phylogenetic context. Using
 field observations of one polymorphic species (N. gracilis) and
 phylogenetic comparative analysis of 85 species across the genus, we
 investigate correlations between color polymorphism and ecological factors
 including altitude, light environment, and herbivory. In N. gracilis,
 color does not correlate to amount of prey-capture, but red pitchers
 experience less herbivory. Throughout the genus, color polymorphism with
 redder lower pitchers appears to be evolutionarily favored. We found a
 lack of phylogenetic signal for most traits, either suggesting that most
 traits are labile or reflecting the uncertainty regarding the underlying
 tree topology. This work highlights ecological correlates of the vast
 phenotypic diversity of this group of tropical plants. We point to a need
 for future work examining herbivores of Nepenthes and experimental
 investigations on color polymorphism.
description: Nepenthes gracilis
 prey/symbiont capture dataData for Nepenthes
 gracilis pitchers sampled in Singapore in summer 2014, associated with
 Methods section 1.b "Assessment of insect accumulation rates in
 different pitcher variants", including metadata on the pitchers as
 well as the counts of arthropods from the initially emptied fluid and the
 fluid collected one month later (this collection date designated by a
 '2' in the name of the variable in the column
 header).pitcherdata.csvCanopy dataData associated with assessment of relationship between pitcher color and canopy coverage, from January 2014 survey of Nepenthes gracilis in Kent Ridge Park, Singapore.Canopy.csvHerbivory dataData associated with assessment of relationship between pitcher color and herbivory, from January 2016 survey of Nepenthes gracilis in Kent Ridge Park, Singapore.HerbivoryLogit.csvCharacter matrixCharacter matrix of 89 taxa (including two outgroups) used for comparative phylogenetic methods described in Methods section 2; this additionally contains some data (peristome width, peristome slope, and wax coverage) taken from Bauer et al. (2012).BauerData (final submission).csvBEAST tree without ITSPhylogenetic tree inferred by BEAST using trnK and PTR1 genes for 85 Nepenthes species and two outgroups (Ancistrocladus abbreviatus and Triphyophyllum peltatum), used in phylogenetic comparative analyses.BEAST_tree (resubmission).nwkBEAST tree with ITSPhylogenetic tree inferred by BEAST using trnK, PTR1, and ITS genes for 85 Nepenthes species and two outgroups (Ancistrocladus abbreviatus and Triphyophyllum peltatum)--not used in phylogenetic comparative analyses appearing in the manuscript.NepITSburninTree.nwkBEAST tree (no ITS), annotatedPhylogenetic tree inferred with BEAST using trnK and PTR1 genes for 85 Nepenthes species and 2 outgroups (Ancistrocladus abreviatus and Triphyophyllum peltatum), annotated in TreeAnnotator to include posterior probabilities.Reannotated_Neptree_nonITSAncestral state reconstructionR script for conducting ancestral state reconstructions on the data.anc_states.RTests of correlated evolutionR script for conducting tests of correlated evolution on the data; includes Pagel's (1994) test and binary phylogenetic generalized linear mixed model (binary PGLMM).correlated_evo.RCount transitions between character statesR script for conducting stochastic character mapping (SIMMAP) on data to count transitions between character states, used in analysis of color polymorphism trait (three states: "similar coloration", "redder lowers", and "redder uppers").count_transitions.RCalculate correlations between morphological traits and altitudeR script for conducting phylogenetic generalized least squares (pgls) between continuous morphological traits and altitude or other continuous traits, as well as for utilizing brunch package to assess correlations between binary (primarily color-related) traits and altitude.pgls_and_brunch.RMap traits onto phylogenyR script for mapping quantitative or qualitative traits onto the Nepenthes phylogeny.map_traits.RConduct PCAR script for conducting principal components analysis (PCA), either a standard PCA or a phylogenetic PCA on continuous trait data to assess differences between altitude classes or pitcher diet (not discussed in manuscript).PCA.RAnalyze phylogenetic signal in traitsR script for conducting tests of phylogenetic signal for both continuous (using Blomberg's K and Pagel's lambda) and binary traits (Fritz and Purvis's D).phylosig.Rmy_funcsSupporting functions for R scripts associated with phylogenetic comparative analyses.my_themesSupporting script used for R scripts associated with phylogenetic comparative analyses.