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Effects of the last glacial period on genetic diversity and genetic differentiation in Cryptomeria japonica in East Asia

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Abstract

To understand how historical and environmental factors have shaped genetic diversity and spatial genetic patterns of tree species, we characterized the genetic diversity and the genetic structure of a coniferous species, Cryptomeria japonica, which is distributed in Japan (two taxonomic groups) and some parts of southeastern China (C. japonica var. sinensis). We investigated population samples for three groups using high-throughput SNP genotyping, sequencing of multiple genes, and then estimated level of genetic diversity, the genetic differentiation, and the divergence time between the three groups. We also investigated the natural distribution during LGM using species distribution modeling. The genetic variation in the Chinese population, var. sinensis, was lower compared to Japanese populations but it harbored some unique genotypes. The species distribution modeling showed that the Chinese population has decreased since Last Glacial Maximum (LGM) because of lower precipitation than present time, but in Japan the favored environment have remained available for this species even in the LGM. Estimated divergence times of the three groups mostly correspond with the time since the Last Glacial. Our data supports the hypothesis that the glacial period, particularly limitations associated with precipitation, strongly influenced the distribution of C. japonica populations. Our findings suggest that climate change plays an important role in speciation processes of C. japonica.

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Acknowledgments

We thank Y. Taguchi and M. Koshiba for technical assistance for DNA analysis. This study was partly supported by the Program for the Promotion of Basic and Applied Research for Innovations in Bio-oriented Industry and JSPS KAKENHI program (grant nos. 26292087, 26291082 and 15H02833), the National Key Research and Development Program of China (grant no. 2016YFE0127200), and Environment Research grant of the Sumitomo Foundation.

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Authors and Affiliations

  1. Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan

    Yoshihiko Tsumura

  2. Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Hitachi, Ibaraki, 319-1301, Japan

    Megumi Kimura

  3. Kansai Research Center, Forestry and Forest Products Research Institute, Kyoto, 612-0855, Japan

    Katsuhiro Nakao

  4. Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, 305-8687, Japan

    Kentaro Uchiyama & Tokuko Ujino-Ihara

  5. Central South University of Forestry and Technology, Changsha, 410004, China

    Yafeng Wen & Wenjun Han

  6. Zhejiang A & F University, Lin’an, Hangzhou, 311300, China

    Zaikang Tong

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  1. Yoshihiko Tsumura
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Correspondence to Yoshihiko Tsumura.

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Communicated by F. Gugerli

Data archive

All SNPs information and sequence data were deposited in DDBJ (accession numbers, AB874696-AB889383 and LC477701-LC479084).

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Tsumura, Y., Kimura, M., Nakao, K. et al. Effects of the last glacial period on genetic diversity and genetic differentiation in Cryptomeria japonica in East Asia. Tree Genetics & Genomes 16, 19 (2020). https://doi.org/10.1007/s11295-019-1411-0

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