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Detecting east–west genetic differentiation in Castanopsis (Fagaceae) on the main islands of Japan and north–south on the Ryukyu Islands, based on chloroplast haplotypes

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Abstract

Castanopsis (Fagaceae) is a plant genus that includes dominant tree species in the broadleaved evergreen forests of Japan. In this study, we investigated the genetic diversity and genetic structure of 76 natural populations of C. sieboldii and C. cuspidata, using variations in chloroplast DNA (cpDNA) sequences and chloroplast microsatellites (cpSSR) to elucidate the phylogeographic patterns reflected by seed flow. Most chloroplast haplotypes were shared between the two species on the main islands, although biparentally inherited microsatellite (nSSR) analyses showed a species-specific pattern in the previous study. The current patterns of haplotype sharing of cpDNA suggest the retention of an ancestral polymorphism that existed in Castanopsis before the two species split or historical introgression in the refugia during the glacial periods. Haplotype network was defined by three groups: Taiwan, southern parts of the Ryukyu Islands, and the central parts of the Ryukyu Islands to the main islands. The observed north–south genetic differentiation in cpDNA on the Ryukyu Islands was not detected by previous nSSR analyses. These results suggest that the lower levels of seed-mediated gene flow between the islands resulted in clear genetic differentiation of cpDNA on the Ryukyu Islands. Moreover, the cpSSR analysis indicated east–west genetic differentiation on the main islands, a pattern found in previous nSSR analyses of Castanopsis and several plant and animal species inhabiting Castanopsis forests in Japan, suggesting the existence of eastern refugia in the last glacial period. Our cpSSR investigation and their higher intraspecific variation provide a useful phylogeographic tool for these species.

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Acknowledgments

The authors are grateful to Hiroshi Yoshimaru, Yoshiaki Tsuda, Akihiro Seo, Kentaro Kimura, Hiroshi Takada, Sota Matsunaga, Ryouichi Kusano, Tsutomu Karukome, Tsai-Wen Hsu, Ho-Ming Chang, and Keiichi Oono for collecting samples and to Takashi Tsuduki, Yuriko Taguchi, and Yasuyuki Komatsu for laboratory work. This research was supported, in part, by a grant for research on Genetic Guidelines for Restoration Programs using Genetic Diversity Information from the Ministry of Environment, Japan, Grants-in-Aid from the Japan Society for the Promotion of Science (Nos. 1701416, 21770087, 2240030, 26440214, and 15J40011 to K. A.), and the Research Project “A new cultural and historical exploration into human-nature relationships in the Japanese archipelago” of the Research Institute for Humanity and Nature, Kyoto, Japan.

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Online Resource 1. Voucher information of the Castanopsis populations investigated (PDF 82 kb)

606_2016_1319_MOESM2_ESM.pdf

Online Resource 2. Details of preliminary screening analyses of 16 Castanopsis samples (one individual per locality: numbers 2, 5, 18, 24, 30, 34, 38, 45, 49, 54, 56, 57, 63, 68, 73, and 76 in Table 1) using universal primers for the chloroplast DNA (cpDNA) and chloroplast microsatellite (cpSSR) loci (PDF 823 kb)

Online Resource 3. Alignments of chloroplast haplotypes in Castanopsis (PDF 89 kb)

606_2016_1319_MOESM4_ESM.pdf

Online Resource 4. Geographic distributions of the chloroplast DNA (cpDNA) and chloroplast simple sequence repeat (cpSSR) haplotypes in the Castanopsis populations. (a) C. sieboldii individuals and (b) C. cuspidata individuals are shown (PDF 143 kb)

Information on electronic supplementary material

Information on electronic supplementary material

Online resource 1. Voucher information of the Castanopsis populations investigated.

Online resource 2. Details of preliminary screening analyses of 16 Castanopsis samples (one individual per locality: numbers 2, 5, 18, 24, 30, 34, 38, 45, 49, 54, 56, 57, 63, 68, 73, and 76 in Table 1) using universal primers for the chloroplast DNA (cpDNA) and chloroplast microsatellite (cpSSR) loci.

Online resource 3. Alignments of chloroplast haplotypes in Castanopsis.

Online resource 4. Geographic distributions of the chloroplast DNA (cpDNA) and chloroplast simple sequence repeat (cpSSR) haplotypes in the Castanopsis populations. (a) C. sieboldii individuals and (b) C. cuspidata individuals are shown.

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Aoki, K., Ueno, S., Kamijo, T. et al. Detecting east–west genetic differentiation in Castanopsis (Fagaceae) on the main islands of Japan and north–south on the Ryukyu Islands, based on chloroplast haplotypes. Plant Syst Evol 302, 1093–1107 (2016). https://doi.org/10.1007/s00606-016-1319-1

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