台灣島嶼因經歷複雜的地質歷史與冰河事件影響物種多樣性及族群遺傳結構，過往研究探討地質及冰河效應對分布不同海拔之物種遺傳結構的影響，玉山圓柏為台灣主要分布於海拔3,000公尺以上之高山物種，針對此一物種進行研究有助於了解台灣地質及冰河效應對於高海拔物種的影響，為了更準確地闡述玉山圓柏之演化歷史，以多基因分析（3個粒線體DNA基因、2個葉綠體DNA片段以及5個細胞核DNA基因）探討玉山圓柏之物種親緣和族群動態。
結果顯示玉山圓柏、刺柏及清水圓柏間可能因保有來自於共同祖先之遺傳特徵（incomplete lineage sorting），造成無明顯物種分群。玉山圓柏不同之族群共有相同之單型，推測玉山圓柏在冰河時期進入台灣後，且因具有較長之世代、較少之世代交替，使得族群間具有相似之遺傳結構。冰河期可能向較低海拔地區擴展其族群，使得族群呈現擴張情形，隨著冰期的結束，逼迫其向高海拔地區遷徙，造成族群瓶頸效應/奠基者效應，降低其族群數量。族群間多為低度分化，推測為冰河時期進入台灣後，族群快速擴張所造成，儘管隨機遺傳漂變逐漸使得族群開始分化，族群間仍保有共組之遺傳多樣性，使得彼此間並無顯著之遺傳分化。

The complexities of geological history and the effects of the past glacial periods shaped the species’ diversities and populations structures of Taiwan. Most of studies focused on species’ genetic structure at different altitudes in responsed to the changes of geology and climate.In Taiwan, Juniperus squamata Buch.-Ham. is an alpine species that is mainly distributed at mountain peaks over 3,000 m. The research of J. squamata provides informations for futher elucidating the genetic structure of alpine species in Taiwan. Multiple-locus analyses（three mitochondrial genes, two chloroplast intergenic spacers and five nuclear genes）were utilized to elucidate the evolutionary history of J. squamata precisely.
The results revealed that shared ancestral polymorphisms（incomplete lineage sorting）among J. squamata, J. formosana Hayata and J. chinensis var. tsukuiensis Masamune contributed to the lack of each monophyly. Longer generation time and fewer alternation of generation may attribute to the shared haplotypes among different populations in J.squamata. J. squamata may expand to lower altitude areas during the glacial periods. As the end of glacial periods, it retreated to higher altitude areas and suffered the bottleneck/founder events. Low levels of genetic differentiations were detected among populations that may be due to glacial demographic expansion. Despite of genetic drift, shared ancestral polymorphsims among populations still make these populations less genetic differentiation.

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