Relating phytochemical diversity metrics with plant enemies

To determine if phytochemical diversity at the scale of individual trees and orchards was related to the incidence of the studied plant enemies, we obtained several metrics. At the tree scale, aside from grouping the trees under chemotypes, we calculated the alpha diversity (Shannon–Weaver diversity index) and beta diversity (defined as the chemical differentiation among individuals) (García-Rodríguez et al., 2012; Wetzel & Whitehead, 2020), for each tree using the concentration of each compound relative to tetradecane in each leaf sample. We used the PAST statistical software to calculate alpha and beta diversity (Hammer, 2019). We also calculated: (a) the total concentration of all PSMs; (b) the concentration of monoterpenoids + sesquiterpenoids + phenylpropanoids; (c) the concentration of persins, and (d) the concentration of furans. We performed Pearson’s correlation analysis with all those metrics and the incidence of plant enemies using the Statistica 6.0 software (StatSoft), Excel, or R programming language (R-Core Team, 2018). Due to the uneven occurrence of plant enemies among the orchards (possibly due to recent pesticide application), we only included orchards where at least one sampled tree had a particular plant enemy. This reduced the sample size to 222 trees for branch borer, 223 for PCB, 194 for red mite, 222 for thrips, and 166 for whitefly. The sample size for fruit rot and scab was 236 trees.

At the orchard scale, we calculated the diversity (Shannon, Simpson, and Evenness) and dominance for each orchard based on the number and abundance of the chemotypes present in it. To determine if the trees grouped at the orchard level were correlated to the average incidence of plant enemies, we calculated the average diversity of trees and the average chemical differentiation of the trees within each orchard to obtain Average Chemical Distance (ACD) and Standard Deviation for Chemical Distance (STD CD). For that, we calculated a distance matrix using city-block (Manhattan) distance with the PAST software. Those metrics were correlated with plant enemy incidence using Statistica 6.0 software. Due to the uneven incidence of plant enemies among the orchards, the sample size was reduced to 16 orchards for branch borer, 16 for PCB, 14 for red mite, 16 for thrips, and 12 for whitefly. The sample size for fruit rot and scab was 17 orchards.