Phylogenetic Structure Analysis Based on the Blue-Light Receptor Cryptochrome: Insights into How Light Shapes the Vertical Structure of Subtropical Forest Community

Understanding the mechanisms that assemble diverse forest communities is a central goal in ecology. Phylogenetic analyses based on DNA barcodes have advanced this field, but their use of sequences evolving at constant rates may not capture adaptations to specific environmental drivers. Light is a critical factor shaping forest structure, particularly in the vertical dimension. This study introduces a novel phylogenetic approach using the blue-light receptor gene, cryptochrome (Cry), which is directly involved in plant light perception and adaptation. We reconstructed a Cry-based phylogeny for 96 tree species in a 20 ha subtropical forest dynamics plot and analyzed community structure using the net relatedness index (NRI) and nearest taxon index (NTI) across horizontal habitats, successional stages, and vertical canopy layers. Compared to traditional DNA barcoding, the Cry phylogeny revealed distinct patterns, showing consistent phylogenetic structure across different habitats—a finding indicative of convergent evolution in light-sensing systems. Furthermore, the Cry-based analysis demonstrated a stronger and more consistent signal in the forest’s vertical structure, with significant phylogenetic clustering in upper canopy layers, directly linking light adaptation to community stratification. Over time, both NRI and NTI values increased, suggesting succession leads to greater phylogenetic overdispersion and highlighting an increased role for environmental filtering among closely related taxa. Our results validate Cry as a powerful functional gene marker for phylogenetics, providing unique insights into how light environment filters species and shapes the vertical assembly of forest communities.