핵 리보솜 DNA ITS 부위에 의한 조팝나무속 식물종의 계통 관계 분석 Analysis of the Phylogenetic Relationships in the Genus Spiraea Based on the Nuclear Ribosomal DNA ITS Region원문보기
조팝나무속(genus Spiraea) 식물은 다년생 목본으로 주로 아시아와 유럽에 분포하고 있다. 한국의 14종을 포함한 전 세계 38분류군에 대해 핵 내 리보솜 전사 서열(ITS)로 이 속의 유전적 관계를 평가하였다. 이 분자생물학적 자료로 분류군의 분지군은 잘 분리되었다. 47 계통(38 분류군: 14개 한국 분류군, 33개 세계 분류군, 9개 중복 분류군). 전체 689 bp 중에서452자리는 절약-정보적이었고, 527자리는 변이를 나타내었으나 절약-비정보적이었고, 159자리는 분류군 전체에서 변이가 전혀 없었다. 비록 계통도에서 잘 분리되었지만 형태적 특성과 지리적 분포와는 일치하지 않았다. 분리되는 자리수는 430이었으며 핵산 다양도(${\pi}$)는 0.281이였다. 중립가설 하에서 Tajima 검증 통계값(D) 은 0.5보다 큰 2.325였다. 따라서 자연 도태가 유전적 변이를 증가시키는 방향으로 작용하고 있었다.
조팝나무속(genus Spiraea) 식물은 다년생 목본으로 주로 아시아와 유럽에 분포하고 있다. 한국의 14종을 포함한 전 세계 38분류군에 대해 핵 내 리보솜 전사 서열(ITS)로 이 속의 유전적 관계를 평가하였다. 이 분자생물학적 자료로 분류군의 분지군은 잘 분리되었다. 47 계통(38 분류군: 14개 한국 분류군, 33개 세계 분류군, 9개 중복 분류군). 전체 689 bp 중에서452자리는 절약-정보적이었고, 527자리는 변이를 나타내었으나 절약-비정보적이었고, 159자리는 분류군 전체에서 변이가 전혀 없었다. 비록 계통도에서 잘 분리되었지만 형태적 특성과 지리적 분포와는 일치하지 않았다. 분리되는 자리수는 430이었으며 핵산 다양도(${\pi}$)는 0.281이였다. 중립가설 하에서 Tajima 검증 통계값(D) 은 0.5보다 큰 2.325였다. 따라서 자연 도태가 유전적 변이를 증가시키는 방향으로 작용하고 있었다.
Genus Spiraea is composed of many long-lived woody species that are primarily distributed throughout Asia and Europe. In this study, we evaluated a representative sample of the 38 taxa in the world, including 14 in Korea, with nuclear ribosomal DNA internal transcribed spacer sequences (ITS) to esti...
Genus Spiraea is composed of many long-lived woody species that are primarily distributed throughout Asia and Europe. In this study, we evaluated a representative sample of the 38 taxa in the world, including 14 in Korea, with nuclear ribosomal DNA internal transcribed spacer sequences (ITS) to estimate genetic relationships within the genus. The molecular data allowed us to resolve well-supported clades in the taxa. In 47 world accessions (38 taxa: 14 Korean taxa, 33 world taxa, and 9 overlapping taxa), total alignment length was 689 positions, of which 452 were parsimony informative, 527 variable, 75 singleton, and 159 constant characters. Although the phylogenic tree showed that many taxa of genus Spiraea were well separated from each other, many branches were not congruent with the morphological characteristics and geographical distributions of the genus. There were 430 segregating sites and the nucleotide diversity (${\pi}$) value was 0.281. Under the neutral mutation hypothesis, the probability that the Tajima test statistic (D) is positive (2.325) is more than 0.5. Therefore, there may be a site at which natural selection, which increases genetic variation, is operating.
Genus Spiraea is composed of many long-lived woody species that are primarily distributed throughout Asia and Europe. In this study, we evaluated a representative sample of the 38 taxa in the world, including 14 in Korea, with nuclear ribosomal DNA internal transcribed spacer sequences (ITS) to estimate genetic relationships within the genus. The molecular data allowed us to resolve well-supported clades in the taxa. In 47 world accessions (38 taxa: 14 Korean taxa, 33 world taxa, and 9 overlapping taxa), total alignment length was 689 positions, of which 452 were parsimony informative, 527 variable, 75 singleton, and 159 constant characters. Although the phylogenic tree showed that many taxa of genus Spiraea were well separated from each other, many branches were not congruent with the morphological characteristics and geographical distributions of the genus. There were 430 segregating sites and the nucleotide diversity (${\pi}$) value was 0.281. Under the neutral mutation hypothesis, the probability that the Tajima test statistic (D) is positive (2.325) is more than 0.5. Therefore, there may be a site at which natural selection, which increases genetic variation, is operating.
* AI 자동 식별 결과로 적합하지 않은 문장이 있을 수 있으니, 이용에 유의하시기 바랍니다.
문제 정의
The purpose of this research is to do molecular data support the current classification of the species within the genus Spiraea in Korea. In addition, molecular evidence assumes an important role in phylogenetic reconstruction of species in this genus.
제안 방법
Maximum parsimony: Heuristic searches were implemented in MEGA version 5 [16,17]under the maximum parsimony (MP) criteria with the accelerated transformation (ACCTRAN) option to optimize the state of unordered (Fitch) characters, 100 random sequence addition replicates, the tree bisection-reconnection (TBR) branch swapping, and gaps treated as a fifth character. Unweighted MP methods do not always take full advantage of the information contained in DNA sequences due to the presence of homoplasious characters.
Then we calculated the ML model parameters using the data partition of interest and a neighbor-joining topology. These estimated values were fixed, and a full heuristic ML search was conducted with 10 random addition sequence replicates, retaining all minimal trees, and TBR branch swapping. After this first ML search was completed, I reestimated model parameters on the ML tree and used these new values to search again.
대상 데이터
All positions containing gaps and missing data were eliminated. There were a total of 689 positions in the final dataset. Evolutionary analyses were conducted in MEGA5.
이론/모형
Codon-based tests of neutrality for analysis between ITS sequences of genus Spiraea were conducted using the Nei-Gojobori method.
Disparity index was calculated a simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences [6]. Estimates of evolutionary divergence between sequences were conducted using the maximum composite likelihood model [16].
Substitution pattern and rates were estimated under the Kimura 2-parameter model. The estimated Transition/Transversion biases (R) varied from 0.
성능/효과
0 g of fresh leaf material. A species of the closely related genus Stephanandra (Stephanandra incise (Thunb) Zabel) was included in the phylogenetic reconstruction as an outgroup.
ITS region for fourteen taxa of Spireae in Korea was successful in all of the species. Aligned nucleotide sequences of ITS were varied within Spireae varying from 625 in S.
The base furtherance did not showed a significant difference to the by a total taxa (Table 2). The mean nucleotide frequencies for fourteen taxa of genus Spireae in Korea are A=16.9%, C=30.8%, G=34.3%, and T=18.0% (Table 2).
참고문헌 (19)
Evans R. C. and T. A. Dickinson. 1999. Floral ontogeny and morphology in subfamily Spiraeoideae Endl. (Rosaceae). Int. J. Pl. Sci. 160, 981-1012.
Jorgensen, R. A. and P. D. Cluster. 1989. Modes and tempos in the evolution of nuclear ribosomal DNA: new characters for evolutionary studies and new markers for genetic and population studies. Ann. Mo. Bot. Gard. 75, 1238-1247.
Kim, T. J. 1991. A taxonomic study of the genus Spiraea in Korea. M.S. Thesis, Chungnam National University, Cheongju, Korea.
Kim, T. J. and B. Y. Sun. 1996. Taxonomy of the genus Spiraea in Korea. Kor. J. Plant Tax. 26, 191-212.
Kumar, S. and S. R. Gadagkar. 2001. Disparity Index: A simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences. Genetics 158, 1321-1327.
Lee, Y. M. 1992. Taxonomic study on the genus Spiraea in Korea: Specially referred to morphology and flavonoid characteristics. Ph. D. Thesis, Seoul National University, Seoul, Korea.
Lu, L. T. 1996. The evolution and distribution of subfam. Spiraeoideae (Rosaceae) of China, with special reference to distribution of the subfamily in the world. Acta Phytotaxonomica Sinica 34, 361-375.
Oh, S. H., L. Chen, S. H. Kim, Y. D. Kim, and H. Shin. 2010. Phylogenetic relationship of Physocarpus insularis (Rosaceae) endemic on Ulleung Island: Implications for conservation biology. J. Plant Biol. 53, 95-105.
Posada, D. and K. A. Crandall. 1998 MODELTEST: testing the model of DNA substitution. Bioinformatics 14, 817-818.
Potter, D., S. M. Still, T. Grebene, D. Ballian, G. Bozic, J. Franjiae, and H. Kraigher. 2007. Phylogenetic relationships in tribe Spiraeeae (Rosaceae) inferred from nucleotide sequence data. Pl. Syst. Evol. 266, 105-118.
Poyarkova, T. A. and G. N. Gatculira. 2008. Morphology and variability of pollen of the genus Spiraea L. (Rosaceae) in Siberia and the far east. Contempory Problems of Ecology 1, 420-424.
Rehder, A. 1940. Manual of Cultivated Trees and Shrubs.pp. 996, 2nd eds. Collier Macmillan, New York.
Richardson, J. E., R. T. Pennington, T. D. Pennington, and P. M. Hollingsworth. 2001. Rapid diversification of a species-rich genus of neotropical rain forest trees. Science 293, 2242-2245.
Swofford, D. L. 2002. PAUP* Version 4.0b10 for Macintosh. pp. 280, Sinauer Associates, Sunderland, MA.
Tamura, K., D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar. 2011. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol. Biol. Evol. 28, 2731-2739.
Tamura, K., M. Nei, and S. Kumar. 2004. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc. Natl. Acad. Sci. USA 101, 11030-11035.
White, T. J. T., S. Bruns, S. Lee, and J. Taylor. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, pp. 315-322, In Innis, M., D. Gelafand, J. Sninsky, and T. White (eds.), PCR Protocols: A Guide to Methods and Applications, Academic Press, San Diego, California, USA.
Zhang, Z., L. Fan, J. Yang, X. Hao, and Z. Gu. 2006. Alkaloid polymorphism and its sequence variation in the Spiraea japonica complex (Rosaceae) in China: traces of the biological effects of the Himalaya-Tibet plateau uplift. Am. J. Bot. 93, 762-769.
AI-Helper
※ AI-Helper는 부적절한 답변을 할 수 있습니다.