Molecular defense responses to natural enemies determine seedling survival in a subtropical forest

Negative density dependence (NDD) has been accepted as a key mechanism for biodiversity maintenance in natural forests and different lineages of natural enemies (fungus, bacterium, insect and virus) may be involved. Previous NDD related studies usually correlated seedling survival to the density of host-specific pests or pathogens along the physical distance to conspecific neighbors, and molecular defense responses of focal seedlings to natural enemies were seldom concerned. By employing a community functional genomic strategy, we extracted copy numbers of homologous genes in defense responses from transcriptomic data of 99 tree species and their inherent impacts on seedling survival were evaluated using linear mixed-effects models (LMMs) and general linear mixed-effects models (GLMMs). The copy number of fungus-defense, insect-defense, and virus-defense genes showed significant negative correlations with survival rates of the seedling community and the copy number of insect-defense genes significantly and negatively correlated with survival rates of top-twenty common species. Seedlings tended to have high survival rates when surrounded by seedling neighbors with similar insectdefense CNV matrices and adult neighbors with distinct bacterium-defense and virus-defense CNV matrices.We conclude that both gene copy number and dissimilarities to adult and seedling neighbors in defense response to natural enemies contributed to seedling survival, indicating the critical contributions of molecular defense responses of plants to species coexistence and diversity maintenance in subtropical forests.