Modern genomic approaches allow for the detection of cryptic speciation in which species pairs with a conservative morphology have actually separated into deeply diverged lineages. Such discoveries have important ramifications for the conservation of endemic and endangered species. Vatica guangxiensis is an endangered species of the family Dipterocarpaceae endemic to southwest China. The species is restricted to three known natural populations and faces the severe threat of extinction. We sequenced more than 80% of known individuals (229), including all available adults and saplings, of V. guangxiensis across the three sites of occurrence using over 10,000 genome-wide SNPs to explore the population genomic status of V. guangxiensis and potential cryptic speciation. We detected deep genomic differentiation between populations from Guangxi and Yunnan provinces with an estimated divergence at ~3.5 Mya and a lack of subsequent gene flow. Our results support the historic taxonomical treatment that populations in Yunnan and Guangxi constitute two distinct taxa. All populations exhibit a loss of genetic diversity and excess of low frequency alleles, suggesting recent bottlenecks. Forward simulations suggest imminent crashes in the genetic diversity of populations and a need for immediate conservation. Our study unravels the historical differentiation of two species that had been overlooked for decades because of their morphological conservatism. It highlights the terminal endangerment and the urgent need for conservation of extremely small tropical or subtropical populations of plant species with a strong signal of genomic vulnerability akin to V. guangxiensis.
The last stand: genomes reveal terminal endangerment of tropical species in Southwest China