Neighborhood variables and neighborhood functional CNV dissimilarity
Based on the census data in 2010, we defined all the adult trees (≥ 1 cm d.b.h.) in a circle of 20 m radius around the focal seedling as its adult neighbors, and all seedlings in the same 1 m2seedling plot of the focal seedling as its seedling neighbors. Two measures of conspecific neighborhood density were calculated for each focal seedling: 1) the number of conspecific seedling neighbors (S_con); and 2) the sum of basal area of conspecific adult neighbors (A_con).
The species pairwise distance matrices were calculated using the functional CNV matrices by the method of Gower (1971) as the proxy of species dissimilarity using FD package in R4.0.2. We used Blomberg´sk statistic to measures phylogenetic signal (Blomberg et al. 2003) for the first two principal coordinates of each species pairwise distance matrix using the picante package in R 4.0.2. The species pairwise distance matrices of each defense response GO were employed to calculate relative nearest taxon functional diversity (NTFd’) as neighborhood functional CNV dissimilarity for each focal seedling by the methods of Webb et al. (2006) and Wang et al. (2020) for both seedling (S_NTFd’) and adult (A_NTFd’) neighbors. The Null distribution of minimum neighborhood dissimilarity was produced by shuffling the species names on the species pairwise distance matrix for 999 times. The Mean (MNull) and standard deviation (SdNull) of the null distribution were calculated. The NTFd’ index was generated from observed value of minimum neighborhood dissimilarity by subtracting MNull and dividing by SdNull. A positive NTFd’ value indicates that species are more functionally dissimilar (higher functional CNV diversity) and a negative NTFd’ value indicates that species are more functionally similar (lower functional CNV diversity). All the four neighborhood variables of focus seedlings calculated for each year interval.