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Adaptive and Slightly Deleterious Evolution in a Conifer, Cryptomeria japonica

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Abstract

In order to evaluate effects of the population structure and natural selection on organisms having long generation times, we surveyed DNA polymorphisms at five loci encoding 9-cis-epoxycarotenoid dioxygenase (NCED), ammonium transporter, calmodulin, aquaporin, and the second major allergen with polymethylgalacturonase enzyme activity in the pollen (Cryj2) in a conifer, Cryptomeria japonica. The average nucleotide diversity at silent sites across 12 loci including the previously analyzed seven loci was 0.0044. The population recombination rate (4Nr, where N and r are the effective population size and recombination rate per base per generation, respectively) was estimated as 0.00046 and a slow reduction in the population size was indicated, according to the maximum likelihood method implemented in LAMARC. At NCED, the McDonald-Kreitman (MK) test revealed an excess of replacement polymorphisms, suggesting contributions of slightly deleterious mutations. In contrast, the MK test revealed an excess of replacement divergence at Cryj2 and a maximum likelihood approach using the PAML package revealed that certain amino acid sites had a nonsynonymous/synonymous substitution rate ratio (ω) > 4.0, indicating adaptive evolution at this locus. The overall analysis of the 12 loci suggested that adaptive, neutral, and slightly deleterious evolution played important roles in the evolution of C. japonica.

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Acknowledgments

We thank Hitoshi Araki and two anonymous referees for helpful comments on the manuscript. This work was partially supported by Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science (nos. 16370101, 19370099).

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Authors and Affiliations

  1. Department of Biology, Faculty of Sciences, Kyushu University, Ropponmatsu, Fukuoka, 810-8560, Japan

    Akihiro Fujimoto, Tomoyuki Kado & Hidenori Tachida

  2. Forestry and Forest Products Research Institute, Kukizaki, Ibaraki, 305-8687, Japan

    Hiroshi Yoshimaru & Yoshihiko Tsumura

Authors
  1. Akihiro Fujimoto
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  2. Tomoyuki Kado
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  5. Hidenori Tachida
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Correspondence to Hidenori Tachida.

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Fujimoto, A., Kado, T., Yoshimaru, H. et al. Adaptive and Slightly Deleterious Evolution in a Conifer, Cryptomeria japonica . J Mol Evol 67, 201–210 (2008). https://doi.org/10.1007/s00239-008-9140-2

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  • DOI: https://doi.org/10.1007/s00239-008-9140-2

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