在植物中，模式物種阿拉伯芥和其野外近緣種的相繼研究使其成為研究遺傳和演化的良好素材。本研究探討阿拉伯芥chalcone synthase ( CHS )基因家族所受的天擇效應與模式以及其它內在的演化力量的影響，並與近緣物種A. halleri ssp. gemmifera 的結果做比對。本研究選用阿拉伯芥第5 條染色體上的 CHS 基因座、與第1 條和第4 條染色體上的CHS-like 基因座所組成的基因家族成員代表，研究發現阿拉伯芥CHS 基因家族皆有過多的低頻率多型性，造成Tajima’s D過度負值且顯著的現象，在其他前人研究的阿拉伯芥基因中也具有同樣的現象，推論此為阿拉伯芥族群曾快速擴張的內部演化力量結果，因此效應作用在整個基因組中。本研究以noncoding與coding區和非同義及同義置換區域的Tajima’s D 值進行比對以檢測基因是否天擇作用影響。研究顯示CHS基因家族中的CHS基因在阿拉伯芥與A. halleri ssp. gemmifera 同源基因中皆受到負向天擇力量，並且在構成酵素活性區的序列附近皆無非同義置換變異顯示其基因的保守性。CHS基因家族中的CHS-like基因(第4條染色體)在阿拉伯芥中偏向負向天擇作用，但在A. halleri ssp. gemmifera中則傾向正向天擇作用顯示在物種分化後，同源基因在不同物種中受到不同的天擇效應。相對地第1條染色體上的另一CHS-like 基因在阿拉伯芥中受到正向天擇作用，而在A. halleri ssp. gemmifera中則是受到制衡性天擇。研究顯示CHS基因家族中的三個基因受到的天擇力量並不一致，且在阿拉伯芥與A. halleri ssp. gemmifera近緣物種間的分化亦受到不同的天擇效應。

　　As a model plant, Arabidopsis thaliana and its wild relatives have played an important role in the study of genomics and evolution of plants. Members of a gene family determining the expression of chalcone synthase (CHS), a key enzyme of the flavonoids pathway, have been identified. This study examines the genetic diversity at chalcone synthase gene in the fifth chromosome, and chalcone synthase-like genes in the first and fourth chromosomes of Arabidopsis thaliana and its relatives. Significantly negative Tajima’s D values are detected in the three members of CHS gene family of Arabidopsis thaliana due to excessive low-frequency polymorphisms among nucleotide sequences, a phenomenon prevailing in most genes in this inbreeding species and thus indicating effects of recent demographic expansion. Tajima’s D values are estimated from noncoding and coding regions, as well as from nonsynonymous and synonymous substitution sites for examing modes of natural selection. CHS gene is under the negative selection in Arabidopsis thaliana and A. halleri ssp. gemmifera. In both species, no variation existed in the active sites of the CHS gene. CHS-like gene (chromosome 4) is under negative selection in Arabidopsis thaliana, while driven by positive selection in A. halleri ssp. gemmifera. In contrast, the other CHS-like gene (chromosome 1) is shaped by positive selection in Arabidopsis thaliana, while under balancing selection in the A. halleri ssp. gemmifera. Apparently, different evolutionary forces have shaped the three members of the CHS gene family in Arabidopsis thaliana and related A. halleri ssp. gemmifera.

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