TY - JOUR
T1 - Adaptive and slightly deleterious evolution in a conifer, Cryptomeria japonica
AU - Fujimoto, Akihiro
AU - Kado, Tomoyuki
AU - Yoshimaru, Hiroshi
AU - Tsumura, Yoshihiko
AU - Tachida, Hidenori
N1 - Funding Information:
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).
PY - 2008/8
Y1 - 2008/8
N2 - 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.
AB - 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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U2 - 10.1007/s00239-008-9140-2
DO - 10.1007/s00239-008-9140-2
M3 - Article
C2 - 18629428
AN - SCOPUS:50249124481
SN - 0022-2844
VL - 67
SP - 201
EP - 210
JO - Journal of Molecular Evolution
JF - Journal of Molecular Evolution
IS - 2
ER -