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
Clay caterpillar attack rate Bird attacks on clay caterpillars bird_attack Numeric
S. exigua growth rate Average mass of S. exigua in mg Avg_spod_mass_mg Numeric
Herbivore count Total number of herbivores Abundance_Herb Numeric
Predator count Total number of predators Abundance_Pred Numeric

Methods

Spodoptera mass was collected after a 10-day laboratory feeding assay. Briefly, Spodoptera exigua, a generalist herbivore, were hatched from eggs and immediately fed leaves from each individual plant. At the end of 10 days, the number of surviving larvae and final mass of each larvae were recorded. See You, An, and Li (2020) for details. Clay caterpillars were deployed in 2022 and assessed for bird attacks each week 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

Clay caterpillar table

head(long_clay)
YearPlantSpecieslocationbird_attackcat_idPlot
20221Acmispon_glaberExterior011
20221Acmispon_glaberExterior011
20221Acmispon_glaberExterior11
20221Acmispon_glaberExterior011
20221Acmispon_glaberInterior021
20221Acmispon_glaberInterior021

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: S. exigua growth rate, predator density, clay caterpillar attack. To do this, we will run a series of generalized linear mixed models for each response variable listed above and main fixed effects being Species. Additional fixed effects plus random effects will be added depending on main effect.

2.1- Total arthropod density ~ Species

Year will be added as a fixed effect with Plant and Plot as random effects. The model used is:

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

2.2- Herbivore density ~ Species

Year will be added as a fixed effect with Plant and Plot as random effects. The model used is:

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

2.3.1- Predator density ~ Species

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

All species

Species by species

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

2.3.2- Predator:herbivore ratio ~ Species

log(Predator:Herbivore ratio) ~ Species + Year + (1|Plant) + (1|Plot))

2.4- Spodoptera growth rate ~ Species

log(Avg Spodoptera biomass) ~ Species + Year + (1|Plant) + (1|Plot)

2.4.1- Caterpillar attack (Bird only) ~ Species

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

2.4.2- Caterpillar attack (non-bird) ~ Species

Caterpillar attack (non-bird) ~ Species + Caterpillar position + (1|Plant) + (1|Plot) + (1|Caterpillar), family = binomial

2.4.3- Caterpillar attack (Total) ~ Species

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

2.5- Results

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
nonbird_attack Species Plant,plot,cat_id <0.001
nonbird_attack cat_position Plant,plot,cat_id 0.46
total_attack Species Plant,plot,cat_id <0.05
total_attack cat_position Plant,plot,cat_id <0.01

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 both non-transformed and log-transformed means + SE.

3.1- Species means tables

Transformed

Species-level means for log-transformed arthropod densities, log-transformed Spodoptera growth rates, and caterpillar attack rates
Species Mean_log_arthtot Mean_logherb lsMean_logpred Mean_log_predratio Mean_logspod Mean_bird_attack Mean_nonbird_attack Mean_tot_attack
Acmispon_glaber 3.653564 3.218808 1.93 -1.6090014 3.0854664 0.1333333 0.1777778 0.3111111
Artemisia_californica 4.626658 4.142166 1.88 -2.0938425 0.0950700 0.1741936 0.0709677 0.2451613
Diplacus_aurantiacus 3.740925 2.761536 2.17 -0.7124839 -1.0485532 0.1468532 0.1608392 0.3076923
Encelia_californica 3.681380 2.879265 1.68 -1.3244492 -0.1710167 0.1403509 0.0789474 0.2192982
Eriogonum_fasciculatum 3.743377 2.946644 1.89 -1.1680015 0.6585116 0.1551724 0.0862069 0.2413793
Grindelia_camporum 3.998855 3.652692 1.80 -2.0071538 1.4422856 0.1578947 0.0827068 0.2406015
Isocoma_menziesii 4.150024 3.537228 2.34 -1.2032468 -0.9869171 0.2000000 0.1043478 0.3043478
Malacothamnus_fasciculatus 5.077814 4.595207 1.65 -2.7636971 -0.0727702 0.0884956 0.1504425 0.2389381
Malacothrix_saxatilis 2.884375 2.016001 1.61 -0.7758746 0.1013485 0.0935252 0.0719424 0.1654676
Mirabilis_laevis 3.674488 2.713377 1.04 -1.8457312 0.2502837 0.1260504 0.0504202 0.1764706
Salvia_apiana 4.572842 4.097501 1.60 -2.4026636 0.1099108 0.1532258 0.1370968 0.2903226
Salvia_mellifera 4.063673 3.683271 1.76 -1.8893854 -0.4259525 0.1338583 0.2519685 0.3858268
Sisyrinchium_bellum 2.246985 1.479547 1.45 -0.5702608 -1.1365932 0.1369863 0.0958904 0.2328767

Untransformed

Untransformed species-level means for arthropod densities, Spodoptera growth rate and caterpillar attack rates
Species Mean_totarth Mean_herb lsMean_pred Mean_pred_ratio Mean_spod Mean_bird_attack Mean_nonbird_attack Mean_tot_attack
Acmispon_glaber 150.44444 137.000000 6.889510 0.4513524 34.1545455 0.1333333 0.1777778 0.3111111
Artemisia_californica 133.08475 76.610169 6.553505 0.1866512 1.6357692 0.1741936 0.0709677 0.2451613
Diplacus_aurantiacus 50.80357 21.428571 8.758284 0.7720872 0.5826087 0.1468532 0.1608392 0.3076923
Encelia_californica 69.15094 38.811321 5.365556 0.6598656 1.9954545 0.1403509 0.0789474 0.2192982
Eriogonum_fasciculatum 61.17391 29.826087 6.619369 0.4667163 11.9970000 0.1551724 0.0862069 0.2413793
Grindelia_camporum 107.40741 92.666667 6.049647 0.3004549 4.6794444 0.1578947 0.0827068 0.2406015
Isocoma_menziesii 85.30233 54.627907 10.381237 0.5913882 1.0812500 0.2000000 0.1043478 0.3043478
Malacothamnus_fasciculatus 237.95000 190.750000 5.206980 0.1710104 3.2444444 0.0884956 0.1504425 0.2389381
Malacothrix_saxatilis 28.64103 14.564103 5.002811 0.7379180 2.6064706 0.0935252 0.0719424 0.1654676
Mirabilis_laevis 62.27778 31.814815 2.829217 0.2870965 4.1636364 0.1260504 0.0504202 0.1764706
Salvia_apiana 162.62500 142.125000 4.953032 0.4341741 6.0601010 0.1532258 0.1370968 0.2903226
Salvia_mellifera 108.28000 89.180000 5.812437 0.2254128 2.6283333 0.1338583 0.2519685 0.3858268
Sisyrinchium_bellum 17.05128 9.820513 4.263115 0.8953910 0.5353333 0.1369863 0.0958904 0.2328767

3.2- Correlation matrixes

We will now create correlation matrixes on both the transformed and untransformed species-level means to determine the strength of relationships between each variable.

NOTE All correlation coefficients are Pearson

Untransformed means

Mean_totarth Mean_herb lsMean_pred Mean_pred_ratio Mean_spod Mean_bird_attack Mean_nonbird_attack Mean_tot_attack
Mean_totarth 1.0000000 0.9752149 0.0131714 -0.7196914 0.2779108 -0.1410309 0.3893428 0.2955927
Mean_herb 0.9752149 1.0000000 -0.0282993 -0.6528801 0.3655877 -0.1886470 0.4664402 0.3443757
lsMean_pred 0.0131714 -0.0282993 1.0000000 0.1720340 0.0665812 0.6226748 0.2437314 0.5371064
Mean_pred_ratio -0.7196914 -0.6528801 0.1720340 1.0000000 -0.1275691 0.0223715 -0.1870783 -0.1645103
Mean_spod 0.2779108 0.3655877 0.0665812 -0.1275691 1.0000000 -0.0730947 0.2605272 0.2083300
Mean_bird_attack -0.1410309 -0.1886470 0.6226748 0.0223715 -0.0730947 1.0000000 -0.1357126 0.3678163
Mean_nonbird_attack 0.3893428 0.4664402 0.2437314 -0.1870783 0.2605272 -0.1357126 1.0000000 0.8713780
Mean_tot_attack 0.2955927 0.3443757 0.5371064 -0.1645103 0.2083300 0.3678163 0.8713780 1.0000000

Transformed

Mean_log_arthtot Mean_logherb lsMean_logpred mean_log_predratio Mean_logspod Mean_bird_attack Mean_nonbird_attack Mean_tot_attack
Mean_log_arthtot 1.0000000 0.9760085 0.2519501 -0.8411371 0.1034415 0.1655057 0.2463326 0.3131610
Mean_logherb 0.9760085 1.0000000 0.2688026 -0.8778528 0.1937696 0.1839687 0.3230519 0.3943111
lsMean_logpred 0.2519501 0.2688026 1.0000000 0.2081021 -0.0342749 0.5639223 0.3094026 0.5696503
mean_log_predratio -0.8411371 -0.8778528 0.2081021 1.0000000 -0.3085769 0.1031407 -0.1975353 -0.1343287
Mean_logspod 0.1034415 0.1937696 -0.0342749 -0.3085769 1.0000000 -0.1182681 0.0413333 -0.0197709
Mean_bird_attack 0.1655057 0.1839687 0.5639223 0.1031407 -0.1182681 1.0000000 -0.1357126 0.3678163
Mean_nonbird_attack 0.2463326 0.3230519 0.3094026 -0.1975353 0.0413333 -0.1357126 1.0000000 0.8713780
Mean_tot_attack 0.3131610 0.3943111 0.5696503 -0.1343287 -0.0197709 0.3678163 0.8713780 1.0000000

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.
You, Yanrong, Chunpeng An, and Chuanyou Li. 2020. “Insect Feeding Assays with Spodoptera Exigua on Arabidopsis Thaliana.” BIO-PROTOCOL 10 (5). https://doi.org/10.21769/BioProtoc.3538.