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Inferences of demographic history and fine-scale landscape genetics in Cycas panzhihuaensis and implications for its conservation


Understanding the population genetic structure and demographic history helps in the management and restoration of endangered species. Cycas panzhihuaensis (Panzihihua sago palm) is narrowly distributed in the eastern Sichuan Basin of China. The only extant population is in the Panzhihua Cycad Nature Reserve (PCNR), which is close to Panzhihua City, and is threatened by the mining industry and slash-and-burn agriculture. To protect this rare species, the local government implemented an ex situ conservation project. In this study, amplified fragment length polymorphism (AFLP) was used to explore the genetic diversity of wild and cultivated populations. Two evolutionarily significant units (ESUs) in PCNR were determined based on significant differences in genetic diversity and demographic histories. The western ESU has low genetic diversity and shares common genotypes with a part of the eastern ESU. The founder effect is suggested as the best-fit scenario to explain the current genetic distribution among the eastern and western ESUs. Small carrying capacity limits both census and effective population sizes, and the gene surfing hypothesis explains the high frequency of fixed alleles without private alleles in multiple loci in the western subpopulation. Every cultivated population, established for either conservation or horticultural purposes, has only genotypes from a single ESU. Supplementary collection for ex situ conservation is suggested to preserve the genetic features of C. panzhihuaensis.

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Our deepest gratitude goes to Dr. Shong Huang for his valuable assistance and helpful suggestions. We also thank Dr. J.G. Shellnutt for providing geological information of Panzhihua areas. This research is finically supported by the Society of Subtropical Ecology, Sichuan Panzhihua Cycad National Nature Reserve Administration, and National Science Council in Taiwan (NSC 102-2621-B-003-005-MY3). This article was also subsidized by the National Taiwan Normal University (NTNU), Taiwan.

Conflict of interest

The authors declare that they have no competing interest.

Compliance with ethical standards

The authors declare that all experiments described herein comply with the law of government in which they were carried out.

Data archiving statement

Data used in this study are publically available in Supplemental File 4.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Pei-Chun Liao.

Additional information

This article is part of the Topical Collection on Gene Conservation

Yong-Qiong Yang, Bing-Hong Huang and Zhi-Xiang Yu contributed equally to this work.

Communicated by P. Ingvarsson

Electronic supplementary material

Below is the link to the electronic supplementary material.

Fig. S1

Distribution of allele frequency of each population shown in a normal quantile plot and bar plot. Thin lines in the normal quantile plot are distribution of expectations. Population Wuding is excluded in this analysis because of small sample size (only two samples) (PDF 426 kb)

Fig. S2

Correlation between the genetic distance (number of differences) and geographic distance (km2) of sampled individuals in the PCNR of C. panzhihuaensis in Panzhihua City, Sichuan Province in China (PDF 324 kb)

Table S1

Sampling information (DOCX 30 kb)

Table S2

AFLP primers information (DOCX 15 kb)

Table S3

Model test for the diversification rate of C. panzhihuaensis lineages. The best-fit models were marked in bold (DOCX 19 kb)


The AFLP data used in this study (TXT 56 kb)

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Yang, YQ., Huang, BH., Yu, ZX. et al. Inferences of demographic history and fine-scale landscape genetics in Cycas panzhihuaensis and implications for its conservation. Tree Genetics & Genomes 11, 78 (2015).

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  • Cycas panzhihuaensis
  • Demographic history
  • Diversification
  • Ex situ conservation
  • Landscape genetics
  • Population structure