巨蛎属Crassostrea牡蛎物种分化及菲律宾蛤仔Ruditapes philippinarum群体遗传多样性研究

	巨蛎属Crassostrea牡蛎物种分化及菲律宾蛤仔Ruditapes philippinarum群体遗传多样性研究
	胡利莎
学位类型	硕士
导师	王海艳
	2016-05-24
学位授予单位	中国科学院大学
学位授予地点	北京
学位专业	生物工程
关键词	巨蛎属菲律宾蛤仔物种分化系统地理学遗传多样性
摘要	西北太平洋常见巨蛎属Crassostrea有长牡蛎Crassostrea gigas gigas、葡萄牙牡蛎Crassostrea gigas angulata、熊本牡蛎Crassostrea sikamea、近江牡蛎Crassostrea ariakensis和香港巨牡蛎Crassostrea hongkongensis，是潮间带代表性种。本研究结合线粒体基因和核糖体基因对巨蛎属五种牡蛎的物种形成机制进行了探讨分析。另外对熊本牡蛎Crassostrea sikamea和近江牡蛎Crassostrea ariakensis进行了系统地理学分析，揭示了各种的群体遗传结构，探讨了各种的群体历史动态，推测了各种形成目前地理分布格局的影响因素。采用两种线粒体基因对我国沿海菲律宾蛤仔Ruditapes philippinarum野生群体进行了遗传多样性研究，探讨了形成目前遗传多样性水平的影响因素。 1、巨蛎属Crassostrea五种牡蛎的物种分化研究本研究采用线粒体COI基因、线粒体16S rRNA基因、核糖体28S rRNA基因以及三种基因的联合基因对巨蛎属的长牡蛎Crassostrea gigas gigas、葡萄牙牡蛎Crassostrea gigas angulata、熊本牡蛎Crassostrea sikamea、近江牡蛎Crassostrea ariakensis和香港巨牡蛎Crassostrea hongkongensis五种牡蛎进行了系统发育和物种分化分析。系统发育结果表明：联合基因在系统发育分析中能得到更为客观准确的结果，五种牡蛎中亲缘关系最近的长牡蛎和葡萄牙牡蛎聚在一起，然后与熊本牡蛎相聚，最后与近江牡蛎和香港巨牡蛎所在的分支相聚。通过化石校准估算五种牡蛎的分化大约发生在渐新世-更新世，近江牡蛎与香港巨牡蛎所在分支大约在29.3百万年前与熊本牡蛎、长牡蛎和葡萄牙牡蛎所在分支形成分化，在大约19.4百万年前近江牡蛎与香港巨牡蛎分化，大约17.5百万年前熊本牡蛎分化出来，亲缘关系最近的长牡蛎和葡萄牙牡蛎的分化大约在3.5百万年前，推测物种的分化与冰期-间冰期循环存在有关，冰期的隔离作用导致物种最终的分化。 2、熊本牡蛎Crassostrea sikamea分子系统地理学研究本研究采用线粒体COI基因和核ITS-1基因标记对熊本牡蛎20个群体进行了分子系统地理学研究。基于COI基因的种群间遗传分化指数分析、分子方差分析结果显示：中国种群、韩国种群和日本种群间存在显著的遗传差异，而基于ITS-1基因的中国、韩国和日本种群间遗传分化不显著，两种基因标记的差异可能与两基因的进化速度不同有关。熊本牡蛎群体间的分化符合地理距离遗传模式。中国、韩国、日本三种群均经历过历史上的种群扩张事件，中国种群扩张最早，韩国种群扩张最晚，熊本牡蛎种群扩张大约在更新世晚期。本研究认为熊本牡蛎当前地理分布格局的形成受历史冰期、海洋洋流以及地理距离等多方面因素的影响。 3、近江牡蛎Crassostrea ariakensis分子系统地理学研究本研究采用线粒体COI基因和16S rRNA基因标记对近江牡蛎10个群体进行了分子系统地理学研究，结果检测到2个显著分化的系统发育类群，分别对应北方和南方群体；南北群体存在显著的地理隔离遗传模式。本研究结果表明南北类群的分化是冰期隔离以及海流环境综合因素导致的，而不是先前认为的长江冲淡水的阻碍作用。 4、菲律宾蛤仔Ruditapes philippinarum群体遗传多样性研究对我国沿海地区10个菲律宾蛤仔野生群体线粒体16S rRNA和COI基因部分序列进行测序，分别得到了长度为473bp和632bp的片段。结果表明，16S rRNA 193条序列A+T平均含量为66.6%，共检测到21个变异位点，193个个体具有22种单倍型； COI基因183条序列A+T平均含量为64.8%，共检测到126个变异位点，183个个体具有67种单倍型。基于群体间遗传距离利用Mega5.1软件构建10个群体的NJ 树，聚类结果表明，大连群体和荣成群体聚为一支，其余8个群体聚为一支。AMOVA分析表明，大连群体和荣成群体间分化不显著，而荣成、大连群体与其余8个群体间的分化达到极显著水平(P<0.01)，说明我国沿海的菲律宾蛤仔野生群体存在一定的遗传分化。
其他摘要	Five species of the genus Crassostrea, such as Crassostrea gigas gigas, Crassostrea gigas angulata, Crassostrea sikamea, Crassostrea ariakensis and Crassostrea hongkongensis, are widely distributed along the Northwest Pacific. As the representative intertidal species, they are vulnerable to the fluctuations of sea-level. Speciation mechanisms of the five Crassostrea species were discussed by using mitochondrial and nuclear DNA sequences. Phylogeographic analysis of Crassostrea sikamea and Crassostrea ariakensis were conducted to assess the population genetic structure and demographic history and surmise the factors on shaping the phylogeographical patterns in present of each species. Two mitochondrial genes were used to investigate the genetic diversity of wild populations of Ruditapes philippinarum along the coast of China. 1. Speciation of five Crassostrea species Phylogenetic and phylogeographic analysis of five Crassostrea species were conducted by COI gene, 16S rRNA gene, 28S rRNA gene and combination of the three genes. The phylogenetic results revealed that, the combined gene may reflecte more information and could be more accurate in phylogenetic analysis. Based on the combined gene we get two great clusters, one contains Crassostrea ariakensis and Crassostrea hongkongensis, the other one contains Crassostrea sikamea and other two species-Crassostrea gigas gigas, Crassostrea gigas angulata, which are with the closest relationship. The divergence times dated from the Oligocene-Pleistocene epochs according to the molecular clock-based evolution age estimate. The divergence time of the two branches (one branch include Crassostrea ariakensis and Crassostrea hongkongensis, the other branch include Crassostrea sikamea, Crassostrea gigas gigas and Crassostrea gigas angulata) dated to about 29.3 million years ago. About 19.4 million years ago, Crassostrea ariakensis and Crassostrea hongkongensis were divergenced to two species. About 17.5 million years ago, Crassostrea sikamea divergenced from the branch. Crassostrea gigas gigas and Crassostrea gigas angulata were divergenced about 3.5 million years ago. The isolation of marginal sea during the glacial epoch leads to the eventual differentiation of species. 2. Phylogeography of Crassostrea sikamea We analysised population genetic structure and demographic history of 20 populations of Crassostrea sikamea along the margin of Northwestern Pacific based on mt COI gene and nuclear ITS-1 gene. The analysis of pairwise F_ST, AMOVA based on COI gene showed that, significant genetic differentiation were found among Chinese populations, Korea’s populations and Japanese populations. While, the results based on ITS-1 gene showed no significant genetic differentiation among the three groups. Based on COI gene, the analysis of IBD showed that the genetic differentiation among three groups is related to the geographic isolation by distance. All the three groups have experienced population expansion events in the history, the expansion time of Chinese populations is the earliest and the Korea’s population is the latest. Population expansion of Crassostrea sikamea populations dated back to the late Pleistocene. We surmise that genetic structure of Crassostrea sikamea is not only affected by the population expansion and geographic expansion at Pleistocene, to a certain extent, also by the geographical distance and ocean current. 3. Phylogeography of Crassostrea ariakensis We analysised population genetic structure and demographic history of 10 populations of Crassostrea ariakensis along the margin of Northwestern Pacific based on mt COI gene and 16S rRNA gene. Two distinct lineages were detected from the minimum haplotype network, and the analysis of IBD showed that the genetic differentiation between the two distinct lineages is related to the geographic isolation by distance. Our results show that the genetic differentiation of the north and south groups is caused by a combination of the historical isolation of sea basins and Current environment rather than the putative Changjiang River outflow barrier. 4. Genetic diversity of Ruditapes philippinarum Partial sequences of the mitochondrial 16S rRNA gene and COI gene of ten Ruditapes philippinarums populations in China were sequenced, 473bp from 16S rRNA gene, and 632bp from COI gene were obtained, respectively. The average contens of A+T (16S rRNA gene 66.6% and COI gene 64.8%) were significantly higher than those of G+C. In 16S rRNA gene fragment 21 variation sites were detected and 22 haplotypes were defined. In COI gene fragment 126 variation sites were detected and 67 haplotypes were defined. Based on the genetic distance among populations, the NJ phylogenetic trees were obtained. The trees suggested that Dalian and Rongcheng populations clustered to one cluster, the rest 8 populations to the other cluster. AMOVA analysis showed that genetic differentiations between Dalian populations and Rongcheng populations were not significant, while it is extremely significant among Dalian populations (Rongcheng populations) and the rest eight populations (P<0.01), indicating that there were some genetic differentiations in different wild populations of Ruditapes philippinarum in China.
学科领域	生物学
文献类型	学位论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/116962
专题	海洋生物分类与系统演化实验室
作者单位	中国科学院海洋研究所
第一作者单位	中国科学院海洋研究所
推荐引用方式 GB/T 7714	胡利莎. 巨蛎属Crassostrea牡蛎物种分化及菲律宾蛤仔Ruditapes philippinarum群体遗传多样性研究[D]. 北京. 中国科学院大学,2016.

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