Deep plastid phylogeographic divergence of beaked hickory (Carya sinensis) calls for transboundary conservation in a biodiversity hotspot

Abstract

Conservation of endangered plants is crucial for maintenance of biodiversity and uninterrupted provision of ecosystem services in a changing world. However, the lack of comprehensive phylogeographic information for most of the endangered species significantly hampers effective conservation action, especially for species distributed across national borders. Beaked hickory (Carya sinensis), an endangered tree species endemic to China and Vietnam, exemplifies these challenges. We conducted phylogeographic analysis of three genomic datasets (i.e. plastid, mitochondrial, and nuclear ribosomal DNA) and ecological niche modeling to investigate the genetic diversity, phylogeographic structure, and population history of C. sinensis. Our findings revealed three distinct plastid clades: Clade A in Vietnam, Clade B in China, and Clade C spanning both countries. Genetic diversity was low at species and within-clade levels, but multiple private haplotypes were observed in each clade. The three clades diverged between 6 and 8 million years ago, making C. sinensis a far older species than others within genus Carya. Bottlenecks were detected in all three clades during the Last Glacial Maximum, likely driven by the late Pleistocene glacial oscillations. Clade C also experienced a recent expansion (~800 years ago), possibly resulting from anthropogenic activities. With suitable habitats projected to decline under future climate change scenarios, we propose a precise evidence-based in and ex situ conservation strategy as part of a practical transboundary conservation framework. Additionally, we recommend treating the three clades as distinct conservation units for C. sinensis. This integrative approach could serve as a model for the transboundary conservation of other threatened plant species.