大黄属CHS类基因的基因重复及适应性进化
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摘要
基因重复为植物应对环境胁迫机制的更新进化提供了丰富的遗传原材料,是植物进化的根本动力。植物通过基因重复,以及重复拷贝之间的表达分化,不仅为植物分化产生重要的生物功能,也为植物产生高度分化的适应性性状提供分子遗传基础。本研究选择经过快速辐射进化成种的典型代表、主要分布在青藏高原的大黄属物种作为研究对象,研究该类群中抗逆相关基因-类黄酮代谢途径的关键酶-查尔酮合成酶编码基因CHS类基因的进化式样。主要结果如下：
(1)使用克隆方法,在16个大黄属物种以及8个相关属物种中克隆获得了36条CHS类基因序列。系统发育分析表明,大黄属及其它属形成了明显的属特异性分支；大黄属类群没有形成种特异性的结构关系,而是属内物种聚在一起,来自于同一个祖先分支的两个拷贝分别聚类为明显的两大分支,分别为A分支和B分支,表明大黄属类群在其物种起源后,发生了一次快速、独立的基因重复事件；来自两种大黄(苞叶大黄和塔黄)基因组DNA的Gel bloting结果进一步证实了大黄属CHS-like发生了一次基因重复事件,基因组中CHS重复基因至少有2个拷贝。
(2)大黄属两个CHS基因拷贝CHSA和CHSB的同义替代率没有显著差别,而非同义替换率差异显著,重复基因CHSB有更高的非同义替换率,表明两者在进化选择上受到的约束明显不同；CHSB分支的ω是CHSA分支的3倍,likelihood分析结果也进一步表明两个分支之间差异显著。这些结果表明,大黄属B分支在经过基因重复后,非同义替代率显著增加,受到的选择压力显著高于A分支。同时,应用分支-位点模型,发现大黄CHSB分支编码氨基酸的一个位点受到了强烈的正选择(后验概率p=0.997)
(3)大黄属CHS基因exon2 DNA片段构建的系统发育关系中,大黄属种间遗传分化小,多呈平行分支,系统树反应的大黄属发育系统关系和基于叶绿体基因片段构建的系统进化关系基本相似,显示出典型的物种快速辐射多样化特征。
Gene duplication provides raw materials for further innovative evolution in plants in response to various stressful environments and natural selection. In this study, we aimed to examine evolutionary history of the CHS-like genes in the Rheum, a genus with a radiative history with its most species occurring mainly in the Qinghai-Tibetan Plateau. The main results and conclusions are listed as following,
(1)A total of 36 CHS-like sequences were obtained through sequencing the clones of the PCR CHS amplification of 16 Rheum species and eight ones from the other closely related genera. Phylogenetic analyses of these sequences suggested that all CHS-like sequences from Rheum comprised a monophyletic lineage and within the genus, two subclades with high supports were recovered. These analyses indicated that since origin of the genus Rheum, CHS had undergone an independent duplication. DNA Gel blotting analyses further confirmed this suggestion that at least two CHS-like members are present in two species.
(2) Based on the branch-model, the ratio of the non-synonymous and synonymous substitutions within the subclades A (ω1=0.1454) and B (ω2=0.4532) ratios were significantly different from each other and also the background ratioω0 (0.0222). It is suggested that an increase in the nonsynonymous substitution rate occurred in the lineage ancestral to CHSB after gene duplication. Branch-site model analyses also indicated that one site (G243) within the CHSB was driven significantly by positive selection with the posterior probability (P=0.997).
(3) Within each subclade, the relationships between different species were rarely recovered and the pattern is a typical "paralleling" phylogeny, suggesting a radiative diversificiation. This result is consistent with the previous phylogenetic analysis based on the chloroplast DNA sequences.
(1)使用克隆方法,在16个大黄属物种以及8个相关属物种中克隆获得了36条CHS类基因序列。系统发育分析表明,大黄属及其它属形成了明显的属特异性分支；大黄属类群没有形成种特异性的结构关系,而是属内物种聚在一起,来自于同一个祖先分支的两个拷贝分别聚类为明显的两大分支,分别为A分支和B分支,表明大黄属类群在其物种起源后,发生了一次快速、独立的基因重复事件；来自两种大黄(苞叶大黄和塔黄)基因组DNA的Gel bloting结果进一步证实了大黄属CHS-like发生了一次基因重复事件,基因组中CHS重复基因至少有2个拷贝。
(2)大黄属两个CHS基因拷贝CHSA和CHSB的同义替代率没有显著差别,而非同义替换率差异显著,重复基因CHSB有更高的非同义替换率,表明两者在进化选择上受到的约束明显不同；CHSB分支的ω是CHSA分支的3倍,likelihood分析结果也进一步表明两个分支之间差异显著。这些结果表明,大黄属B分支在经过基因重复后,非同义替代率显著增加,受到的选择压力显著高于A分支。同时,应用分支-位点模型,发现大黄CHSB分支编码氨基酸的一个位点受到了强烈的正选择(后验概率p=0.997)
(3)大黄属CHS基因exon2 DNA片段构建的系统发育关系中,大黄属种间遗传分化小,多呈平行分支,系统树反应的大黄属发育系统关系和基于叶绿体基因片段构建的系统进化关系基本相似,显示出典型的物种快速辐射多样化特征。
Gene duplication provides raw materials for further innovative evolution in plants in response to various stressful environments and natural selection. In this study, we aimed to examine evolutionary history of the CHS-like genes in the Rheum, a genus with a radiative history with its most species occurring mainly in the Qinghai-Tibetan Plateau. The main results and conclusions are listed as following,
(1)A total of 36 CHS-like sequences were obtained through sequencing the clones of the PCR CHS amplification of 16 Rheum species and eight ones from the other closely related genera. Phylogenetic analyses of these sequences suggested that all CHS-like sequences from Rheum comprised a monophyletic lineage and within the genus, two subclades with high supports were recovered. These analyses indicated that since origin of the genus Rheum, CHS had undergone an independent duplication. DNA Gel blotting analyses further confirmed this suggestion that at least two CHS-like members are present in two species.
(2) Based on the branch-model, the ratio of the non-synonymous and synonymous substitutions within the subclades A (ω1=0.1454) and B (ω2=0.4532) ratios were significantly different from each other and also the background ratioω0 (0.0222). It is suggested that an increase in the nonsynonymous substitution rate occurred in the lineage ancestral to CHSB after gene duplication. Branch-site model analyses also indicated that one site (G243) within the CHSB was driven significantly by positive selection with the posterior probability (P=0.997).
(3) Within each subclade, the relationships between different species were rarely recovered and the pattern is a typical "paralleling" phylogeny, suggesting a radiative diversificiation. This result is consistent with the previous phylogenetic analysis based on the chloroplast DNA sequences.
引文
李安仁.1998.中国植物志第25卷第1册,科学出版社
李吉均,施雅风,李炳元.1995.青藏高原隆升与全球变化,甘肃人民出版社,兰州
刘瑛心.1985.中国沙漠植物志.第一卷.北京：科学出版社,321～324
马德滋,刘惠兰.1986.宁夏植物志.第一卷.银川：宁夏人民出版社,88～90
马毓泉.1990.内蒙古植物志.第二卷,呼和浩特：内蒙古人民出版社,145～156
吴征镒.1983.西藏植物志.第一卷.北京：科学出版社,595～600
吴征镒.1984.云南种子植物名录.上册.昆明：云南人民出版社,283～284
吴家坤,张登科,杨永康等.1992.国产大黄属的新分类群.西北植物学报,12(4)：309～315
施雅风,李吉均,李炳元.1998.青藏高原晚新生代隆升与环境变化.广东：广东科技出版社
王玉金,刘建全.2004.利用叶绿体DNA trnL—F序列初步探讨菊科风毛菊属的系统发育.植物分类学报,42,136-153
谢宗强.2000.国产大黄属植物的生态地理分布.面向21世纪的中国生物多样性保护(许智宏)中国林业出版社
周以良(主编).1992.黑龙江省植物志.第四卷.哈尔滨：东北林业大学出版社,255-261
Arabidopsis Genome Initiative.2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408,796-815.
Barrier M., Robichaux R. H., Purugganan M. D.2001. Accelerated regulatory gene evolution in an adaptive radiation. Proc Natl Acad Sci U S A 98,10208-10213.
Blanc G., Wolfe K. H.2004. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16,1667-1678.
Bowers J. E., Chapman B. A., Rong J. and Paterson A. H.2003. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422,433-438.
Burki F, Kaessmann H.2004. Birth and adaptive evolution of a hominoid gene that supports high neurotransmitter flux. Nature genetics,36,1061～1063.
Chen S.1993. Polygonaceae. In, Wang, W., Wu, S., Lang, K., Li, P., Pu, F., Chen, S. (eds) Vascular plants of the Hengduan Mountains. Science Press, Beijing, pp 349-369
Clegg M.T., Cummings M. P., Durbin M. L.1997. The evolution of plant nuclear genes. Proc. Natl. Acad. Sci. USA.94,7791-7798.
Dara G.T. and Rama S. S.2004. Rapid evolution though gene duplication and subfunctionalization of the test-specific a4 proteasome subunits in Drosophila. Genetics 168, 1421-1432
Doyle J. J. and Doyle J. L.1987. A rapid isolation procedure for small quantities of fresh leaf material. Phytochem. Bull 19,11-15.
Durbin M. L., McCaig B., Clegg M. T.2000. Molecular evolution of the chalcone synthase multigene family in the morning glory genome. Plant Mol Biol 42,79-92.
Ermolaeva M. D., Wu M., Eisen J. A. and Salzberg S. L.2003. The age of the Arabidopsis thaliana genome duplication. Plant Mol Biol 51,859-866.
Felsenstein J.1981. Evolutionary trees from DNA sequences, a maximum likelihood approach. J. Mol. Evol.17,368-376..
Ferrer J. L., Jez J. M., Bowman M. E., Dixon R.A., Noel J. P.1999. Structure of chalcone synthase and the molecular basis of plant polyketide biosynthesis, Nat. Struct. Biol.6, 775-784.
Frankel N., Hasson E., Iusem N. D., Rossi M. S.2003. Adaptive evolution of the water stress-induced gene Asr2 in Lycopersicon species dwelling in arid habitats. Mol. Biol. Evol. 20,1955-1962.
Freeling M. and Thomas B. C.,2006. Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Research 16,805-814.
Fujita M., Fujita Y., Noutoshi Y., Takahashi F., Narusaka Y.2006. Crosstalk between abiotic and biotic stress responses, a current view from the points of convergence in the stress signaling networks. Curr Opin Plant Biol.9,436-442.
Gavrilets S. and Vose A.2005. Dynamic patterns of adaptive radiation. Proc. Natl. Acad. Sci. USA 102,18040-18045.
Gerlee P., Lundh T., Zhang B., Anderson A. R. A.2009. Gene divergence and pathway duplication in the metabolic network of yeast and digital organism. J. R. Soc. Interface 6,1233-1245
Goff S. A., Ricke D., Lan T. H., Presting G., Wang R., Dunn M., Glazebrook J., Sessions A., Oeller P., Varma H, et al.2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296,92-100.
Good-Avila S. V., Souza V., Gaut B. S., Eguiarte L. E.2006. Timing and rate of speciation in Agave (Agavaceae). Proc Natl Acad Sci U S A 103,9124-9129.
Grant V.1981. Plant Speciation (Columbia Univ. Press, New York) 2nd Ed. P.563.
Hahn M. W.2009. Distinguishing Among Evolutionary Models for the Maintenance of Gene Duplicates. Journal of Heredity 100 (5),605-617
Ha M., Kim E. D., Chen Z. J.2009. Duplicate genes increase expression diversity in closely related species and allopolyploids. Proc Natl Acad Sci USA 106 (7),2295-2300
Hanada K., Zou C., Lehti-Shiu M. D., Shinozaki K., Shiu S. H.2008. Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol 148,993-1003.
Harborne J. B.1994. The Flavonoids, Advances in Research since 1986. Chapman and Hall, London.
Harrison T. M., Copeland P., Kidd F., Yin A.1992. Raising Tibet. Science 255,1663-1670.
Hasegawa M., Kishino H., Yano T.,1985. Dating the human-ape split by a molecular clock of mitochondrial DNA. J. Mol. Evol.22,160-174.
Helariutta Y., Kotilainen M., Elomaa P., Kalkkinen N., Bremer K., Teeri T. H., Albert V. A.1996. Duplication and functional divergence in the chalcone synthase gene family of Asteraceae, Evolution with substrate change and catalytic simplification. Proc Natl Acad Sci USA 93, 9033-9038.
He X. and Zhang J.2005. Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics 169,1157-1164.
Hittinger C. T., Carroll S. B.2007. Gene duplication and the adaptive evolution of a classic genetic switch. Nature 449,677-681.
Hof K., Van B., Ronald G., Gravendeel B.2008. Chalcone Synthase Gene Lineage Diversification Confirms Allopolyploid Evolutionary Relationships of European Rostrate Violets. Mol. Biol. Evol.2510,2099-2108.
Hughes C, and Eastwood R.2006. Island radiation on a continental scale, exceptional rates of plant diversification after uplift of the Andes. Proc Natl Acad Sci U S A 103,10334-10339.
Innan H. and Kondrashov, F.2010. The evolution of gene duplications, classifying and distinguishing between models. Nature Reviews Genetics, doi,10.1038/nrg2689.
Iwashina T., Omori Y., Kitajima J., Akiyama S., Suzuki T., Ohba, H.2004. Flavonoids in translucent bracts of Himalayan Rheum nobile (Polygonceae) as ultraviolet shields. J. Plant Res.117,101-107
Jaillon O., Aury J. M., Noel B., et al.2007. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449,463-467.
Kong H. Z., Leebens-Mack J., Ni W. M., Pamphilis C. W., Ma H.2004. Highly heterogeneous rates of evolution in the SKP1 gene family in plants and animals, functional and evolutionary implications. Mol. Biol. Evol.21,117-128.
Ku H. M., Vision T., Liu J. Tanksley S. D.2000. Comparing sequenced segments of the tomato and Arabidopsis genomes, large-scale duplication followed by selective gene loss creates a network of synteny. Proc Natl Acad Sci U S A 97,9121-9126.
Kumar S., Tamura K., Jakobsen I. B., Nei M.,2001. MEGA2, molecular evolutionary genetics analysis software. Bioinformatics 17,1244-1245.
Langdale J. A., Taylor W. C., Nelson T.1991. Cell-specific accumulation of maize phospoenolpyruvate carboxylase is corrected with demethylation at a specific site>3kb upstream of the gene. Mol. Gen. Genet.225,49-55.
Li A. R.1998. Flora Republicae popularis Sinicae. Beijing, Science Press.
Liu R. R., Tian, X. M., Wang, A. L., Wan, D. S., Liu, J. Q.2010. Uniformity of katypotypes in Rheum (Polygonaceae), a species-rich genus in the Qinghai-Tibetan Plateau and adjacent regions. Caryologia 62,261-266
Li W. H.1997. Molecular evolution. Sinauer, Sunderland, M.A.
Li W. H., Yang J., Gu X.2005. Expression divergence between duplicate genes. TRENDS in Genetics 21(11),602-607
Li P., Bousquet J.,1992. Relative-rate test for nucleotide substitutions between two lineages. Mol. Biol. Evol.9,1185-1189.
Lockton S. and Gaut B. S.2005. Plant conserved non-coding sequences and paralogue evolution. Trends Genet 21,60-65.
Losina-Losinskaya A. S.,1936. The genus Rheum and its species. Acta Instituti Botanici
Academiae Scientiarum Unionis Rerum Publicarum Soveticarum Socialisticarum, Ser.1, 5-141.
Lukens L., and Zhan S.2007. The plant genome's methylation status and response to stress, Implications for plant improvement. Current Opinion in Plant Biology,10,317-322.
Lynch M. and Force A.2000. The probability of duplicate gene preservation by subfunctionalization. Genetics 154,459-473.
Lynch M. and Conery J. S.2000. The evolutionary fate and consequences of duplicate genes. Science 290,1151-1155.
Maere S., De Bodt S., Raes J., Casneuf T., Van Montagu M., Kuiper M., Van deeper Y.2005. Modeling gene and genome duplications in eukaryotes. Proc Natl Acad Sci USA 102, 5454-5459
Maryam F., David F., Soria-Hernanz M. A., Matthew B. H., Martha R. W., Heidi G. E.2005. Molecular evolution of the chalcone synthase gene family and identification of the expressed copy in flower petal tissue of Viola cornuta. Plant Science 168,1127-1134.
Masterson J.1994. Stomatal Size in Fossil Plants-Evidence for Polyploidy in Majority of Angiosperms. Science 264,421-424.
McGrath C.L., Casola C., and Hahn M.W.2009. Minimal effect of ectopic gene conversion among recent duplicates in four mammalian genomes. Genetics (in press), doi: 10.1534/genetics.109.101428.
Moore R. C. and Purugganan M. D.2003. The early stages of duplicate gene evolution. Proc Natl Acad Sci USA 100,15682-15687
Moore R. C. and Purugganan M. D.2005. The evolutionary dynamics of plant duplicate genes. Curr Opin Plant Biol 8,122-128
Morton B. R., Gaut B. S., Clegg M. T.1996. Evolution of alcohol dehydrogenase genes in the palm and grass families. Proc. Natl. Acad. Sci. U. S. A.93,11735-11739.
Nei M. and Gojobori T.1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol.3,418-426.
Nei M.2005. Selectionism and neutralism in molecular evolution. Mol. Biol. Evol.22, 2318-2342.
Nielsen R. and Yang Z.1998. Likelihood models for detecting positively selected amino acid sites
and application to the HIV-1 envelop gene. Genetics 148,929-936.
Ni Z., Kim E. D., Ha M., Lackey E., Liu J., Zhang Y., Sun Q., Chen Z. J.2009. Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature 457,327-331.
Nozawa M, Suzuki Y., Nei M.2009. Reliabilities of identifying positive selection by the branch-site and the site-prediction methods. Proc Natl Acad Sci USA 106:6700-6705.
Ohno S.,1970. Evolution by gene duplication. New York, Springer-Verlag.
Ohba H. and Malla S. B.1988.The Himalayan Plants. University of Tokyo Press, Tokyo.
Ohta T.1993. Pattern of nucleotide substitution in growth hormone-prolactin gene family, a paradigm for evolution by gene duplication. Genetics 134,1271-1276.
Omori Y. and Ohba H.,1999. Thermal condition of the inflorescence of a glasshouse plant, Rheum nobile Hook. f. and Thoms., and microclimatic features of its habitat in Jaljale Himal, east Nepal. Newslett Himalayan Bot.25,5-1.
Omori Y, Takayama H., Ohba H.2000. Selective light transmittance of translucent bracts in the Himalayan giant glasshous plant Rheum nobile HooK. F. and Thomson Polygonaceae.. Bot. J. Linn. Soc.132,19-27.
Papp B. et al.2003. Evolution of cis-regulatory elements in duplicated genes of yeast. Trends Genet.19,417-422.
Paterson A. H., Bowers J. E., Chapman B. A.2004. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci USA 101,9903-9908.
Paterson A. H., Chapman B. A., Kissinger J. C., Bowers J. E., Feltus F. A. and Estill J. C.2006. Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon. Trends Genet 22, 597-602.
Raes J., Vandepoele K., Simillion C., Saeys Y., Van de Peer Y.2003. Investigating ancient duplication events in the Arabidopsis genome. J Struct Funct Genomics 3,117-129
Richardson J. E., Pennington R. T., Pennington T. D., Hollingsworth P. M.2001. Rapid diversification of a species-rich genus of neotropical rain forest trees. Science 293, 2242-2245.
Rieseberg L. H. and Willis J. H.2007. Plant speciation. Science 317,910-914
Rizzon C., Ponger L., Gaut B. S.2006. Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice. PLoS Comput Biol 2, e115
Saitou N. and Nei M.,1987. The neighbor-joining method, a new method for reconstructing phylogenetic trees. Mol. Biol. Evol.4,406-425.
Sandve S. and Fjellhem S.2010. Did gene family expansions during the Eocene-Oligocene boundary climate cooling play a role in Pooideae adaptation to cool climates? Molecular Ecology doi:10.1111/j.1365-294X.2010.04629.x
Sawyer,S. A.1989. Statistical tests for detecting gene conversion. Mol. Biol. Evol.6,526-538.
Sawyer S.A.2000. GENECONV, Statistical Tests for Detecting Gene Conversion-Version 1.81. Department of Mathematics, Washington University, St. Louis, Mo.
Schein M., Yang Z. H., Mitchell-Olds T., Schmid K. J.2004. Rapid evolution of a pollenspecific oleosin-like gene family from Arabidopsis thaliana and closely related species. Mol. Biol. Evol.21,659-669.
Schluter D.2000. The ecology of adaptive radiation. Oxford University Press, Oxford, UK.
Seehausen O.2006. African cichlid fish, a model system in adaptive radiation research. Proc R Soc B273,1987-1998
Seoighe C. and Gehring C.2004. Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome. Trends Genet 20,461-464
Shen Y. Y., Liang L., Zhu Z. H., Zhou W. P., Irwin M. D., Zhang Y. P.2010. Adaptive evolution of energy metabolism genes and the origin of flight in bats. Proc Natl Acad Sci USA 107, 8666-8671
Shiu S. H., Byrnes J. K., Pan R., Zhang P., Li W. H.2006. Role of positive selection in the retention of duplicate genes in mammalian genomes. Proc Natl Acad Sci USA 103, 2232-2236
Shiu S. H., Shih M. C, Li W. H.2005. Transcription factor families have much higher expansion rates in plants than in animals. Plant Physiol.139,18-26
Simillion C., Vandepoele K., Van Montagu M. C., Zabeau M., Van de Peer Y.2002. The hidden duplication past of Arabidopsis thaliana. Proc Natl Acad Sci USA 99,13627-13632
Speth E. B., Lee Y. N., He S.Y.2007. Pathogen virulence factors as molecular probes of basic
plant cellular functions. Curr Opin Plant Biol 10,580-586.
Swofford D. L.,2001. PAUP*, Phylogenetic Analysis Using Parsimony PAUP and other methods..Version4.0 beta. Sinauer Associates, Sunderland, Mass.
Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. J.1997. The CLUSTAL-X windows interface, flexible strategies for multiple sequence alignment aides by quality analysis tools. Nucleic Acids Res.25,4875-4882.
Tuskan G. A., Difazio S., Jansson S., Bohlmann J., Grigoriev I., Hellsten U., Putnam N., Ralph S., Rombauts S., Salamov A., et al.2006. The genome of black cottonwood, Populus trichocarpa (Torr.& Gray). Science 313,1596-1604
Tsukaya H.2002. Optical and anatomical characteristics of bracts from the Chinese "glasshouse" plant, Rheum alexandrae Batalin Polygonaceae., Yunnan, China. J. Plant Res.115,59-63.
Ursula N. K., Barzen E., Bernhardt J.1987. Chalcone Synthase Genes in Plants:A Tool to Study Evolutionary Relationships. J Mol Evol.26,213-225
Vision T. J., Brown D. G., Tanksley S. D.2000. The origins of genomic duplications in Arabidopsis. Science 290,2114-2117
Vladimir-Shulaev D. C, Gad-Miller, Ron-Mittler.2008. Metabolomics for plant stress response. Physiologia Plantarum 132,199-208.
Wang A. L., Yang M. H., Liu J. Q.2005 Molecular Phylogeny, Recent Radiation and Evolution of Gross Morphology of the Rhubarb genus Rheum Polygonaceae. Inferred from Chloroplast DNA trnL-F Sequences. Ann. Bot.96,489-498.
Wang J., Qu L., Chen J., Gu, H., Chen Z.2000. Molecular evolution of the exon 2 of CHS genes and the possibility of its application to plant phylogenetic analysis. Chinese Sci. Bull. 45,1735-1742.
Wang X., Shi X., Hao B., Ge S. Luo J.2005. Duplication and DNA segmental loss in the rice genome, implications for diploidization. New Phytol.165,937-946.
Wang Y. J. and Liu J. Q.2004. A preliminary investigation on the phylogeny of Saussurea Asteraceae, Cardueae. based on chloroplast DNA trnL-F sequences. Acta Phytotaxonomica Sinica42(2),136-153.
Wang Y. J., Pan J. T., Liu S. W., Liu J. Q.2004. A new species of Saussurea (Asteraceae) from Tibet in west China and its systematic position according to ITS sequence analysis. Botanical Journal of the Linnean Society 147,349-356.
Wapinski I., Pfeffer A., Friedman N., Regev A.2007. Natural history and evolutionary principles of gene duplication in fungi. Nature 449,54-61
Wong WSW, Yang Z, Goldman N, Nielsen R.2004. Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 168:1041-1051.
Xiao H., Jiang N., Schaffner E., Stockinger E. J., Van der Knaap E.2008. A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science 319,1527-1530.
Yamaguchi-Shinozaki K. and Shinozaki K.2006. Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annual Review of Plant Biology 57, 781-803.
Yang J. and Gu H.2006. Duplication and divergent evolution of the CHS and CHS like genes in the chalcone synthase CHS superfamily. Chin Sci Bull.51,505-509.
Yang J., Gu H. Y., Yang Z. H.2004. Likelihood Analysis of the Chalcone Synthase Genes Suggests the Role of Positive Selection in Morning Glories Ipomoea. J. Mol Evol.58, 54-63.
Yang J., Huang J.X., Gu H.Y., Yang Z.2002. Duplication and adaptive evolution of the chalcone synthase genes of Dendranthema Asteraceae.. Mol. Biol. Evol.19,1752-1759.
Yang J., Wang Z. L., Zhao X.Q., Wang D.P., Qi D. L., Xu B. H., Ren Y. H., Tian H. F.2008. Natural selection and adaptive evolution of Leptin in the Ochotona family driven by the cold environmental stress. PLoS one 3, e1472.
Yang Z. H. and Nielsen R.2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol.19,908-917.
Yang Z. H., Nielsen R., Goldman N.2009. In defense of statistical methods for detecting positive selection. Proc Natl Acad Sci USA 106:E95, author reply E96.
Yang Z. H., Wong S.W., Nielsen R.2005. Bayes empirical Bayes inference of amino acid sites under positive selection. Mol. Biol. Evol.22,1107-1118.
Yu J., Wang S., Lin H.2005. The Genomes of Oryza sativa, a history of duplications. PLoS Biol. 3, e38.
Yu L., Wang X.Y., Jin W., Luan P. T., Ting N., Zhang Y. P.2010. Adaptive Evolution of Digestive RNASE1 Genes in Leaf-Eating Monkeys Revisited, New Insights from Ten Additional Colobines. Mol. Biol. Evol.27(1),121-131
Zhang J. M., Dean A. M., Brunet F., Long M. Y.2004. Evolving protein functional diversity in new genes of Drosophila. Proc. Natl. Acad. Sci. USA 101,16246-16250.
Zhang J. Z.2003. Evolution by gene duplication, an update. Trends in Ecology and Evolution,18 (6),292-298.
Zhang J. Z.2004. Frequent false detection of positive selection by the likelihood method with branch-site models. Mol. Biol. Evol.21,1332-1339.
Zhong Y., Zhao Q., Shi S. H., Huang Y. L., Hasegawa M.2002. Detecting evolutionary rate heterogeneity among mangroves and their close terrestrial relatives. Ecol. Lett.5,427-432.
Zhou D. W., Zhou J., Meng L. H., Wang Q. B., Xie X., Guan Y. C., Ma Z. Y., Zhong Y., Chen F., Liu J. Q.2009. Duplication and adaptive evolution of the COR15 genes within the highly cold-tolerant Draba lineage Brassicaceae. Gene 441,36-44.
Zou C., Lehti-Shiu M. D., Thomashow M., Shiu S. H.2009. Evolution of Stress-Regulated Gene Expression in Duplicate Genes of Arabidopsis thaliana. PLoS Genet.57, e1000581. doi,10.1371/journal.pgen.1000581.
李吉均,施雅风,李炳元.1995.青藏高原隆升与全球变化,甘肃人民出版社,兰州
刘瑛心.1985.中国沙漠植物志.第一卷.北京：科学出版社,321～324
马德滋,刘惠兰.1986.宁夏植物志.第一卷.银川：宁夏人民出版社,88～90
马毓泉.1990.内蒙古植物志.第二卷,呼和浩特：内蒙古人民出版社,145～156
吴征镒.1983.西藏植物志.第一卷.北京：科学出版社,595～600
吴征镒.1984.云南种子植物名录.上册.昆明：云南人民出版社,283～284
吴家坤,张登科,杨永康等.1992.国产大黄属的新分类群.西北植物学报,12(4)：309～315
施雅风,李吉均,李炳元.1998.青藏高原晚新生代隆升与环境变化.广东：广东科技出版社
王玉金,刘建全.2004.利用叶绿体DNA trnL—F序列初步探讨菊科风毛菊属的系统发育.植物分类学报,42,136-153
谢宗强.2000.国产大黄属植物的生态地理分布.面向21世纪的中国生物多样性保护(许智宏)中国林业出版社
周以良(主编).1992.黑龙江省植物志.第四卷.哈尔滨：东北林业大学出版社,255-261
Arabidopsis Genome Initiative.2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408,796-815.
Barrier M., Robichaux R. H., Purugganan M. D.2001. Accelerated regulatory gene evolution in an adaptive radiation. Proc Natl Acad Sci U S A 98,10208-10213.
Blanc G., Wolfe K. H.2004. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16,1667-1678.
Bowers J. E., Chapman B. A., Rong J. and Paterson A. H.2003. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422,433-438.
Burki F, Kaessmann H.2004. Birth and adaptive evolution of a hominoid gene that supports high neurotransmitter flux. Nature genetics,36,1061～1063.
Chen S.1993. Polygonaceae. In, Wang, W., Wu, S., Lang, K., Li, P., Pu, F., Chen, S. (eds) Vascular plants of the Hengduan Mountains. Science Press, Beijing, pp 349-369
Clegg M.T., Cummings M. P., Durbin M. L.1997. The evolution of plant nuclear genes. Proc. Natl. Acad. Sci. USA.94,7791-7798.
Dara G.T. and Rama S. S.2004. Rapid evolution though gene duplication and subfunctionalization of the test-specific a4 proteasome subunits in Drosophila. Genetics 168, 1421-1432
Doyle J. J. and Doyle J. L.1987. A rapid isolation procedure for small quantities of fresh leaf material. Phytochem. Bull 19,11-15.
Durbin M. L., McCaig B., Clegg M. T.2000. Molecular evolution of the chalcone synthase multigene family in the morning glory genome. Plant Mol Biol 42,79-92.
Ermolaeva M. D., Wu M., Eisen J. A. and Salzberg S. L.2003. The age of the Arabidopsis thaliana genome duplication. Plant Mol Biol 51,859-866.
Felsenstein J.1981. Evolutionary trees from DNA sequences, a maximum likelihood approach. J. Mol. Evol.17,368-376..
Ferrer J. L., Jez J. M., Bowman M. E., Dixon R.A., Noel J. P.1999. Structure of chalcone synthase and the molecular basis of plant polyketide biosynthesis, Nat. Struct. Biol.6, 775-784.
Frankel N., Hasson E., Iusem N. D., Rossi M. S.2003. Adaptive evolution of the water stress-induced gene Asr2 in Lycopersicon species dwelling in arid habitats. Mol. Biol. Evol. 20,1955-1962.
Freeling M. and Thomas B. C.,2006. Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Research 16,805-814.
Fujita M., Fujita Y., Noutoshi Y., Takahashi F., Narusaka Y.2006. Crosstalk between abiotic and biotic stress responses, a current view from the points of convergence in the stress signaling networks. Curr Opin Plant Biol.9,436-442.
Gavrilets S. and Vose A.2005. Dynamic patterns of adaptive radiation. Proc. Natl. Acad. Sci. USA 102,18040-18045.
Gerlee P., Lundh T., Zhang B., Anderson A. R. A.2009. Gene divergence and pathway duplication in the metabolic network of yeast and digital organism. J. R. Soc. Interface 6,1233-1245
Goff S. A., Ricke D., Lan T. H., Presting G., Wang R., Dunn M., Glazebrook J., Sessions A., Oeller P., Varma H, et al.2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296,92-100.
Good-Avila S. V., Souza V., Gaut B. S., Eguiarte L. E.2006. Timing and rate of speciation in Agave (Agavaceae). Proc Natl Acad Sci U S A 103,9124-9129.
Grant V.1981. Plant Speciation (Columbia Univ. Press, New York) 2nd Ed. P.563.
Hahn M. W.2009. Distinguishing Among Evolutionary Models for the Maintenance of Gene Duplicates. Journal of Heredity 100 (5),605-617
Ha M., Kim E. D., Chen Z. J.2009. Duplicate genes increase expression diversity in closely related species and allopolyploids. Proc Natl Acad Sci USA 106 (7),2295-2300
Hanada K., Zou C., Lehti-Shiu M. D., Shinozaki K., Shiu S. H.2008. Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol 148,993-1003.
Harborne J. B.1994. The Flavonoids, Advances in Research since 1986. Chapman and Hall, London.
Harrison T. M., Copeland P., Kidd F., Yin A.1992. Raising Tibet. Science 255,1663-1670.
Hasegawa M., Kishino H., Yano T.,1985. Dating the human-ape split by a molecular clock of mitochondrial DNA. J. Mol. Evol.22,160-174.
Helariutta Y., Kotilainen M., Elomaa P., Kalkkinen N., Bremer K., Teeri T. H., Albert V. A.1996. Duplication and functional divergence in the chalcone synthase gene family of Asteraceae, Evolution with substrate change and catalytic simplification. Proc Natl Acad Sci USA 93, 9033-9038.
He X. and Zhang J.2005. Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics 169,1157-1164.
Hittinger C. T., Carroll S. B.2007. Gene duplication and the adaptive evolution of a classic genetic switch. Nature 449,677-681.
Hof K., Van B., Ronald G., Gravendeel B.2008. Chalcone Synthase Gene Lineage Diversification Confirms Allopolyploid Evolutionary Relationships of European Rostrate Violets. Mol. Biol. Evol.2510,2099-2108.
Hughes C, and Eastwood R.2006. Island radiation on a continental scale, exceptional rates of plant diversification after uplift of the Andes. Proc Natl Acad Sci U S A 103,10334-10339.
Innan H. and Kondrashov, F.2010. The evolution of gene duplications, classifying and distinguishing between models. Nature Reviews Genetics, doi,10.1038/nrg2689.
Iwashina T., Omori Y., Kitajima J., Akiyama S., Suzuki T., Ohba, H.2004. Flavonoids in translucent bracts of Himalayan Rheum nobile (Polygonceae) as ultraviolet shields. J. Plant Res.117,101-107
Jaillon O., Aury J. M., Noel B., et al.2007. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449,463-467.
Kong H. Z., Leebens-Mack J., Ni W. M., Pamphilis C. W., Ma H.2004. Highly heterogeneous rates of evolution in the SKP1 gene family in plants and animals, functional and evolutionary implications. Mol. Biol. Evol.21,117-128.
Ku H. M., Vision T., Liu J. Tanksley S. D.2000. Comparing sequenced segments of the tomato and Arabidopsis genomes, large-scale duplication followed by selective gene loss creates a network of synteny. Proc Natl Acad Sci U S A 97,9121-9126.
Kumar S., Tamura K., Jakobsen I. B., Nei M.,2001. MEGA2, molecular evolutionary genetics analysis software. Bioinformatics 17,1244-1245.
Langdale J. A., Taylor W. C., Nelson T.1991. Cell-specific accumulation of maize phospoenolpyruvate carboxylase is corrected with demethylation at a specific site>3kb upstream of the gene. Mol. Gen. Genet.225,49-55.
Li A. R.1998. Flora Republicae popularis Sinicae. Beijing, Science Press.
Liu R. R., Tian, X. M., Wang, A. L., Wan, D. S., Liu, J. Q.2010. Uniformity of katypotypes in Rheum (Polygonaceae), a species-rich genus in the Qinghai-Tibetan Plateau and adjacent regions. Caryologia 62,261-266
Li W. H.1997. Molecular evolution. Sinauer, Sunderland, M.A.
Li W. H., Yang J., Gu X.2005. Expression divergence between duplicate genes. TRENDS in Genetics 21(11),602-607
Li P., Bousquet J.,1992. Relative-rate test for nucleotide substitutions between two lineages. Mol. Biol. Evol.9,1185-1189.
Lockton S. and Gaut B. S.2005. Plant conserved non-coding sequences and paralogue evolution. Trends Genet 21,60-65.
Losina-Losinskaya A. S.,1936. The genus Rheum and its species. Acta Instituti Botanici
Academiae Scientiarum Unionis Rerum Publicarum Soveticarum Socialisticarum, Ser.1, 5-141.
Lukens L., and Zhan S.2007. The plant genome's methylation status and response to stress, Implications for plant improvement. Current Opinion in Plant Biology,10,317-322.
Lynch M. and Force A.2000. The probability of duplicate gene preservation by subfunctionalization. Genetics 154,459-473.
Lynch M. and Conery J. S.2000. The evolutionary fate and consequences of duplicate genes. Science 290,1151-1155.
Maere S., De Bodt S., Raes J., Casneuf T., Van Montagu M., Kuiper M., Van deeper Y.2005. Modeling gene and genome duplications in eukaryotes. Proc Natl Acad Sci USA 102, 5454-5459
Maryam F., David F., Soria-Hernanz M. A., Matthew B. H., Martha R. W., Heidi G. E.2005. Molecular evolution of the chalcone synthase gene family and identification of the expressed copy in flower petal tissue of Viola cornuta. Plant Science 168,1127-1134.
Masterson J.1994. Stomatal Size in Fossil Plants-Evidence for Polyploidy in Majority of Angiosperms. Science 264,421-424.
McGrath C.L., Casola C., and Hahn M.W.2009. Minimal effect of ectopic gene conversion among recent duplicates in four mammalian genomes. Genetics (in press), doi: 10.1534/genetics.109.101428.
Moore R. C. and Purugganan M. D.2003. The early stages of duplicate gene evolution. Proc Natl Acad Sci USA 100,15682-15687
Moore R. C. and Purugganan M. D.2005. The evolutionary dynamics of plant duplicate genes. Curr Opin Plant Biol 8,122-128
Morton B. R., Gaut B. S., Clegg M. T.1996. Evolution of alcohol dehydrogenase genes in the palm and grass families. Proc. Natl. Acad. Sci. U. S. A.93,11735-11739.
Nei M. and Gojobori T.1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol.3,418-426.
Nei M.2005. Selectionism and neutralism in molecular evolution. Mol. Biol. Evol.22, 2318-2342.
Nielsen R. and Yang Z.1998. Likelihood models for detecting positively selected amino acid sites
and application to the HIV-1 envelop gene. Genetics 148,929-936.
Ni Z., Kim E. D., Ha M., Lackey E., Liu J., Zhang Y., Sun Q., Chen Z. J.2009. Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature 457,327-331.
Nozawa M, Suzuki Y., Nei M.2009. Reliabilities of identifying positive selection by the branch-site and the site-prediction methods. Proc Natl Acad Sci USA 106:6700-6705.
Ohno S.,1970. Evolution by gene duplication. New York, Springer-Verlag.
Ohba H. and Malla S. B.1988.The Himalayan Plants. University of Tokyo Press, Tokyo.
Ohta T.1993. Pattern of nucleotide substitution in growth hormone-prolactin gene family, a paradigm for evolution by gene duplication. Genetics 134,1271-1276.
Omori Y. and Ohba H.,1999. Thermal condition of the inflorescence of a glasshouse plant, Rheum nobile Hook. f. and Thoms., and microclimatic features of its habitat in Jaljale Himal, east Nepal. Newslett Himalayan Bot.25,5-1.
Omori Y, Takayama H., Ohba H.2000. Selective light transmittance of translucent bracts in the Himalayan giant glasshous plant Rheum nobile HooK. F. and Thomson Polygonaceae.. Bot. J. Linn. Soc.132,19-27.
Papp B. et al.2003. Evolution of cis-regulatory elements in duplicated genes of yeast. Trends Genet.19,417-422.
Paterson A. H., Bowers J. E., Chapman B. A.2004. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci USA 101,9903-9908.
Paterson A. H., Chapman B. A., Kissinger J. C., Bowers J. E., Feltus F. A. and Estill J. C.2006. Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon. Trends Genet 22, 597-602.
Raes J., Vandepoele K., Simillion C., Saeys Y., Van de Peer Y.2003. Investigating ancient duplication events in the Arabidopsis genome. J Struct Funct Genomics 3,117-129
Richardson J. E., Pennington R. T., Pennington T. D., Hollingsworth P. M.2001. Rapid diversification of a species-rich genus of neotropical rain forest trees. Science 293, 2242-2245.
Rieseberg L. H. and Willis J. H.2007. Plant speciation. Science 317,910-914
Rizzon C., Ponger L., Gaut B. S.2006. Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice. PLoS Comput Biol 2, e115
Saitou N. and Nei M.,1987. The neighbor-joining method, a new method for reconstructing phylogenetic trees. Mol. Biol. Evol.4,406-425.
Sandve S. and Fjellhem S.2010. Did gene family expansions during the Eocene-Oligocene boundary climate cooling play a role in Pooideae adaptation to cool climates? Molecular Ecology doi:10.1111/j.1365-294X.2010.04629.x
Sawyer,S. A.1989. Statistical tests for detecting gene conversion. Mol. Biol. Evol.6,526-538.
Sawyer S.A.2000. GENECONV, Statistical Tests for Detecting Gene Conversion-Version 1.81. Department of Mathematics, Washington University, St. Louis, Mo.
Schein M., Yang Z. H., Mitchell-Olds T., Schmid K. J.2004. Rapid evolution of a pollenspecific oleosin-like gene family from Arabidopsis thaliana and closely related species. Mol. Biol. Evol.21,659-669.
Schluter D.2000. The ecology of adaptive radiation. Oxford University Press, Oxford, UK.
Seehausen O.2006. African cichlid fish, a model system in adaptive radiation research. Proc R Soc B273,1987-1998
Seoighe C. and Gehring C.2004. Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome. Trends Genet 20,461-464
Shen Y. Y., Liang L., Zhu Z. H., Zhou W. P., Irwin M. D., Zhang Y. P.2010. Adaptive evolution of energy metabolism genes and the origin of flight in bats. Proc Natl Acad Sci USA 107, 8666-8671
Shiu S. H., Byrnes J. K., Pan R., Zhang P., Li W. H.2006. Role of positive selection in the retention of duplicate genes in mammalian genomes. Proc Natl Acad Sci USA 103, 2232-2236
Shiu S. H., Shih M. C, Li W. H.2005. Transcription factor families have much higher expansion rates in plants than in animals. Plant Physiol.139,18-26
Simillion C., Vandepoele K., Van Montagu M. C., Zabeau M., Van de Peer Y.2002. The hidden duplication past of Arabidopsis thaliana. Proc Natl Acad Sci USA 99,13627-13632
Speth E. B., Lee Y. N., He S.Y.2007. Pathogen virulence factors as molecular probes of basic
plant cellular functions. Curr Opin Plant Biol 10,580-586.
Swofford D. L.,2001. PAUP*, Phylogenetic Analysis Using Parsimony PAUP and other methods..Version4.0 beta. Sinauer Associates, Sunderland, Mass.
Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. J.1997. The CLUSTAL-X windows interface, flexible strategies for multiple sequence alignment aides by quality analysis tools. Nucleic Acids Res.25,4875-4882.
Tuskan G. A., Difazio S., Jansson S., Bohlmann J., Grigoriev I., Hellsten U., Putnam N., Ralph S., Rombauts S., Salamov A., et al.2006. The genome of black cottonwood, Populus trichocarpa (Torr.& Gray). Science 313,1596-1604
Tsukaya H.2002. Optical and anatomical characteristics of bracts from the Chinese "glasshouse" plant, Rheum alexandrae Batalin Polygonaceae., Yunnan, China. J. Plant Res.115,59-63.
Ursula N. K., Barzen E., Bernhardt J.1987. Chalcone Synthase Genes in Plants:A Tool to Study Evolutionary Relationships. J Mol Evol.26,213-225
Vision T. J., Brown D. G., Tanksley S. D.2000. The origins of genomic duplications in Arabidopsis. Science 290,2114-2117
Vladimir-Shulaev D. C, Gad-Miller, Ron-Mittler.2008. Metabolomics for plant stress response. Physiologia Plantarum 132,199-208.
Wang A. L., Yang M. H., Liu J. Q.2005 Molecular Phylogeny, Recent Radiation and Evolution of Gross Morphology of the Rhubarb genus Rheum Polygonaceae. Inferred from Chloroplast DNA trnL-F Sequences. Ann. Bot.96,489-498.
Wang J., Qu L., Chen J., Gu, H., Chen Z.2000. Molecular evolution of the exon 2 of CHS genes and the possibility of its application to plant phylogenetic analysis. Chinese Sci. Bull. 45,1735-1742.
Wang X., Shi X., Hao B., Ge S. Luo J.2005. Duplication and DNA segmental loss in the rice genome, implications for diploidization. New Phytol.165,937-946.
Wang Y. J. and Liu J. Q.2004. A preliminary investigation on the phylogeny of Saussurea Asteraceae, Cardueae. based on chloroplast DNA trnL-F sequences. Acta Phytotaxonomica Sinica42(2),136-153.
Wang Y. J., Pan J. T., Liu S. W., Liu J. Q.2004. A new species of Saussurea (Asteraceae) from Tibet in west China and its systematic position according to ITS sequence analysis. Botanical Journal of the Linnean Society 147,349-356.
Wapinski I., Pfeffer A., Friedman N., Regev A.2007. Natural history and evolutionary principles of gene duplication in fungi. Nature 449,54-61
Wong WSW, Yang Z, Goldman N, Nielsen R.2004. Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 168:1041-1051.
Xiao H., Jiang N., Schaffner E., Stockinger E. J., Van der Knaap E.2008. A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science 319,1527-1530.
Yamaguchi-Shinozaki K. and Shinozaki K.2006. Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annual Review of Plant Biology 57, 781-803.
Yang J. and Gu H.2006. Duplication and divergent evolution of the CHS and CHS like genes in the chalcone synthase CHS superfamily. Chin Sci Bull.51,505-509.
Yang J., Gu H. Y., Yang Z. H.2004. Likelihood Analysis of the Chalcone Synthase Genes Suggests the Role of Positive Selection in Morning Glories Ipomoea. J. Mol Evol.58, 54-63.
Yang J., Huang J.X., Gu H.Y., Yang Z.2002. Duplication and adaptive evolution of the chalcone synthase genes of Dendranthema Asteraceae.. Mol. Biol. Evol.19,1752-1759.
Yang J., Wang Z. L., Zhao X.Q., Wang D.P., Qi D. L., Xu B. H., Ren Y. H., Tian H. F.2008. Natural selection and adaptive evolution of Leptin in the Ochotona family driven by the cold environmental stress. PLoS one 3, e1472.
Yang Z. H. and Nielsen R.2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol.19,908-917.
Yang Z. H., Nielsen R., Goldman N.2009. In defense of statistical methods for detecting positive selection. Proc Natl Acad Sci USA 106:E95, author reply E96.
Yang Z. H., Wong S.W., Nielsen R.2005. Bayes empirical Bayes inference of amino acid sites under positive selection. Mol. Biol. Evol.22,1107-1118.
Yu J., Wang S., Lin H.2005. The Genomes of Oryza sativa, a history of duplications. PLoS Biol. 3, e38.
Yu L., Wang X.Y., Jin W., Luan P. T., Ting N., Zhang Y. P.2010. Adaptive Evolution of Digestive RNASE1 Genes in Leaf-Eating Monkeys Revisited, New Insights from Ten Additional Colobines. Mol. Biol. Evol.27(1),121-131
Zhang J. M., Dean A. M., Brunet F., Long M. Y.2004. Evolving protein functional diversity in new genes of Drosophila. Proc. Natl. Acad. Sci. USA 101,16246-16250.
Zhang J. Z.2003. Evolution by gene duplication, an update. Trends in Ecology and Evolution,18 (6),292-298.
Zhang J. Z.2004. Frequent false detection of positive selection by the likelihood method with branch-site models. Mol. Biol. Evol.21,1332-1339.
Zhong Y., Zhao Q., Shi S. H., Huang Y. L., Hasegawa M.2002. Detecting evolutionary rate heterogeneity among mangroves and their close terrestrial relatives. Ecol. Lett.5,427-432.
Zhou D. W., Zhou J., Meng L. H., Wang Q. B., Xie X., Guan Y. C., Ma Z. Y., Zhong Y., Chen F., Liu J. Q.2009. Duplication and adaptive evolution of the COR15 genes within the highly cold-tolerant Draba lineage Brassicaceae. Gene 441,36-44.
Zou C., Lehti-Shiu M. D., Thomashow M., Shiu S. H.2009. Evolution of Stress-Regulated Gene Expression in Duplicate Genes of Arabidopsis thaliana. PLoS Genet.57, e1000581. doi,10.1371/journal.pgen.1000581.
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