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Phylogeography of horseshoe crab, Tachypleus tridentatus in the Indo-West Pacific
No full text西太平洋長期以來被公認為生物歧異度中心，探索各物種地理親緣關係，可瞭解此地區生物多樣性形成機制。本研究以分子遺傳標誌，粒線體 AT-rich片段，探討現今印度西太平洋地區活化石三棘鱟之遺傳變異。總樣本數為82隻個體採集自台灣、泰國暹羅灣(GT)及安達曼海(AB)三個地區，共五個族群；其中台灣地區包含金門(TK)、澎湖東衛(TD)及澎湖鐵線尾(TT)三個族群。
本研究以鄰接演算法建構三棘鱟族群之單型親緣關係及以最短距離網狀圖，並由化石紀錄及分子鐘評估分歧時間，支持漸新世晚期到中新世早期（21-27百萬年前）印度洋及西太平洋間族群的顯著分歧，並支持印度西太平洋板塊間之隔離作用。另推論中新世晚期到中期（17-21百萬年前）南中國海盆的持續擴張在阻礙三棘鱟基因交流上扮演關鍵角色。由族群成長係數及單峰之mismatch distribution分析支持暹羅灣族群急遽擴張現象，並推論其為受到冰期造成的海面及棲地波動的影響。另外發現鐵線尾三棘鱟族群曾發生嚴重的瓶頸效應，推論源於近年來族群數量衰減及於封閉海灣長久近親繁殖造成的結果。最後藉由三棘鱟地理親緣關係以及族群遺傳數據提出對印度西太平洋三棘鱟在保育上之建議。The Indo-West-Pacific region (IWP) hosts the highest marine biodiversity on earth. The concordance among different species can be used to deduct the common mechanism that forms the IWP marine biodiversity. Genetic variation of mitochondrial AT- rich region in the “living-fossil” horseshoe crab, Tachypleus tridentatus, were revealed for 82 individuals collected from 5 populations in 3 regions, including southern Burma coast of Andaman Sea (AB), Angsila in Gulf of Thailand (GT), and Kinmen (TK), Donwei (TD), Tehsiwei (TT) in Taiwan.
Haplotype phylogeny constructed by neighbour-joining algorithm, the network derived from the minimum spanning network, and dating by fossil records demonstrated that a significantly deep divergence between the populations in Indian and Pacific Ocean, suggesting a pattern of Indian-Pacific tectonic plate divergence from late Oligocene to early Miocene (21-27 Ma). In addition, it also indicated that Taiwan population formed a significantly different clade from Gulf of Thailand divergence time indicates that South China Sea Basin might play an important role in retarding gene flow of between the T. tridentatus populations of southern and northern South China Sea from early Miocene to middle Miocene (17-21 Ma). The demography parameter and unimodal mismatch distribution indicates the sudden range expansion of T. tridentatus population in Gulf of Thailand and affected by sea level and habitat fluctuation during glaciations. The mismatch distribution indicated the bottleneck effect on Donwei population due to recent population size decline and inbreeding in this close bay. The implications of phylogeography and demography towards the T. tridentatus conservation in the IWP are also highlighted.Chapter 1 Introduction 1
1.1 Evolutionary history of Horseshoe crab 1
1.2 Life history and phylogeography of horseshoe crab 3
1.3 Marine biogeography in the Indo-West Pacific 5
1.4 Glacial effect on population demography of Tachypleus tridentatus 6
1.5 The question about phylogeography of horseshoe crab in the IWP 7
Chapter 2 Materials and Methods 9
2.1 Collection of Samples 9
2.2 DNA extraction, Polymerase chain reaction (PCR), and Sequencing 9
2.3 Phylogeny construction 10
2.4 Network analysis 11
2.5 Population genetics analyses 12
2.6 Demography 12
Chapter 3 Results 14
3.1 Phylogeny and Network Reconstruction 14
3.2 Population Structure 15
3.3 Demography 16
Chapter 4 Discussions 18
4.1 Ancient divergence of Tachypleus tridentatus? 18
4.2 Unexpected divergence in the South China Sea 19
4.3 Glacial effects on population demography 21
4.4 Implications for conservation 24
Chapter 5 Conclusion 26
Reference 28
Table 32
Figure 40
Appendix 4
Synthesis, Properties, and Solar-Cell Applications of Pentiptycene Incorporated Poly(p-phenylene vinylene)s
No full text在本論文主要為含五苯荑之對苯乙烯聚合物之合成，並探討不同五苯荑比例對其光電性質之影響 ，以期應用於有機共軛高分子太陽能電池元件中。
本實驗室致力於五苯荑分子的官能化，並成功合成出雙溴五苯荑，曾利用雙溴五苯荑經Heck偶合反應合成出含五苯荑之聚對苯乙烯，但聚合效率不佳，因此我們轉為開發反應活性較高的雙碘五苯荑或不同核心架構的雙乙烯五苯荑來合成含五苯荑之聚對苯乙烯。在合成部分，以五苯荑醌為起始物，經過一系列的中心苯環官能基轉換，我們成功合成出雙碘五苯荑及雙乙烯五苯荑。雙碘五苯荑能以芳香環取代反應之方式有效地提升總產率，因此利用雙碘五苯荑進行含五苯荑之聚對苯乙烯的合成，成功合成出不同含五苯荑比例的PEN-ROPPV和PEN-3ROPPV高分子。於光物理性質部分，受到五苯荑立體效應影響，兩高分子相較於一般聚對苯乙烯在吸收和螢光光譜皆有藍位移，而PEN-3ROPPV含有較低比例的五苯荑，故相較於PEN-ROPPV較為紅位移；兩分子薄膜之吸收和螢光光譜與稀釋溶液態相當類似，文獻中指出五苯荑立體效應能有效避免高分子鏈間作用。電化學方面，兩分子之氧化為一不可逆之過程。根據兩分子之HOMO及LUMO，符合作為太陽能電池之基本條件，唯獨在能帶間隙上較寬，不利於吸收可見光。予體和受體之互混溶性為影響塊材異質接面太陽能電池因素之一，引進五苯荑欲提升對聚苯乙烯與PCBM之互溶混性，但在元件效率之表現，兩者皆相當低，推測可能原因有二：(一)、高分子無法有效吸收可見光導致捕光效率差；(二)、形態上予體和受體互溶混性並未構成有效通路。因此若要有效提升元件效率則需進行結構上的改質。In this thesis, we report the synthesis and electronic properties of pentiptycene-incorporated poly(phenylene vinylene)s (PPVs). We have also investigated the performance of these PPV-type derivatives as active materials for bulk heterojunction (BHJ) solar cells.
Our lab has been devoted to the synthesis of new pentiptycene building blocks, including dibromopentiptycene. We previously used dibromopentiptycene to synthesize pentiptycene-incorporated poly(phenylene vinylene)s by Heck coupling reactions, but the overall yield and polydispersity are poor. As a result, we turn to the more reactive diiodopentiptycene and the alterative building block divinylpentiptycene. We used pentiptycene quinone as the starting material and successfully obtained diiodopentiptycene and divinylpentiptycene through multistep synthesis, and particularly the SNAr reaction of a pentiptycene triflate. Two pentiptycene incorporated PPVs PEN-ROPPV and PEN-3ROPPV have been successfully prepared. These two polymers are blue-shifted in absorption and fluorescence spectra as compared to alkyl or alkoxy-substituted PPVs. The spectra of PEN-3ROPPV are somewhat red-shifted than those of PEN-ROPPV due to its lower fraction of the pentiptycene group. Their spectra in thin film are similar to those in dilute solutions, indicating negligible aggregation of polymers backbone.The cyclic voltammetric anodic curves of these two polymers are irreversible. The energy levels of their HOMOs and LUMOs are suitable for application in BHJ solar cells with PCBM as the electron acceptor. However, the power conversion efficiency are low partly owing to poor light harvesting of the sun light. Another possible factor that is responsible to the low efficiency of solar cells is the morphology even though we had expected that pentiptycene could interact well with PCBM
Evolutionary History and Conservation Genetics of Horseshoe Crabs in the Indo-West Pacific
No full text印度西太平洋具有高度海洋生物多樣性，不同物種間的公同性研究有助於瞭解此一區域海洋生物多樣性形成機制。鱟是具有古老演化史的海洋節肢動物，世界上共有四種，其中三種（三棘鱟Tachypleus tridentatus、巨鱟T. gigas、圓尾鱟Carcinoscorpius rotundicauda）廣泛分布於印度西太平洋地區，且其具有重要的海岸生態與經濟價值。然而，棲地流失與族群衰退亦有必要研究其遺傳連通性及族群動態以作為保育依據。在我的論文中有，有主要三個目標：（1）應用地理親緣學研究三種印度西太平洋鱟的種化機制及其遷徙路徑（第二章中探討）；（2）比較古氣候及古地質變遷對於西北太平洋的三棘鱟及印尼馬來群島的巨鱟族群動態史的影響（第三章）；（3）將遺傳連通性作為設計鱟在東海及難中國海北部海洋保護區網絡及其他保育措施的依據（第四章）。
首先以粒線體細胞色素c氧化酵素（COI）及AT-rich region，分別作為分析三種鱟種間及種內親緣關係的材料。根據化石及生物地理學紀錄，作為亞洲鱟與美洲鱟（Limulus polyphemus） 共同祖先的分化時間點依據，再利用COI序列的遺傳變異定年出圓尾鱟及另兩種亞洲鱟的分化時間約為兩千四百五十萬年前至三千三百六十萬年前之間；而同屬的兩種鱟三棘鱟及巨鱟分化時間則為兩千零五十萬年至兩千七百六十萬年間。而不管以COI或是以AT-rich region親緣分析的結果顯示，三棘鱟相較於巨鱟譜系都較淺近。而巨鱟種內的親緣關係中，除了分化程度較三棘鱟高，亦形成兩個系群，其中一個系群純由印度洋族群所組成，且較為古老，顯示巨鱟源自於印度洋。而以族群分化係數（FST）分析，結果則顯示巨鱟在印度洋及太平洋的族群間亦有顯著差異。
粒線體DNA AT-rich region遺傳變異另外也用於遺傳連通性及族群動態的分析上，採集自大陸沿岸及台灣海峽的三棘鱟共有114隻個體，而日本則有296隻樣本。藉由貝氏天際線點圖（Bayesian Skyline plot）分析結果顯示，在其3萬5千前來的族群歷史中，歷經上次最大冰期過後除日本族群外的西北太平洋有效族群數開始緩慢成長；而日本族群則自上次日本小冰期過後（約三千五百年前至四千五百年前）才有鱟的遷入。而許多日本鱟族群具有極低的遺傳多樣性，可能是因與其他西北太平洋族群之間缺乏遺傳連通性（族群間之FST有顯著差異）引起。
不同空間尺度的遺傳連通性及族群動態可有助於測量海洋生物的擴散能力，並可藉此瞭解族群是否存在因棲地衰退所造成的危機，並以此作為擬定保育行動的依據。而本論文也分析三棘鱟在東海及難中國海北部的遺傳連通性，以選擇較適合的海洋保護區位置及間距來設計海洋保護區網絡；此一分析也可作為西北太平洋海洋生物的區域性保育措施的參考。The Indo-West-Pacific region (IWP) hosts the highest marine biodiversity on earth. The concordance among different species can be used to deduct the common mechanism that forms the IWP marine biodiversity. The horseshoe crab is an ancient marine arthropod, which has a wide geographic distribution cross the IWP and a long evolutionary history and importance in costal ecosystem and economics. However, loss of habitats and population degradation urged the need to study genetic connectivity and population demography for conservation. In my PhD dissertation there are three aims to be addressed: (1) To apply with phylogeographic methods of three species of horseshoe crabs (Tachypleus tridentatus, T. gigas, and Carcinoscorpius rotundicauda) probing in the speciation mechanism of the colonization routes (Chapter 2). (2) To compare how the effect of paleoclimate and paleogeology change on historical demography between two species horseshoe crab, T. tridentatus in the northwestern Pacific and T. gigas in the Indo-Malay Archipelago (Chapter 3). (3) To transfer the pattern of the genetic connectivity into design of reserves network and other conservation actions for horseshoe crabs along East and northern South China Sea (Chapter 4).
Phylogenetic relationship of three species of horseshoe crabs was revealed by mitochondrial (mt) COI, and AT-rich region. Based on dating Asian horseshoe crabs and Atlantic horseshoe crab (Limulus polyphemus) by fossil and biogeographic records of common ancestor and genetic variation of COI sequence, there were deep divergence at 24.7 ~33.6 million year ago (mya) between C. rotundicauda and two Tachypleus species, and 20.3~ 27.6 mya between T. gigas and T. tridentatus. The phylogenetic trees constructed by each marker all exhibited that only T. tridentatus had shallow genealogy relative to T. gigas. The deep divergent phylogeny of might be due to more isolation created by complicated sea basins and plate tectonic in Indo-Malay Archipelago than northwestern Pacific and also indicated the southern origin of Asian horseshoe crab according to the basal lineage in Indian Ocean. Pairwise difference (FST) also indicated that there was a significant differentiation between Indian and Pacific T. gigas populations.
Genetic variation of mt AT-rich region was examined for genetic connectivity and demography of 114 T. tridentatus individuals from Mainland China coast and Taiwan Strait, and 296 individuals from Japan coast. There was gradual growth in effective population size of horseshoe crab in Mainland China and Taiwan Strait after Last Glacial Maxima during the past 35 thousands years ago by using Bayesian Skyline plot, while horseshoe crabs began to colonize after last minor glacial period to Japan (3500~4500 years ago). The extremely low of genetic diversity in most Japan populations could result from loss of genetic connectivity measured by FST from other populations in the northwestern Pacific.
Based on genetic connectivity and historical demography in different spatial scale, it improve the measurement of the dispersal capacity of marine organism and realizing the risk and gain the information of conservation actions for those marine organism with lower dispersal capacity like horseshoe crab could sensitive to surfer from habitat degradation. A greater understanding of genetic connectivity could be used to realize the dispersal pattern and apply for reserve network design of T. tridentatus in East China Sea and north South China Sea. This dissertation also provides a conservation awareness to build a baseline for marine organisms, which are especially facing habitat deconstruction in the northwestern Pacific.Acknowledgment……………………………………….........…………...……….…..i
中文摘要……………………………………………………...…………..……….….ii
Abstract ……………………………………………………...…………..……….......vi
List of Tables....……………….………………..………...……………………….....viii
List of Figures………………….…………………………...………………..….…....ix
Chapter 1 General Introduction……………………………………..…………………1
Chapter 2 Evolutionary history of three species of horseshoe crabs in the Indo-West Pacific.…………………………………………………...…………….…..14
Chapter 3 Demographic history of Tachypleustridentatus and T. gigasin the Indo-West Pacific.……………………….………………………………………..….28
Chapter 4 Genetic connectivity and design of reserves network of Tachypleustridentatus in the East and South China Seaboards….………45
Chapter 5 General discussion and conclusion…………………………………..……62
References……………….……….……..…………..…………………………….….66
Appendixes……………….……….……..…………..………….……………………8
Population Subdivision of the Tri-Spine Horseshoe Crab, Tachypleus tridentatus, in Taiwan Strait
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