Description of research

This study seeks to determine the relationship of several indirect effects on arthropod herbivore density across 3 years in a common garden of Coastal Sage Scrub plants.

The metadata used for our analyses was collected annually in April-May for three consecutive years from 2021-2023 in a common garden at Concordia University Irvine. The common garden consisted of 13 species of woody shrubs native to the Coastal Sage Scrub ecosystem, arranged in 20 plots, each with 1 individual plant per species.

Data collected, abbreviations used and variable type assigned for the metadata can be found in the table below.

Data Description Column Name Variable Type
Plant # Individual plant Plant Factor
Plant Species Plant Species Species Factor
Plot Individual Plot Plot Factor
Year Year data collected Year Factor
Bird attack rate Bird attacks on clay caterpillars bird_attack Numeric
Herbivore count Total number of herbivores Abundance_Herb Numeric
Predator count Total number of predators Abundance_Pred Numeric

Methods

Clay caterpillars were deployed in 2022 and assessed for bird attacks weekly over a period of 4 weeks with one caterpillar on the interior and one on the exterior of each plant as described in Dean, et al., 2024. Arthropods were collected from plants using a vacuum method as previously described in Pratt et al. (2017), sorted from plant material, identified to taxonomic order and assigned to one of 5 feeding guilds: Herbivore, Predator, Omnivore, Detritovore, Playnivore.

1- Load packages and data tables

2- Among-species variation

We will first test whether species vary in Herbivore density as well as direct/indirect effects on herbivore density of interest: Predator density and clay caterpillar attack rates for birds. To do this, we will run a series of generalized linear mixed models for each response variable listed above with the main fixed effect of interest being Species. Additional fixed effects plus random effects will be added depending on main effect.

2.1- Herbivore density ~ Species

log(Herbivore count + 1) ~ Species + Year + (1|Plant) + (1|Plot)

2.2- Predator density ~ Species

NOTE Predator density relationship with herbivore count is curvilinear, therefore we ran the model with a polynomial assumption. Figure included in 3.3 for reference.

log(Predator count + 1) ~ Species + poly(log(Herbivore count + 1), 2) + Year + (1|Plant) + (1|Plot)

2.3- Caterpillar attack (Bird) ~ Species

Caterpillar attack (Bird only) ~ Species + Caterpillar position + (1|Plant) + (1|Plot) + (1|Caterpillar), family = binomial

3- Species means correlations of Herbivore density and indirect effects

We will create a correlation matrix to assess relationships between direct, indirect effects and herbivore density using species-level means.

NOTE Least square means were used for predator abundance to control for the effect of herbivore abundance included in the model

NOTE For variables transformed in the model (herbivore, predator and spodoptera) we report non-transformed means

3.1- Species means tables

Trait species means and p-values of species effect for each trait

Species Mean_herb lsMean_pred Mean_bird_attack
P-value (species effect) <0.001 <0.001 0.81
Acmispon_glaber 137.00 6.89 0.13
Artemisia_californica 76.61 6.55 0.17
Diplacus_aurantiacus 21.43 8.76 0.15
Encelia_californica 38.81 5.37 0.14
Eriogonum_fasciculatum 29.83 6.62 0.16
Grindelia_camporum 92.67 6.05 0.16
Isocoma_menziesii 54.63 10.38 0.20
Malacothamnus_fasciculatus 190.75 5.21 0.09
Malacothrix_saxatilis 14.56 5.00 0.09
Mirabilis_laevis 31.81 2.83 0.13
Salvia_apiana 142.13 4.95 0.15
Salvia_mellifera 89.18 5.81 0.13
Sisyrinchium_bellum 9.82 4.26 0.14

3.2- Correlation matrixes

We will now report p-values for correlation matrixes on untransformed species-level means to determine the strength of relationships between each variable.

NOTE All correlation coefficients are Pearson

P-values

Mean_herb lsMean_pred Mean_bird_attack
Mean_herb NA 0.9273587 0.4567026
lsMean_pred 0.9273587 NA 0.0265001
Mean_bird_attack 0.4567026 0.0265001 NA

Plot

3.3- Regression plots

Predator density ~ Herbivore density (all species, log-transformed)

lsMean Predator density ~ Mean Herbivore density

Bird attack ~ Herbivore density

Bird attack ~ Predator density

Appendix

A.1- Full stats for Among-species variation in Herbivores, Predators, Spodoptera and Caterpillar attack

Among-species variation in Herbivores, Predators, Spodoptera and Caterpillar attack
Response Fixef Ranef P.value
Arth_tot_density Species Plant,plot <0.001
Arth_tot_density Year Plant,plot <0.001
Herb_density Species Plant,plot <0.001
Herb_density Year Plant,plot <0.001
Pred_density Species Plant,plot <0.001
Pred_density Herb_density Plant,plot <0.001
Pred_density Year Plant,plot <0.001
Pred_ratio Species Plant, plot <0.001
Pred_ratio Year Plant,plot <0.001
Spod_growth Species Plant,plot <0.001
Spod_growth Year Plant,plot <0.001
Bird_attack Species Plant,plot,cat_id 0.81
Bird_attack cat_position Plant,plot,cat_id <0.001
Vertebrate_attack Species Plant,plot,cat_id 0.45
Vertebrate_attack cat_position Plant,plot,cat_id <0.001
Arthropod_attack Species Plant,plot,cat_id <0.001
Arthropod_attack cat_position Plant,plot,cat_id <0.05
total_attack Species Plant,plot,cat_id <0.05
total_attack cat_position Plant,plot,cat_id <0.01
Pratt, Jessica D., Andrew Datu, Thi Tran, Daniel C. Sheng, and Kailen A. Mooney. 2017. “Genetically Based Latitudinal Clines in Artemisia Californica Drive Parallel Clines in Arthropod Communities.” Ecology 98 (1): 79–91. https://doi.org/10.1002/ecy.1620.