Abstract: The endangerment of most species is primarily attributed to anthropogenic habitat destruction and reductions in genetic diversity; however, studies focusing on the genomic divergence underlying the distinct distribution patterns of closely related species pairs remain limited. In this study, we employed comparative and evolutionary genomic approaches to investigate genomic divergence between endangered species and their widespread congeners in the genera Acer and Dipteronia. We found that temperature fluctuations, precipitation, and elevation are the primary environmental variables driving ecological niche divergence between endangered and widespread species in both genera. Next, we aimed to identify genomic characteristics that may underlie the differential adaptability of these species to environmental selection. Our analyses revealed that widespread species expanded key gene families, such as bZIP, bHLH, and WRKY, through tandem or dispersed duplication, with several copies potentially associated with drought and temperature tolerance. Additionally, endangered species consistently exhibited a more pronounced loss of Gamma WGT-derived gene triads, whereas the corresponding genes retained in widespread species are potentially associated with drought, cold, and fungal resistance. Beyond these tandem, dispersed, and WGT-associated duplications, transposable element (TE)-mediated gene duplication further contributed to lineage-specific gene family expansion in widespread species, as exemplified by the FAR-RED IMPAIRED RESPONSE 1 (FAR1) family, which contains substantially more members in A. saccharum than in the endangered A. yangbiense. These findings demonstrate the efficacy of comparative genomic frameworks for elucidating the drivers of endangerment in the genera Acer and Dipteronia.

Key words: genomic differences, Acer, Dipteronia, environmental selection, gene family evolution, WGT-triads retention