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Genetic differentiation and evolution of broad-leaved evergreen shrub and tree varieties of Daphniphyllum macropodum (Daphniphyllaceae)

Heredity volume 131, pages 211–220 (2023)Cite this article

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Abstract

Tree form evolution is an important ecological specialization for woody species, but its evolutionary process with adaptation is poorly understood, especially on the microevolutionary scale. Daphniphyllum macropodum comprises two varieties: a tree variety growing in a warm temperate climate with light snowfall and a shrub variety growing in a cool temperate climate with heavy snowfall in Japan. Chloroplast DNA variations and genome-wide single-nucleotide polymorphisms across D. macropodum populations and D. teijsmannii as an outgroup were used to reveal the evolutionary process of the shrub variety. Population genetic analysis indicated that the two varieties diverged but were weakly differentiated. Approximate Bayesian computation analysis supported a scenario that assumed migration between the tree variety and the southern populations of the shrub variety. We found migration between the two varieties where the distributions of the two varieties are in contact, and it is concordant with higher tree height in the southern populations of the shrub variety than the northern populations. The genetic divergence between the two varieties was associated with snowfall. The heavy snowfall climate is considered to have developed since the middle Quaternary in this region. The estimated divergence time between the two varieties suggests that the evolution of the two varieties may be concordant with such paleoclimatic change.

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Fig. 1: Distributions of analyzed populations and chloroplast DNA haplotypes, genetic clusters elucidated by sNMF, and approximate maximum tree height of the population.
Fig. 2: Comparison of the three group divergence scenarios.
Fig. 3: Genetic relationships among populations, constructed based on DA distance using the neighbor-joining method.
Fig. 4: Genetic relationships among individuals detected by principal component analysis (PCA).
Fig. 5: The effective population size and number of migrants per generation in the three island groups are denoted by circles and arrows, respectively, in the best scenario (isolation with migration, IM).

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Data availability

Genotype data of SNPs and the script for demographic analysis used for this study will be available at Dryad: https://doi.org/10.5061/dryad.70rxwdc3x.

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Acknowledgements

We are grateful to Harue Abe, Ryosuke Adachi, Hiroya Hatakawa, Arata Momohara, Hisa Saito, Shota Sakaguchi, Shogo Sugiura, Yuta Takano, Azumi Yano, the University of Tokyo Hokkaido Forest and Hokkaido University Nakagawa Experimental Forest for their help in collecting plant materials. This research was supported by a Grant-in-Aid for Scientific Research (18H02230 and 20H03020) for the Japan Society for the Promotion of Science, KAKENHI.

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Authors and Affiliations

  1. Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan

    Watanabe Yoichi

  2. Faculty of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan

    Sae Matsuzawa

  3. Gifu Academy of Forest Science and Culture, 88 Sodai, Mino, Gifu, Japan

    Ichiro Tamaki

  4. Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan

    Atsushi J. Nagano

  5. Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihouji, Tsuruoka, Yamagata, 997-0017, Japan

    Atsushi J. Nagano

  6. Department of Biology, Daejeon University, 62 Daehak-ro, Dong-gu, Daejeon, 34520, South Korea

    Sang-Hun Oh

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Contributions

WY designed the study. Sample collection was performed by WY, SM, IT and S-HO. The molecular experiments were conducted by WY, SM and AJN. Data were generated, analyzed, and visualized by WY, SM and IT. Manuscript was written by WY, with contributions from all authors.

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Correspondence to Watanabe Yoichi.

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Yoichi, W., Matsuzawa, S., Tamaki, I. et al. Genetic differentiation and evolution of broad-leaved evergreen shrub and tree varieties of Daphniphyllum macropodum (Daphniphyllaceae). Heredity 131, 211–220 (2023). https://doi.org/10.1038/s41437-023-00637-2

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