印度西太平洋鱟之演化史與保育遺傳

Abstract

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.