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Phylogeography of a rare orchid, Vexillabium yakushimense: comparison of populations in central Honshu and the Nansei Island chain, Japan

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Abstract

Vexillabium yakushimense is a rare, terrestrial orchid which occurs in east and southeast Asia. In spite of its inconspicuous appearance, several new populations were discovered in central Honshu, Japan. Because these populations are geographically isolated at its northern range limit of distribution, they were suspected to have distinctive genetic characteristics. Given this hypothesis, we quantified the genetic variation of V. yakushimense for populations of central Honshu, and the Nansei Island chain, which represent the most southern locality in Japan. Leaves were collected from nine populations in central Honshu (n = 48) and two populations from the Nansei Island chain (n = 29). We examined genetic variation using cpDNA (1,205 bp) and ITS (511 bp) markers. Based on the cpDNA variation, a total of seven haplotypes were recovered; populations in central Honshu were clearly differentiated from those in the Nansei Island chain. Relatively high allelic richness and haplotype diversity were found in the pooled population of central Honshu. These populations likely maintained an adequate population size for a long period despite a markedly different ecological niche compared to that in the Nansei Island chain. In contrast to cpDNA, little variation was detected in ITS. Further studies on geographic occurrences, reproductive biology and mycorrhizal association are encouraged for its conservation.

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Acknowledgments

We sincerely thank Mr. T. Watanabe, Mr. A. Tono, Mr. S. Yamaguchi, Mrs. Y. Yamaguchi, Mr. K. Watanabe and Makino Herbarium (Dr. N. Murakami, Dr. T. Sugawara, Dr. H. Kato) for their support in field collection, examination of herbarium specimens and DNA analyses. Comments on an early draft by Dr. B.V. Barnes (Professor Emeritus of the University of Michigan) were very helpful. Two refrees provided useful suggestions. This research was funded by the Yokohama National University-National Environment Research Institute Global COE program from April 2010 to March 2012 and the Pro Natura Fund from October 2011 to September 2012.

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Authors and Affiliations

  1. Network Center of Forest and Grassland Survey, Monitoring Site 1000 Project, Japan Wildlife Research Center, Tokyo, Japan

    Ikuyo Saeki

  2. Makino Herbarium, Tokyo Metropolitan University, Tokyo, Japan

    Ikuyo Saeki

  3. Japanese Red Maple Conservation Group, Iida, Japan

    Ikuyo Saeki & Asako Kitazawa

  4. General Research Center, Ocean Exposition Commemorative Park Management, Naha, Japan

    Atsushi Abe & Koya Minemoto

  5. Graduate School of Environment and Information Sciences, Yokohama National University, Yokohama, Japan

    Fumito Koike

  6. Tomakomai Experimental Forest, Hokkaido University, Takaoka, Tomakomai, Hokkaido, 053-0035, Japan

    Ikuyo Saeki

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  1. Ikuyo Saeki
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Correspondence to Ikuyo Saeki.

Appendix 1

Appendix 1

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Table 3 GenBank accession numbers of sequenced individuals of Vexillabium yakushimense
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Saeki, I., Kitazawa, A., Abe, A. et al. Phylogeography of a rare orchid, Vexillabium yakushimense: comparison of populations in central Honshu and the Nansei Island chain, Japan. Plant Syst Evol 300, 1–12 (2014). https://doi.org/10.1007/s00606-013-0854-2

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