中文摘要
本研究根據細胞核DNA之internal transcribed spacer及葉綠體DNA（trnL(UAA)3'exon與trnF(GAA)之間的intergenic spacer, IGS；以及trnL(UAA)5'exon與trnL(UAA)3'exon之間的intron, trn-L）之非轉譯區DNA序列資料，針對龍膽屬內小龍膽組32個分類群之分子親緣關係進行研究，並探討台灣特產種類的起源問題。
研究龍膽屬類群發現，DNA序列自核基因組共獲得約453~479bp，自葉綠體基因組共得到626~740bp，每分類群共獲得約1,100~1,200 bp的資料；合併資料組經排序後得到1450個序列特徵，共計690個變異位置及422個儉約訊息位置，屬內分類群間則具5~227bp的差異。比較核基因組及葉綠體基因組後序列資料發現，前者之G＋C content 為56.4%~61.5%之間，後者則僅33.6%~36.7%；而兩個基因組的核酸取代率差異不大，且依該序列資料所建構之親緣關係亦具一致性。
綜合本研究與前人所報導之核基因組序列資料（ITS1＋ITS2），所建構之親緣關係樹在組層級方面，支持小龍膽組種類為單系群的假說。合併基因組在解析小龍膽組內的系層級關係上，發現菔根系與流蘇系為單系群，帚枝系具有並系群的現象，卵萼系、線葉系，及小龍膽系則呈現為複系群。
台灣特有的小龍膽類群，根據分子親緣關係，應為兩個起源。其中一個分支包含11個分類群（台灣黃花龍膽群），其姊妹群為菔根系，兩者具有相當長的演化距離，表示已隔離分化相當世代；另一起源則僅有台東龍膽一種，其姊妹群為卵萼系的鱗葉龍膽，兩者演化距離短，可能為新近才隔離分化的類群。
上述分子序列資料外，綜合染色體數目及地理分布與生態習性的相關研究發現，台灣黃花龍膽群在種類間具有穩定的形態差異，但卻呈現低的遺傳變異度，顯然為最近才快速種化的類群；而根據生育地隔離現象明顯且變動性高，加上染色體數目為兩組連續變異，且與形態的歸群相關，研判族群之間因生育習性所造成的阻隔，加上染色體數目不整倍化的現象，應為造成台灣黃花龍膽群快速種化的重要機制。

Abstract
Nucleotide sequences of the internal transcribed spacers of nuclear ribosomal DNA and sequences of two chloroplast DNA noncoding regions of the trnL intron (trn-L) and the intergenic spacer between the trnL and the trnF genes of 32 species of sect. Chondrophyllae were determined and analysed phylogenetically, together with some species of other sections of the genus Gentiana. Based on the sequence data, the origination of endemic species of Taiwan is inferred.
The length of nrDNA on ITS1 + ITS2 in the taxa surveyed ranged from 453 to 479 bp and cpDNA on IGS + trn-L from 626 to 740 bp. Totally, about 1100 to 1200 bp sequence data in these taxa are obtained. Of the aligned sequences of 1450 positions, 690 variable sites and 422 parsimony sites existed. Pairwise comparisons among Gentiana species showed that sequences diverge from 5 to 227 bp. Comparison of the substitution rates among sequences revealed that nrDNA and cpDNA possess similar sequence divergence. The G + C content varied from 56.4% to 61.5% in nrDNA and from 32.6% to 36.7% in cpDNA. Both the sequence data from nrDNA and cpDNA give concordant phylogenetic trees.
By incorporating previously released ITS1 and ITS2 sequence data of 20 other species into phylogenetic analyses, the ITS phylogeny supports the monophyly of the sect. Chondrophyllae. Based on NJ tree of combined data (nrDNA + cpDNA) of the sect. Chondrophyllae, both ser. Napuliferae and Fimbriatae are revealed monophyly, but ser. Fastigiatae is the paraphyly. In contrast, series Orbiculatae, Linearifoliae, and Humiles are polyphyletic groups.
All the twelve Taiwanese taxa of sect. Chondrophyllae are endemic. They were shown to have two origins according to the molecular phylogeny. Among them, a well-supported clade of eleven taxa (Taiwanese yellow-flowered gentians) is closely related to the ser. Napuliferae. In contrast, another lineage contains only a single taxon G. tenussima. Its shorter genetic distance to related taxon implies a short isolation history.
Taiwanese yellow-flowered gentians are morphologically differentiation among species. Cytological, phytogeographical, and ecological evidenced while low genetic divergence exists among species, indicates a rapid speciation occurred on these taxa. Based on the facts that the habitat variable, that most of these taxa appear to be obviously isolated, and that the chromosome number also seems to be relevant to morphological differentiation. I propose that isolation of populations and dysploidization in chromosome number are important mechanisms of the speciation of Taiwanese yellow-flowered gentians.

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