| Summary: | <p>Abstract</p> <p>Background</p> <p>This study addresses the apportionment of genetic diversity between <it>Cycas revoluta </it>and <it>C. taitungensis</it>, species that constitute the section <it>Asiorientales </it>and represent a unique, basal lineage of the Laurasian genus <it>Cycas</it>. Fossil evidence indicates divergence of the section from the rest of <it>Cycas </it>at least 30 million years ago. Geographically, <it>C. taitungensis </it>is limited to Taiwan whereas <it>C. revoluta </it>is found in the Ryukyu Archipelago and on mainland China.</p> <p>Results</p> <p>The phylogenies of ribosomal ITS region of mtDNA and the intergenic spacer between <it>atp</it>B and <it>rbc</it>L genes of cpDNA were reconstructed. Phylogenetic analyses revealed paraphyly of both loci in the two species and also in the section <it>Asiorientales</it>. The lack of reciprocal monophyly between these long isolated sections is likely due to persistent shared ancestral polymorphisms. Molecular dating estimated that mt- and cp DNA lineages coalesced to the most recent common ancestors (TMRCA) about 327 (mt) and 204 MYA (cp), corresponding with the divergence of cycad sections in the Mesozoic.</p> <p>Conclusion</p> <p>Fates of newly derived mutations of cycads follow Klopfstein et al.'s surfing model where the majority of new mutations do not spread geographically and remain at low frequencies or are eventually lost by genetic drift. Only successful 'surfing mutations' reach very high frequencies and occupy a large portion of a species range. These mutations exist as dominant cytotypes across populations and species. Geographical subdivision is lacking in both species, even though recurrent gene flow by both pollen and seed is severely limited. In total, the contrasting levels between historical and ongoing gene flow, large population sizes, a long lifespan, and slow mutation rates in both organelle DNAs have all likely contributed to the unusually long duration of paraphyly in cycads.</p>
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