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.