DOI: 10.5061/dryad.k0p2ngfnq
title: Defense traits vary across leaf ages in the thistles (Cardueae)

description: Plants produce a variety of structural and chemical defenses to deter
 herbivores, which can covary across every scale of biological
 organization. Along these lines, it has been suggested that young leaves
 differ from old leaves in their defense strategies, but studies have
 largely focused on woody plants and/or chemical traits. Thus, we lack an
 understanding of how structural and chemical defenses ontogenetically
 covary across a large portion of plant diversity. We investigate the range
 of structural and chemical defenses of thistles (tribe Cardueae), which
 comprise herbaceous species with a wide spectrum of defensive traits. We
 collected structural and chemical trait data across species and leaf ages
 from field collections, herbarium specimens, and the literature. Species’
 young leaves tend to produce similar suites of traits, with greater
 interspecific variation in older leaves. Young leaves are dominated by
 chemical defenses, while older leaves produce a broader range of both
 chemical and physical defense traits. Leaf spininess is associated with a
 distinct chemical profile that differs from that of non-spiny species. Our
 study demonstrates how defense strategies can vary across the leaves of
 herbaceous species and their ages. Expanding such efforts will be critical
 to further our macroevolutionary understanding of variation in plant
 defenses.
description: # Defense traits vary across leaf ages in the thistles (Cardueae) Dataset
 DOI: [10.5061/dryad.k0p2ngfnq](https://doi.org/10.5061/dryad.k0p2ngfnq) ##
 Description of the data and file structure This dataset is associated with
 the manuscript, "Defense traits vary across leaf ages in the thistles
 (Cardueae)", published at Functional Ecology.  It includes the
 dataset used for analysis, including data on all of the traits evaluated
 for each individual plant. We collected data on both physical and chemical
 traits to evaluate how leaf defenses vary across individuals, populations,
 and species in the thistles (Cardueae). We focused on data from seven
 species collected in Indiana, and then supplemented that dataset with
 additional chemical data from 34 herbarium collections. ### Files and
 variables #### File: trait_data_with_counts.csv **Description:**  #####
 Variables * Species:  the species collected * Population:  population ID
 (associated with species) * Individual:  individual ID (must be combined
 with population and species to be unique) * Leaf_age:  divided into
 "young" (upper most fully expanded leaf below the reproductive
 inflorescence), "intermediate" (a leaf mid-way between the young
 and old leaves), and "old" (basal-most leaf that was largely
 undamaged) * trichome_density:  the number of trichomes counted per mm2;
 if trichome density was too high to count, we set this value at 50/mm2
 (centered and scaled) * SLA:  specific leaf area (centered and scaled) *
 ID:  the combined unique ID for each sample, combines species with
 population ID, individual ID, and leaf age * total_long_spines: the total
 number of spines &gt; 3mm in length (centered and scaled) *
 mean_spine_length: the mean length of spines &gt; 3mm in length (centered
 and scaled) * Leaf_length: total length of the leaf in cm *
 rel_spine_length: length of the longest spine/length of the leaf *
 alkaloids: count of number of molecules assigned to alkaloid pathway
 (centered and scaled) * flavonoids: count of number of molecules assigned
 to flavonoid pathway (centered and scaled) * terpenoids: count of number
 of molecules assigned to terpenoid pathway (centered and scaled) *
 phenols: count of number of molecules assigned to phenol pathway (centered
 and scaled) * Cap:  cap ID for mass spec analyses * Year:  year of sample
 collection * FuncHillDiv:  functional Hill diversity (centered and scaled)
 * features_present:  the total number of chemical features present per
 leaf (centered and scaled) * count_Alkaloids: raw total count of alkaloids
 * count_Flavonoids: raw total count of flavonoids * count_Phenols: raw
 total count of phenols * count_Terpenoids: raw total count of terpenoids
 ## Code/software R packages used: lmerTest ggfortify factoextra NbClust
 chemodiv ## Access information Other publicly accessible locations of the
 data: * none Data was derived from the following sources: * none