Data from: Keeping an eye on coloration: ecological correlates of the evolution of pitcher traits in the genus Nepenthes (Caryophyllales)

Gilbert KJ, Nitta JH, Talavera G, Pierce NE

Date Published: November 21, 2017

DOI: https://doi.org/10.5061/dryad.m5ct8

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Title Nepenthes gracilis prey/symbiont capture data
Downloaded 3 times
Description Data 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).
Download pitcherdata.csv (10.97 Kb)
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Title Canopy data
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Description Data associated with assessment of relationship between pitcher color and canopy coverage, from January 2014 survey of Nepenthes gracilis in Kent Ridge Park, Singapore.
Download Canopy.csv (381 bytes)
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Title Herbivory data
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Description Data associated with assessment of relationship between pitcher color and herbivory, from January 2016 survey of Nepenthes gracilis in Kent Ridge Park, Singapore.
Download HerbivoryLogit.csv (13.20 Kb)
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Title Character matrix
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Description Character 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).
Download BauerData (final submission).csv (15.73 Kb)
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Title BEAST tree without ITS
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Description Phylogenetic 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.
Download BEAST_tree (resubmission).nwk (3.465 Kb)
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Title BEAST tree with ITS
Downloaded 4 times
Description Phylogenetic 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.
Download NepITSburninTree.nwk (5.74 Kb)
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Title BEAST tree (no ITS), annotated
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Description Phylogenetic 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.
Download Reannotated_Neptree_nonITS (70.71 Kb)
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Title Ancestral state reconstruction
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Description R script for conducting ancestral state reconstructions on the data.
Download anc_states.R (2.936 Kb)
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Title Tests of correlated evolution
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Description R script for conducting tests of correlated evolution on the data; includes Pagel's (1994) test and binary phylogenetic generalized linear mixed model (binary PGLMM).
Download correlated_evo.R (6.866 Kb)
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Title Count transitions between character states
Downloaded 5 times
Description R 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").
Download count_transitions.R (3.031 Kb)
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Title Calculate correlations between morphological traits and altitude
Downloaded 3 times
Description R 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.
Download pgls_and_brunch.R (2.141 Kb)
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Title Map traits onto phylogeny
Downloaded 2 times
Description R script for mapping quantitative or qualitative traits onto the Nepenthes phylogeny.
Download map_traits.R (8.536 Kb)
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Title Conduct PCA
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Description R 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).
Download PCA.R (10.25 Kb)
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Title Analyze phylogenetic signal in traits
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Description R 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).
Download phylosig.R (7.185 Kb)
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Title my_funcs
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Description Supporting functions for R scripts associated with phylogenetic comparative analyses.
Download my_funcs.R (27.82 Kb)
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Title my_themes
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Description Supporting script used for R scripts associated with phylogenetic comparative analyses.
Download my_themes.R (2.283 Kb)
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When using this data, please cite the original publication:

Gilbert KJ, Nitta JH, Talavera G, Pierce NE (2017) Keeping an eye on coloration: ecological correlates of the evolution of pitcher traits in the genus Nepenthes (Caryophyllales). Biological Journal of the Linnean Society 123(2): 321-337. https://doi.org/10.1093/biolinnean/blx142

Additionally, please cite the Dryad data package:

Gilbert KJ, Nitta JH, Talavera G, Pierce NE (2018) Data from: Keeping an eye on coloration: ecological correlates of the evolution of pitcher traits in the genus Nepenthes (Caryophyllales). Dryad Digital Repository. https://doi.org/10.5061/dryad.m5ct8
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