紅樹林植物的拓殖與分化受到地質歷史及地形的影響甚鉅，例如，東南亞的細蕊紅樹(Ceriops tagal)即可能同時受到馬來半島的陸地阻隔以及南中國海內的古代地理的影響，形成特殊的族群結構。故本研究利用遺傳方法，以東南亞的細蕊紅樹為模型，回溯印度洋-西太平洋地理區的紅樹林親緣地理關係。以母系遺傳的葉綠體DNA進行偵測，可以避免花粉(父系遺傳)的干擾，有效地追蹤細蕊紅樹胎生苗的流傳方向及地理隔離對其傳播的干擾。五百萬年來馬來半島對南中國海(太平洋)及孟加拉灣(印度洋)沿岸的細蕊紅樹形成有效的地理屏障，造成兩海域間族群的明顯分化；而冰河時期馬來半島與婆羅洲形成巨大的巽他大陸(Sundaland)，使現今分布於馬來半島、海南島及婆羅洲等地的細蕊紅樹遺傳同質性高。而阻隔南中國海與安達曼灣的馬來半島最窄處──克拉地峽(Kra Isthmus)僅寬約六十公里，兩岸的細蕊紅樹族群雖明顯的分化並各自享有獨特的基因型，但卻檢測出長距離散播的可能性。嚴格分子鐘的計算與五百萬年前的隔離事件大致吻合，些微的低估可能導因於南中國海與孟加拉灣之間的長距離傳播。根據溯祖理論檢驗出馬來半島南端的族群與其他地區在歷史上有高度的基因交流，亦提供麻六甲海峽為其溝通管道的證據。在兩萬一千年前巽他大陸消失、暹邏灣初形成之際，細蕊紅樹沿著古湄南河口逐漸退縮至現今的暹邏灣沿岸。藉由暹邏灣內的灣流及潮汐力量，胎生苗得以在各族群之間順暢的流動，並藉由族群的拓殖、滅絕等動態變化維持整個暹邏灣內細蕊紅樹的族群穩定，構成一個典型的關聯族群(classical metapopulation)。此外，因週期性的冰河期與間冰期使海平面下降、上升，造成兩海域的族群時而隔離、時而有機會進行長距離的傳播，使其遺傳多樣性得以藉冰河期時的累積突變與間冰期時的基因交換而提高。而孟加拉灣因大陸棚較陡峻、海底較深，因此冰河期海岸變化不大，使其細蕊紅樹族群得以維持穩定。相對地，南中國海因巽他陸棚在冰河期時形成巽他大陸，南中國海面積縮小，間冰期後再度擴張，因此在該海域檢測出族群擴張，但區域之小族群則呈穩定狀態，因此推測其南中國海族群擴張方式主要以拓殖、建立新族群為主，而非增加區域族群之大小。由本研究得知，印度洋-西太平洋的紅樹林的族群遺傳結構的確受到古代地質事件及地形的影響，尤其是南中國海地區，陸棚較淺、較緩，海岸線受冰河影響較大，其族群藉基因交流、拓殖等方式彼此影響，形成關聯族群的結構。因此，根據Levins模型的結論──遷移率的提升有助關聯族群的維持，建議在開發港口、工廠之餘，東南亞各國宜保護各海岸的自然環境，提供紅樹林擴散的踏腳石，提高其遷移率，以維持其關聯族群的穩定性。

The colonization and differentiation of mangrove species are noticeably affected by geographic histories. The Indo-West Pacific (IWP) is the region that contains the most abundant and specious mangrove assemblages. The population of Ceriops tagal endemic in Southeast Asia, like that of many other mangrove species, was structured by the isolation of present Malay Peninsula and ancient Sundaland. I used maternally inherited chloroplast DNA, with which the effects of pollen dispersal could be excluded, to retrace the phylogeographic relationships among populations and dispersal route of propagules of C. tagal. In this dissertation, the Malay Peninsula was demonstrated to effectively isolate the gene flow of populations of C. tagal between the South China Sea (SCS) and the Bay of Bengal (BOB). During the glacials, the emergence of the Sunda Shelf connected the Borneo and the Malay Peninsula, forming a strict barrier named Sundaland. This caused populations within the SCS sharing common ancestral genotypes, and so was the situation in populations of the BOB water mass. The Gulf of Thailand (GOT) began to take shape 21 thousand years ago, and mangroves therefore started to retreat (or expand) to the coasts of the GOT. While populations in the GOT had frequent gene flow due to the tides and seashore currents, the independent demographic dynamics of each local population structured the whole GOT population. The closed gulf maintains the stable historical demography of whole GOT population and thus forms a classical metapopulation. The Kra Isthmus, the narrowest part of the Malay Peninsula, had been submerged under sea level before ca. 5 Mya, and this might lead to unhindered gene flow of mangroves between the SCS and the BOB. The divergent time of the SCS and BOB populations based on strict molecular clock is slightly underestimated when compared with the formation time of the Kra Isthmus. The long distance dispersal between the SCS and the BOB may be the cause of the underestimation of molecular clock. The most likely route for long distance dispersal across the land barrier is that via the Malacca Strait. The high gene flow between populations in the South Malay Peninsula and other areas in the past estimated by the coalescent-method provides an indirect evidence of Malacca Strait as the gate of dispersal. The isolation of populations in the two water masses during the glacials and the acceleration of gene flow due to sea-level rise during the interglacials might cause the high genetic diversity of mangroves in the IWP now. Moreover, while the periodic expansion and contraction of the SCS due to the sink and emergence of the Sundaland caused population expansion in the SCS, this situation never happened in the BOB, and population there maintained demographically stable. The population in the SCS may expand through colonization instead of local population growth because only few local populations were detected to expand. Thus, for conservation application, I suggest that the coasts of the Southeast Asia should be protected in order to provide steppingstone for the dispersal of mangroves.

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