本研究欲探討中海拔物種的親緣地理，選定位於台灣中海拔山區特有種的短肢攀蜥為研究對象。研究的方法是利用粒線體細胞色素b序列及外部型態測量來做分析。結果定序出共16個單倍基因型，細胞色素b序列長度為617 bp，有84個變異位，平均遺傳距離為5.4%。在親緣關係樹上呈現3個主要支系，支系的分布與地理位置有明顯相關，分別為北部、中北部及南部支系。族群遺傳的分析中顯示，族群之間呈現高度分化，且單倍基因型皆只侷限於採集地點。而外部型態測量上，共測量18個特徵，雌雄個體間僅有脇間距長及背部鱗片數有差異。用其它16個特徵做主成分分析及典型區別分析中，主成分分析並無有效將個體區分出來，而典型區別分析中觀霧、南橫、思源啞口和武陵農場的族群則可明顯與其它族群區別出來。短肢攀蜥的親緣地理類型屬於Avise(2000)所定義的第一種，推測造成的原因，可能是避難所效應及低擴散能力所造成。

The study intended to investigate the phylogeography of mid-altitude species, Japalura brevipes, which is the endemic to Taiwan. I used mitochondrial cytochrome b sequences and morphological characters to investigate the phylogeography. The molecular results showed that there are 16 haplotypes. The length of partial cytochrome b sequences is 617 bp including 84 informative sites, and the mean genetic distance is 5.4%. In phylogenetic analyses, three major clades were found in the phylogenetic trees. Moreover, these clades (north, central-north and south) corresponded to the geographic distribution. Analysis of population genetic structure revealed significant differentiation among populations, and most of the haplotypes were restricted to the locally. The morphological analyses showed that there is no difference between sexes at 18 characters, with the exception of the axilla-groin length and dorsal-crest scales. The Principal Component Analysis and Canonical Discriminate Analysis using 16 morphological characters showed the different results. Principal Component Analysis failed to separate populations. However, Canonical Discriminate Analysis could discriminate the populations of Guanwu, Nanheng, Sihyuantkou and Wuling Farm from others. Phylogeography of J. brevipes belonged to category 1 defined by Avise (2000). I infer refuge effect and dispersal ability hypotheses to explain the genetic structure of J. brevipes.

Introduction…………………………………………………1
Methods and Materials……………………………………4
Results……………………………………………………10
Discussion………………………………………………14
References………………………………………………19
Figures……………………………………………………27
Tables……………………………………………………36
Appedix……………………………………………………44

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