Cycas taitungensis and its sister species, C. revoluta (Cycas sect. Asiorientalis), are distributed peripatrically. Previous studies have revealed their phylogeographic pattern and, based on certain plastid DNA markers, have established that they diverged recently. However, the speciation process involving the genomic divergence has not been well clarified. In this study, based on their geographical distribution and estimates of their genetic diversity, two speciation models are proposed: (1) the founder and (2) the bottleneck speciation mode. Using approximate Bayesian computation (ABC) in combination with their estimated genetic diversity and population structure, we infer that the ancestral C. taitungensis populations diverged and southward colonized southeastern Taiwan from ancestral C. revoluta since the middle Pleistocene. These founders preserved ancestral polymorphism, resulting in small differences in genetic diversity and effective population size (Ne), despite a large difference in census population size (Nc) between two species. Based on this case of island cycad species offshore of continental Asia, this study provides new insight into how the speciation process influences the genetic diversity pattern of species with small Nc and Ne.
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