以限制酶位點標定之核酸定序法檢視太平洋構樹之親緣地理

Reconstructing Phylogeography of Pacific Paper Mulberry using RADSeq

李宜軒(Yi-Hsuan Li)

指導教授 ： 鍾國芳

共同指導教授 ： 陳凱儀(Kai-Yi Chen)

國立臺灣大學/生物資源暨農學院/森林環境暨資源學研究所/碩士(2018年)

https://doi.org/10.6342/NTU201800168

摘要

構樹（Broussonetia papyrifera (L.) L’Hér. ex Vent., paper mulberry）為太平洋南島語族重要物質文化樹皮布的主要製作原料，並極有可能隨著南島語族遷徙傳入太平洋，因此，透過研究構樹親緣地理關係，可推論南島語族遷徙路徑。由於過去的研究皆使用單一或少數分子標記作為討論依據，解析度低，因此本研究利用限制酶位點標定之核酸定序法（restriction-site associated DNA sequencing, RADSeq），利用Stacks軟體自137個個體間尋獲6,322個單一核酸多型性（single nucleotide polymorphism, SNP）位點，並進行最大似然性親緣關係分析，成功以全基因組範圍資料再次證實了太平洋構樹皆來自臺灣東南部，與南島語族遷徙相關的「出臺灣說（Out of Taiwan Hypothesis）」相符，且太平洋構樹個體間差異甚小，亦符合太平洋構樹的播遷皆是透過人為無性扦插繁殖之理論，利用此少數差異已可追蹤構樹於遠大洋洲的傳播路徑。過去研究中，以母系遺傳的葉綠體DNA片段作為分子標記，臺灣的構樹基因型明顯具三區地理結構。而本研究所使用之分子標記主要分布於核基因體中，可由花粉攜帶傳播，結果顯示構樹花粉傳播能力強，能將核基因傳播甚遠，造成原發現臺灣島內之地理結構不呈現於新分析結果中，但即便如此，臺灣海峽仍能形成一有效屏障，隔離中國大陸與臺灣族群。從RADSeq分析結果中，亦發現琉球群島族群與臺灣東部族群最為相近，但仍有相當分化，可能是因為第四紀時曾有兩次冰河期陸橋連接，之後又因海平面上升造成族群長期隔離所致。

關鍵字

南島語族遷徙 ； 共生物種 ； 次世代定序 ； Stacks ； 出臺灣說 ； 琉球群島 ； 冰河陸橋

並列摘要

Paper mulberry (Broussonetia papyrifera (L.) L’Hér. ex Vent.), a wind-pollinated dioecious tree native to East Asia, is the cultural necessities of Austronesian-speaking peoples (Austronesians) for making bark cloth (tapa). By studying the geographical relationship among the populations of paper mulberry, the migration path of the Austronesians can be deduced. To increase phylogenetic resolution of previous studies limited by insufficient molecular resolution, we applied restriction-site associated DNA sequencing (RADSeq) collected using next-generation sequencing technology, obtaining 6,322 SNPs from 137 individuals for phylogenetic analysis by Stacks. The outcome reaffirmed that the Pacific paper mulberries were all derived from southeastern Taiwan, and the genetic differences among the Pacific paper mulberry were rare, conforming asexual propagation of the Pacific paper mulberry for tapa making and reaffirming the “out of Taiwan” hypothesis of Austronesian expansion and migration. Tough the genetic differences were rare, we still succeeded in finding the propagation path of paper mulberry in remote Oceania. The previous study, which using the chloroplast marker, showed the strong phylogeographic structure in Taiwan. On the contrary, the lack of phylogeographic structure in Taiwan revealed by RADSeq, which represents the biparental-inherited nuclear genome, suggests high gene flow mediate by efficient pollen dispersal. Nevertheless, Taiwan Strait remains an effective dispersal barrier for pollen dispersal between mainland China and Taiwan. Our RADSeq data also confirm the tight relationship between populations of Ryukyu Islands and eastern Taiwan. However, substantial genetic differentiation is present between the two populations, suggesting a long-term isolation and that the Ryukyus populations were likely established via land bridge during the twice ice age.

並列關鍵字

Austronesian expansion and migration ； commensal species ； next-generation sequencing (NGS) ； Stacks ； Out of Taiwan hypothesis ； Ryukyu Islands ； ice age ； land bridge

參考文獻

張至善. 2012 談樹皮布與構樹. 林業研究專訊, 19, 62-66.

Carson, M.T. 2012 Evolution of an Austronesian landscape: The Ritidian site in Guam. Journal of Austronesian Studies, 3, 55-86.

Hung, H.C. 2005 Neolithic interaction between Taiwan and Northern Luzon: the pottery and jade evidence form the Cagayan Valley. Journal of Austronesian Studies, 1 (1), 109-113.

Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. 1990 Basic local alignment search tool. J Mol Biol, 215 (3), 403-410.

Baird, N.A., Etter, P.D., Atwood, T.S., Currey, M.C., Shiver, A.L., Lewis, Z.A. et al. 2008 Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One, 3 (10), e3376.