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Open Access Research article

Paraphyly of organelle DNAs in Cycas Sect. Asiorientales due to ancient ancestral polymorphisms

Yu-Chung Chiang1, Kuo-Hsiang Hung2, Shann-Jye Moore3, Xue-Jun Ge4, Shong Huang3, Tsai-Wen Hsu5*, Barbara A Schaal6* and TY Chiang7*

Author Affiliations

1 Department of Life Sciences, Pingtung University of Science and Technology, Pingtung, Taiwan, 912, Republic of China

2 Graduate Institute of Bioresources, Pingtung University of Science and Technology, Pingtung, Taiwan, 912, Republic of China

3 Department of Life Science, Taiwan Normal University, Taipei, Taiwan, Republic of China

4 South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China

5 Endemic Species Research Institute, Nantou, Taiwan, Republic of China

6 Department of Biology, Washington University, St Louis, MO 63130, USA

7 Department of Life Sciences, Cheng-Kung University, Tainan, Taiwan, 701, Republic of China

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BMC Evolutionary Biology 2009, 9:161  doi:10.1186/1471-2148-9-161

Published: 10 July 2009



This study addresses the apportionment of genetic diversity between Cycas revoluta and C. taitungensis, species that constitute the section Asiorientales and represent a unique, basal lineage of the Laurasian genus Cycas. Fossil evidence indicates divergence of the section from the rest of Cycas at least 30 million years ago. Geographically, C. taitungensis is limited to Taiwan whereas C. revoluta is found in the Ryukyu Archipelago and on mainland China.


The phylogenies of ribosomal ITS region of mtDNA and the intergenic spacer between atpB and rbcL genes of cpDNA were reconstructed. Phylogenetic analyses revealed paraphyly of both loci in the two species and also in the section Asiorientales. 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.


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.