Are giant sinkholes in China's karst mountains havens or traps for the rare plants that inhabit them? A new study finds they are both—offering refuge from heat and drought while gradually eroding the evolutionary potential of an endangered tree.
In a study published in Current Biology on July 14, researchers from the South China Botanical Garden (SCBG) of the Chinese Academy of Sciences (CAS) and the Guangxi Institute of Botany found that colossal karst sinkholes, known as tiankeng in Chinese, can help preserve the endangered tree Magnolia aromatica, while also limiting gene flow and diminishing its long-term evolutionary potential.
In the karst mountains of southwest China, tiankeng shelter cool, humid forests at the bottom of steep cliffs. These hidden forests shield rare plants from harsh surface conditions. Magnolia aromatica, a rare karst tree distributed across fragmented limestone habitats in Guangxi, Guizhou, and Yunnan provinces, grows both inside and outside these sinkholes. But until now, it has been unclear whether the isolation inside tiankeng poses genetic risks that exceed their protective benefits.
To answer this question, the researchers assembled a high-quality reference genome for Magnolia aromatica and re-sequenced 112 individuals from 26 populations across southwest China, including populations from both inside and outside tiankeng. Their population genomic analyses identified four major evolutionary lineages, two of them associated with the Leye Tiankeng landscape.
The results revealed a paradox: at a broad scale, tiankeng-associated populations retained intermediate levels of genetic diversity and mutation load compared with non-tiankeng lineages, indicating that tiankeng can act as microrefugia that help maintain the species. At a finer scale, however, populations growing inside tiankeng showed lower genomic diversity and a higher burden of deleterious mutations than nearby exterior populations.
"Tiankeng are not simply safe havens," said KANG Ming from SCBG, corresponding author of the study. "They provide a buffered microenvironment that helps endangered plants persist, but their enclosed geography can also isolate populations and gradually wear away the genetic variation needed for future adaptation."
The researchers also found evidence that Magnolia aromatica has adapted to the deep shade of tiankeng interiors. Genes under selection in tiankeng-interior populations were enriched for functions related to photosynthesis and carbon fixation. Controlled shading experiments supported this genomic signal: seedlings died quickly under full or strong light, but survived and grew well under 50% to 90% shade, performing especially strongly under deep shade.
"This helps explain why Magnolia aromatica can thrive in the dim, humid forests at the bottom of tiankeng," said ZHU XianLiang from SCBG, first author of the study. "The species appears to be strongly dependent on shaded environments, especially during early seedling establishment."
The researchers then went on to assess future vulnerability under climate change. Their forecasts suggest that future habitat suitability may shift across the species' range, while some populations may face increasing maladaptation risk. More importantly, the burden of deleterious mutations is projected to rise over time, meaning that genomic erosion could compound the effects of climate change.
According to the researchers, the study provides one of the first genome-scale demonstrations that karst tiankeng can both preserve and constrain evolutionary potential in an endangered tree. It also offers a broader lesson for conserving species in isolated microrefugia: places that protect biodiversity today may not be sufficient to safeguard the evolutionary future of species under rapid environmental change.
The scientists also highlighted the need for conservation strategies that go beyond protecting individual tiankeng. While tiankeng interiors should be protected as important microrefugia, nearby exterior populations and potential dispersal routes also need attention because they may help maintain genetic connectivity and adaptive potential.
"Our results suggest that conservation should protect both the shelter and the connections around it," said KANG. "For endangered karst plants, maintaining gene flow among populations may be just as important as preserving the special habitats where they survive."
