親緣地理學（phylogeography）討論當物種受到歷史地質事件影響時，族群遺傳結構所產生的改變，並利用建構物種的親緣關係與調查族群在地理上的分佈，來檢視族群分化的歷史。在臺灣針對兩棲爬行動物的研究大多支持山脈為臺灣島上對物種分化而言最主要的地理屏障，然而目前卻尚未有針對褐樹蛙（Buergeria robusta）這種棲息生態同時受到陸域及淡水域影響的全島廣布物種進行親緣地理學的研究。本研究採集全島33個採樣點一共564隻褐樹蛙個體，以粒線體DNA中的細胞色素b（cytochrome b）基因片段做為分子遺傳標記，建構基因單型的親緣關係樹（phylogeny）與網狀譜系圖（network），討論褐樹蛙各族群間的遺傳分化程度及分布擴散歷程，並與前人研究的淡水魚類或其他小型兩棲爬行動物相比較。結果顯示褐樹蛙在親緣關係上可以分成七個支系，在地理分佈上可以分成五個區域。其中東部區域由於受到中央山脈的阻隔，與其他區域形成高度分化，而成為一個獨立的系群。在西部族群中，東北部、北部、中部與南部區域之間的遺傳交流極為有限，也各自擁有特殊的單基因型，而雪山山脈、苗栗丘陵與臺灣堆均成為阻礙基因交流的地理屏障。在族群歷史變動的部分，大部分主要遺傳支序皆呈現歷史上的分布範圍擴張，而大多數的地理區域則呈現歷史上的族群數量成長。總結而論，在臺灣造成物種產生遺傳分化的地理障礙，幾乎每一項都會成為褐樹蛙基因交流上的地理障礙，因此本研究認為褐樹蛙的遺傳分化模式兼具陸域生物與水域生物特徵而自成一格的特殊模式。

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