Rivers have shaped the phylogeography of a narrowly distributed cycad lineage in Southwest China

The intricate river systems forming various drainages play a crucial role as natural barriers, impeding the gene flow of extensively distributed taxa. However, there have been limited studies focused on examining the impact of river barriers on the phylogeography of plant lineages with restricted distributions. Cycas chenii X. Gong & W. Zhou, an endemic plant species found alongside rivers in the Yunnan region of China, possesses considerable research significance. By utilizing double digest restriction site associated DNA sequencing, we investigated the genetic diversity, genetic structure, and population historical dynamics for C. chenii to explore the influence of rivers on this species. We found C. chenii displayed greater genetic diversity in comparison to other Cycas species, with the HB population, a sole population situated in southwest Red River Region, exhibiting the highest genetic diversity at the population level. The AMOVA results revealed that the predominant genetic variations existed within populations (84.46%). Mantel test revealed a significant positive correlation between genetic differentiation and geographic distance in C. chenii . Both genetic structure and phylogenetic analyses strongly corroborate the categorization of the ten populations of C. chenii into three distinct clusters, aligning with their respective rivers and geographic distributions. Furthermore, the populations of C. chenii experienced three bottlenecks within the last five million years, which could be correlated with geological events. Based on these findings, specific conservation strategies were proposed for the three evolutionary significant units (ESUs) of C. chenii , each of which encounters distinct conservation challenges.