Phylogeography of the endangered orchid Dendrobium moniliforme in East Asia inferred from chloroplast DNA sequences

Abstract

The aim of the current study was to elucidate the phylogeographic history of Dendrobium moniliforme, an endangered orchid species, based on two chloroplast DNA (cpDNA) markers (trnC-petN and trnE-trnT). One hundred and thirty-five samples were collected from 18 natural populations of D. moniliforme covering the entire range of the Sino-Japanese Floristic Region (SJFR) of East Asia. A total of 35 distinct cpDNA haplotypes were identified in these populations, of which 23 haplotypes were each present in only one sample and thus restricted to a single population. The significantly larger N_ST value (0.586) than G_ST (0.328) (p < 0.05) demonstrated the presence of strong phylogeographic structure. Phylogenetic analyses indicated that all haplotypes were clustered into two lineages. The genetic diversity of D. moniliforme was high at the species level, reflected in its haplotype diversity (H_d=0.8862), nucleotide diversity (P_i=0.00361), total genetic diversity (H_T=0.9011), and significant differentiation (Φ_ST=0.5482). Based on mismatch distribution analysis and neutrality tests, population expansion was evident in all sampled populations and also in all populations sampled in mainland China. Three refuge areas were identified, one each in southwestern China, central-southeastern China, and the CKJ (Taiwan, Japan and Korea) Islands. The results supported the hypothesis that glacial refugia were maintained on different spatial-temporal scales in the SJFR during the last glacial maximum or earlier cold periods, suggesting that Quaternary refugial isolation promoted allopatric speciation of D. moniliforme in East Asia.

Keywords:

• cpDNA
• Dendrobium moniliforme
• haplotype
• phylogeography
• refuge

Acknowledgements

We are grateful to Ms. Chun Gu for revising the manuscript, Dr. Joongku Lee and Dr. Kamezo Saito for providing samples from South Korea and Japan, respectively.

Disclosure statement

The present study determined the phylogeography of Dendrobium moniliforme based on the two chloroplast DNA (cpDNA) markers trnC-petN and trnE-trnT. D. moniliforme possesses great medicinal and horticultural value, but have become a critically endangered species in China. This calls for an in-depth investigation into its phylogeography. The main findings of this study are as follows, which we believe will make it interesting to general readers of Mitochondrial DNA. First, 35 distinct cpDNA haplotypes were identified in 18 natural populations of D. moniliforme covering the entire range of the SJFR of East Asia, and it had high levels of haplotype diversity and total genetic diversity, as well as significant population phylogeographic structure. Second, expansion occurred in all sampled populations around c. 0.56 Mya and in all populations sampled in mainland China around c. 0.54 Mya. Third, all identified haplotypes were clustered into two clades. Fourth, no haplotype was shared between mainland China and Japan, implying that the Chinese and Japanese D. moniliforme populations might have evolved independently. The obtained cpDNA results also suggested that multiple glacial refugia for D. moniliforme existed in East Asia, which have promoted its allopatric speciation during the glacial period.

This study does not have any potential competing interests and all authors have approved the manuscript for submission. Also, we confirm that the content of the manuscript is our original unpublished work and has not been submitted to any other journals for review.

Funding information

This work was supported by the National Natural Science Foundation of China [grant number 31170300], a project funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions.