Data and code from: Phylogenetic patterns of tolerance to herbivory and underlying suite of traits: Phylogenetic signal and trade-offs
Data files
Sep 17, 2026 version files 28.60 KB
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phylo_tolerance.zip
23.08 KB
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README.md
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Abstract
When herbivory is inevitable, plants can cope with it through tolerance, buffering its negative effects on plant fitness. Macroevolutionary patterns of tolerance to herbivory may improve our understanding about its evolution. Here, we explore the phylogenetic patterns of tolerance to herbivory and underlying functional traits, as well as the potential evolutionary constraints in the forms of fitness costs and a trade-off with resistance across the genus Datura. We performed a common garden experiment with simulated herbivory (defoliation) and analyzed data within a phylogenetic comparative explicit framework. Significant phylogenetic signal was detected only for certain tolerance underlying traits: specific leaf area and chlorophyll content, but no overall phylogenetic signal for tolerance was observed. No trade-off between tolerance and resistance was detected, although a negative relationship between tolerance and plant fitness in the absence of damage was found. Our results provide evidence for an absence of correspondence between phylogeny and interspecific plant defense variation, even though some underlying traits were influenced by phylogeny. We propose that the relationship between resistance and tolerance can arise as complementary defenses to variable herbivory pressures mediated by plants’ internal resource allocation, while the cost of tolerance may imply a trade-off with growth or reproductive potential.
Authors: Franco Liñán-Vigo and Juan Núñez-Farfán
Correspondence: Juan Núñez-Farfán; [farfan@unam.mx]
Franco Liñán-Vigo; [f.linanvigo@gmail.com]
Dataset DOI: 10.5061/dryad.xpnvx0kxv
Description of the data
This dataset corresponds to measurements of functional traits and tolerance to herbivory in a common garden experiment where we grew ten Datura (Solanaceae) species.
When plants reached a reproductive stage were randomly allocated to one of two treatments: control and damage. For the control treatment we left plants undamaged. For the damage treatment, we simulated leaf damage (in the pattern and timing of true herbivores). Tolerance is the change in fitness (measured as number of seeds) in response to leaf damage (in log scale).
Functional traits were measured at the harvest date (thirty days after the allocation to one of the two treatments).
For more methodological details, please check the material and methods section of the manuscript.
File structure
The compressed file (phylo_tolerance.zip) contains two folders:
(1) The folder data contains a three files:
- daturadat.csv: this file contains the functional traits for ten species of Datura that grew in a common garden setting.
- resistdat.csv: this file contains data on resistance traits only for the ten species of Datura included in this study. The complete dataset can be found in Kariñho-Betancourt et al. 2015 New Phyt.
- tree10daturas.tre: a pruned phylogenetic tree from the MCC tree of the Datureae tribe from Dupin and Smith 2018 TAXON.
Dupin, J. and Smith, S.D. (2018), Phylogenetics of Datureae (Solanaceae), including description of the new genus Trompettia and re–circumscription of the tribe. Taxon, 67: 359-375. https://doi.org/10.12705/672.6
Kariñho-Betancourt, E., Agrawal, A.A., Halitschke, R. and Núñez-Farfán, J. (2015), Phylogenetic correlations among chemical and physical plant defenses change with ontogeny. New Phytol, 206: 796-806. https://doi.org/10.1111/nph.13300
(2) The folder scripts contains two files:
- analysis.R: the scripts for all the analyses mentioned in the manuscript.
- custom_functions.R: script for supporting plotting functions.
Variables
The following variables are included in the daturadat.csv file:
- plant_id: nominal, individual identifier of the plant.
- family: nominal, maternal line to which each plant belongs.
- spp: nominal, The species to which the plant belongs.
- treatment: nominal. At the reproductive stage plants were randomly allocated to one of these two treatments:
control: The plant did not receive damage.
damage: Forty percent of the standing leaf area was removed. - area0: numeric continuous.
The estimated leaf area for each plant at the reproductive stage.
Units: cm2 - n.leaves0: numeric discrete. The number of fully expanded leaves of each plant.
- fitness: numeric discrete. The total seed output of each plant after thirty days of allocation to one of the treatments.
Units: seeds per plant - area: numeric continuous. The standing leaf area at the harvest date, thirty days after allocation to treatments.
Units: cm2 - n.leaves: numeric discrete. The number of fully expanded leaves of each plant at the harvest date.
- leaf.mass: numeric continuous. Dry mass of standing leaves and petioles at the harvest day.
Units: g - stem.mass: numeric continuous. Dry mass of stems at the harvest date.
Units: g - root.mass: numeric continuous. Dry mass of roots at the harvest date.
Units: g - biomass: numeric continuous. Dry mass of the whole vegetative parts.
It is the result of the sum of the three previous variables.
Units: g - CCI: numeric continuous. Measured with a chlorophyll meter CCM 200 Opti-Science.
The content of chlorophyll was measured in four fully expanded leaves as chlorophyll content index.
The value for each plant represents the mean value of the four measurements. - SLA: numeric continuous. Specific leaf area measured as the area of the leaf divided by its dry mass.
It was measured for four fully expanded leaves (the same leaves as for CCI).
A mean value was obtained for each plant.
Units: cm2·g-1 - lmf: numeric proportion. Leaf mass fraction, result of dividing leaf.mass over biomass.
Units: g of leaves/gram of plant. It can be considered unitless. - smf: numeric proportion. Stem mass fraction, result of dividing stem.mass over biomass.
Units: g of stems/gram of plant. It can be considered unitless. - rmf: numeric proportion. Root mass fraction, result of dividing root.mass over biomass.
Units: g of roots/gram of plant. It can be considered unitless.
The following variables are included in the resistdat.csv file:
- spp: nominal. The species to which the plant belongs.
- hyoscyamineR: numeric continuous. Mean species value of hyoscyamine leaf content at reproductive stage.
Units: µg·g-1 of leaf dry mass. - scopolamineR: numeric continuous. Mean species value of scopolamine leaf content at reproductive stage.
Units: µg·g-1 of leaf dry mass. - trichomesR: numeric continuous. Mean species value of leaf trichome density at reproductive stage.
Units: number of trichomes·cm-2
