Genomic insights into population dynamics and adaptive strategies of the endangered dipterocarp, Hopea chinensis

Asian rainforests are a biodiversity hotspot and are dominated by dipterocarps. Thus, protecting endangered dipterocarp species living on the distribution boundary of dipterocarps is a central factor in maintaining the range of Asian rainforests. Despite the perceived conservation priority of these species, we know little about how they became endangered and how they have adapted to marginal habitats. Here, we focused on the population genomics of Hopea chinensis, an endangered species narrowly distributed at the northern limit of dipterocarps, to (1) reveal its demographic history and infer factors contributing to endangered status; (2) evaluate the genetic consequences of its small remnant population; and (3) identify key genes associated with its adaptation. We found drastic population declines after the Last Glacial Maximum, suggesting the role of human disturbances in the endangered status. Despite high levels of inbreeding, we detected only 441 derived deleterious and 337 derived major-effect mutations, which were not significantly enriched in any KEGG pathway, providing evidence of low genetic loads. Furthermore, selective sweep analysis showed 12 genes associated with cold and drought tolerance and plant defense and immunity. Comparative genomics identified 125 specific and 30 lost gene families in the genome of H. chinensis, many of which were relevant to the responses to biotic and abiotic stresses. Our findings, therefore, reveal the genomic characteristics linked with the endangered status and adaptations for H. chinensis. Together with the population genomic results from two other dipterocarp species, we highlighted the necessity to establish nature reserves to prevent further human disturbances and to comprehensively describe the mutualistic and antagonistic networks associated with endangered dipterocarp species to guide in-situ and ex-situ conservation.