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Phylogeography of the component species of broad-leaved evergreen forests in Japan, based on chloroplast DNA variation

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Abstract

In order to elucidate the past distribution and colonization routes of broad-leaved evergreen (lucidophyllous) forests, we investigated the intraspecific phylogeographic patterns of lucidophyllous forests in Japan and surrounding areas. We selected 6 component species with a similar geographic distributions growing in Castanopsis-dominant forests. We defined possible important refugia during the glacial periods as the regions rich in rare haplotypes (with a frequency of 5% or less), or as regions rich in the number of common haplotypes (with a frequency of more than 5%). We then located the sites of refuge by comparing the intraspecific phylogeographic patterns among 6 component species of lucidophyllous forests with respect to these two parameters (i.e., haplotype uniqueness and the number of haplotypes). The following results were obtained during the course of this study: (1) rare haplotypes were distributed among islands around the main islands of Japan; (2) rare subtypes and the greatest numbers of common haplotypes were observed in Kyushu, a finding which agreed with fossilized pollen data demonstrative of the past existence of refugia in southern Kyushu; and (3) rare haplotypes were found on the Muroto Peninsula, and the second greatest numbers of common haplotypes were observed on the Kii Peninsula, a finding which suggested the existence of additional important refugia along the Pacific coast of Japan during the glacial ages.

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Acknowledgements

We would like to thank Dr. Tamotsu Hattori for his generous support and valuable suggestions, and in particular for providing information regarding the lucidophyllous forest collection sites. We would also like to thank Mr. Seiya Morinaga, Dr. Tsuguo Sakura, Dr. Nobuyuki Tanaka, Mr. Noritoshi Inagaki, Mr. Shungo Kariyama, Dr. Akihiro Seo, Ms. Miho Imada, Ms. Utami Makino, Ms. Yukimi Yoshida, Ms. Rika Takeuchi, Ms. Akemi Nakagoshi, and Ms. Keiko Aoki for their assistance with the collection of plant materials in Japan. We are grateful to Dr. Tzen-Yuh Chiang, Mr. Shann-Jye Moore, Mr. Ho-Ming Chang, Dr. Chang-Fu Hsieh, Ms. I-Ling Lai in Taiwan, and to Dr. Do-Soon Cho in Jeju Island for their assistance with our fieldwork outside of Japan. In addition, we would like to thank Mr. Hidenobu Funakoshi, Mr. Taku Fujita, Dr. Kayo Asami, Mr. Hiroaki Ishida, Mr. Yoshihiro Sawada, and Mr. Hiroji Akamatsu for sending plant samples. Finally, we would like to acknowledge Dr. Masayuki Takamiya for his identification of Arachniodes aristata. This study was financially supported in part by a Grant-in-Aid from the Japan Society for the Promotion of Science No. 13575012 to N.M.

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Authors and Affiliations

  1. Department of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan

    Kyoko Aoki & Noriaki Murakami

  2. Division of Biological Resources, Museum of Nature and Human Activities, Sanda, Japan

    Takeshi Suzuki

  3. Division of Botany, Taiwan Endemic Species Research Institute, Chi-chi, Taiwan

    Tsai-Wen Hsu

Authors
  1. Kyoko Aoki
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  2. Takeshi Suzuki
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  3. Tsai-Wen Hsu
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  4. Noriaki Murakami
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Corresponding author

Correspondence to Kyoko Aoki.

Appendices

Appendix 1

Table 6 lists voucher information regarding the plant samples.

Table 6 Collection sites
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Appendix 2

Tables 7, 8, 9, 10, 11 and 12 show aligned sequences of polymorphic sites.

Table 7 Aligned sequences of polymorphic sites for Prunus zippeliana, a component species of lucidophyllous forests in Japan
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Table 8 Aligned sequences of polymorphic sites for Alpinia japonica, a component species of lucidophyllous forests in Japan
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Table 9 Aligned sequences of polymorphic sites for Daphne kiusiana, a component species of lucidophyllous forests in Japan
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Table 10 Aligned sequences of polymorphic sites for Elaeocarpus sylvestris var. ellipticus, a component species of lucidophyllous forests in Japan
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Table 11 Aligned sequences of polymorphic sites for Arachniodes sporadosora, a component species of lucidophyllous forests in Japan
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Table 12 Aligned sequences of polymorphic sites for Arachniodes aristata, a component species of lucidophyllous forests in Japan
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Aoki, K., Suzuki, T., Hsu, TW. et al. Phylogeography of the component species of broad-leaved evergreen forests in Japan, based on chloroplast DNA variation. J Plant Res 117, 77–94 (2004). https://doi.org/10.1007/s10265-003-0132-4

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