DOI: 10.5061/dryad.7hb5c59
title: Data from: Independent evolution of ancestral and novel defenses in a genus of toxic plants (Erysimum, Brassicaceae)

description: Phytochemical diversity is thought to result from coevolutionary cycles as
 specialization in herbivores imposes diversifying selection on plant
 chemical defenses. Plants in the speciose genus Erysimum (Brassicaceae)
 produce both ancestral glucosinolates and evolutionarily novel
 cardenolides as defenses. Here we test macroevolutionary hypotheses on
 co-expression, co-regulation, and diversification of these potentially
 redundant defenses across this genus. We sequenced and assembled the
 genome of E. cheiranthoides and foliar transcriptomes of 47 additional
 Erysimum species to construct a phylogeny from 9,869 orthologous genes,
 revealing several geographic clades but also high levels of gene
 discordance. Concentrations, inducibility, and diversity of the two
 defenses varied independently among species, with no evidence for
 trade-offs. Closely related, geographically co-occurring species shared
 similar cardenolide traits, but not glucosinolate traits, likely as a
 result of specific selective pressures acting on each defense. Ancestral
 and novel chemical defenses in Erysimum thus appear to provide
 complementary rather than redundant functions.
description: 1_Data_Glucosinolate_MSdata     2_Data_Cardenolide_MSdata     3_Data_NaK-ATPase_Assay     4_Data_Myrosinase_Activtiy     5_Data_Geographic_DistanceMatrix Geographic distance matrix containing pairwise distances [km] between sampling locations of 43 Erysimum species   Erysimum_ExaML_dated.tre Dated, ultrametric ExaML tree file of 48 Erysimum species with Arabidopsis thaliana (ATH) as outgroup. Tree was constructed from 9868 orthologous genes using a genome-guided phylo-transcriptomics pipeline.   1_Rcode_Glucosinolate_MSdata Averaging of glucosinolate MS data, clustering analysis, test for phylogenetic signal in phytochemical similarity   2_Rcode_Cardenolide MSdata Averaging of cardenolide MS data, clustering analysis, test for phylogenetic signal in phytochemical similarity   3_Rcode_NaK-ATPase_Assay Fitting of sigmoid dose-response curves for Na+/K+-ATPase inhibition, estimation of cardenolide concentrations in Erysimum extracts.   4_Rcode_Myrosinase_Activity Averaging of myrosinase activity, test for phylogenetic signal, test for effects of glucosinolate concentration and glucosinolate chemotype on activity.   5_Rcode_Phylogenetic analysis Tests for phylogenetic signal in plant traits (Blomberg's K), mantel tests between phytochemical and phylogenetic similarity, PGLS analyses of trait correlations, and tip-rate correlation.   <strong>6_Code_Phylogeny_Construction</strong>   Code for transcriptome annotation, gene tree construction and cleaning, concatenating, dating, and hybridization analysis.   <strong>6_Data_HyDE_output.txt</strong>   Full list of hybridization tests performed by HyDe. Column 'Significance_corrected' highlights tests significant after Bonferroni correction (s.Bonferroni) or non-significant (n.s.).   <strong>MEGA_alignments_glucosinolate_trees.zip</strong>   Zipped file of MEGA alignment files for all glucosinolate-related gene trees presented in the paper.   <br>