Hui Shang

and 7 more

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 distance to conspecific neighbors, and molecular defense responses of focal seedlings to natural enemies were seldomly concerned. By employing community functional genomics 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 partial linear regression analysis and general linear mixed-effects models. The community-level transcriptomic gene copy number of defense responses to fungus, insect and virus showed significant negative correlations with survival rates of the seedling community and the species-level gene copy number of defense response to insect significantly correlated with survival rates of top-twenty common seedling species. Moreover, presence of adult neighbors with distinct defense response to bacterial and viral pathogens survival of focal seedlings as predicted by NDD, while presence of seedling neighbors with similar defense response to insect tended to promote survival of focal seedlings which may be driven by insect-mediated biotic filtering or competitive exclusion. We conclude that both gene copy number and dissimilarities to adult and seedling neighbors in defense response to natural enemies determined seedling survival, indicating the critical contributions of molecular defense responses of plants to species coexistence and diversity maintenance in subtropical forests.

Lu Jin

and 12 more

Phylogenetic trees have been extensively used in community ecology. However, how the phylogenetic reconstruction affects ecological inferences is poorly understood. In this study, we reconstructed three different types of phylogenetic trees (a synthetic-tree generated using VPhylomaker, a barcode-tree generated using rbcL+matK+trnH-psbA and a genome-tree generated from plastid genomes) that represented an increasing level of phylogenetic resolution among 580 woody plant species from six dynamic plots in subtropical evergreen broadleaved forests of China. We then evaluated the performance of each phylogeny in estimations of community phylogenetic structure, turnover and phylogenetic signal in functional traits. As expected, the genome-tree was most resolved and most supported for relationships among species. For local phylogenetic structure, the three trees showed consistent results with Faith’s PD and MPD; however, only the synthetic-tree produced significant clustering patterns using MNTD for some plots. For phylogenetic turnover, contrasting results between the molecular trees and the synthetic-tree occurred only with nearest neighbor distance. The barcode-tree agreed more with the genome-tree than the synthetic-tree for both phylogenetic structure and turnover. For functional traits, both the barcode-tree and genome-tree detected phylogenetic signal in maximum height, but only the genome-tree detected signal in leaf width. This is the first study that uses plastid genomes in large-scale community phylogenetics. Our results highlight the outperformance of genome-trees over barcode-trees and synthetic-trees for the analyses studied here. Our results also point to the possibility of Type I and II errors in estimation of phylogenetic structure and turnover and detection of phylogenetic signal when using synthetic-trees.