Geographic isolation promoted species divergence of two closely related Cycas species in distinct river basins

PREMISE: Understanding the process of species divergence and the mechanisms that drive genetic differentiation among closely related species is essential for explaining the origins of plant biodiversity. Geographic isolation and niche differentiation are key drivers of species divergence. Cycas chenii and C. guizhouensis are morphologically similar sister species from different river basins in Southwest China. Their distinct habitats in nearby river systems make them a potentially good model system for studying species divergence. METHODS: We used double-digest restriction-site-associated DNA sequencing data and analyzed the data with a range of analyses to investigate the genetic divergence of C. guizhouensis and C. chenii and to assess the significance of geographic factors and ecological differentiation in their divergence. RESULTS: The two species had significant genetic differentiation (genetic differentiation index = 0.34). On the basis of phylogenetic and admixture analyses, the two species are genetically distinct lineages that diverged in the early Miocene. They experienced similar demographic histories over the past several million years. The genetic distance between the two species correlated positively with geographic distance but not with environmental distance. In a niche identity test, the ecological niches of the two species were statistically indistinguishable (Schoener's D = 0.68, I = 0.91, both within the null distribution). CONCLUSIONS: Environmental variation is unlikely to have been the primary factor driving divergence of C. chenii and C. guizhouensis. Geographic separation instead may have been triggered by shifts in river channels during the early Miocene epoch, playing a pivotal role in interspecific differentiation.