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研究生:韋杰鴻
研究生(外文):JIEHONG WEI
論文名稱:中國沿岸髭縞虾虎(Tridentiger barbatus)之族群遺傳
論文名稱(外文):Population genetics of Tridentiger barbatus along the coast of China
指導教授:廖德裕
指導教授(外文):Te-yu Liao
學位類別:碩士
校院名稱:國立中山大學
系所名稱:海洋科學系研究所
學門:自然科學學門
學類:海洋科學學類
論文種類:學術論文
論文出版年:2018
畢業學年度:106
語文別:英文
論文頁數:47
中文關鍵詞:髭縞虾虎(Tridentiger barbatus)洋流中國沿岸親緣地理學族群遺傳
外文關鍵詞:phylogeographyTridentiger barbatuspopulation geneticscoastal Chinacurrent
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對於廣泛分佈的物種,它們的族群間基因交流容易因為海洋中各種因素
而中斷,導致族群分化。過去研究認為複雜的沿岸流系統,長江沖淡水以及更
新世冰期週期海平面變化是造成中國沿岸海洋生物分化的可能因素。髭縞虾虎
(Tridentiger barbatus)是一種廣泛分佈于中國,韓國和日本沿岸的底棲性虾虎,
其族群遺傳結構亦可能受到上述因素的影響。為研究其族群遺傳結構,本研究
從中國沿岸 14 個樣點採集共 258 尾髭縞虾虎個體,并擴增其細胞色素 b,視紫
紅質 (Rhodopsin)和 RAG1 基因序列片段進行分析。以貝葉斯分析法(Bayesian
analysis) 重建的親緣關係樹和 TCS 法重構的單倍型網絡圖均显示髭縞虾虎內部
存在兩個分化較深的譜系(southern lineage 和 northern lineage),這兩個系譜的分
佈模式與中國沿岸夏季洋流模式類似,意味著洋流對髭縞蝦虎魚親緣地理模式
可能有重要影響。細胞色素 b 基因單倍型分佈,pairwise Fst 和 AMOVA 表明
southern lineage 內亦存在分化,可能與近岸洋流和潛在的地理屏障有關。兩系
譜間分化時間約為一百六十五萬年前, 可追溯到更新世時期。兩系譜的 Tajima’
D 和 Fu’s Fs 值均為顯著的負值,表明兩系譜在過去存在突然擴張。貝葉斯天際
線(Bayesian skyline plot)分析結果顯示 southern lineage 和 northern lineage 的突然
擴張時間分別為一萬年前和一萬五千年前,均發生于末次冰期(The last glacial
period)結束后(約 2 萬年前)。這意味著更新世冰期可能對髭縞虾虎的分化和族群
規模有重要影響。
Gene exchange of widespread marine species populations may be easily interrupted
by various conditions in the ocean, which may result in divergences. Previous studies
suggested that complex coastal current system, Changjiang Diluted Water and
Pleistocene Glacial Cycle are possible factors causing divergence of marine
organisms in Coastal China. Tridentiger barbatus is a benthic goby widely spread in
coastal China, Korea and Japan. In this study, we collected 258 individuals of T.
barbatus from 14 sites along the coast of China to explore its genetic structure.
Fragments of cyt b, Rh and RAG1 from all individuals were obtained and analyzed.
Bayesian trees and TCS network revealed two deeply divided lineages (southern
lineage and northern lineage) in T. barbatus, distributions of the two lineages
appeared to match summer coastal current pattern in China. It implied that currents
may have important effect on the phylogeographic pattern of T. barbatus. Cyt b
haplotype distributions and AMOVA showed further divisions within southern
lineage, which may be related to currents and barriers in coastal China. Divergence
time of the two lineages was 1.65 Mya, which may be dated back to Pleistocene
glacial cycles. Tajima’ D and Fu’ Fs statistics were significantly negative in both
southern and northern lineage, suggesting that the two lineages might have undergone
sudden expansions in past. Bayesian skyline plot showed that sudden expansion times
of southern and northern lineage were 0.010 Mya and 0.015 Mya, respectively, which
happened at the end of the last glacial period (about 0.02 Mya). It implied that
Pleistocene glaciation may be important to divergence and population size of T.
barbatus.
Content
論文審定書..................................................................................................................... i
Acknowledgement ......................................................................................................... ii
摘要.............................................................................................................................. iii
Abstract ......................................................................................................................... iv
Contents ......................................................................................................................... v
List of Figures ............................................................................................................... vi
List of Tables ............................................................................................................... vii
1. Introduction ................................................................................................................ 1
2. Material and methods ................................................................................................. 4
2.1. Sampling and DNA extraction............................................................................. 4
2.2 PCR and sequencing ............................................................................................ 4
2.3 Genetic diversities and genealogy........................................................................ 5
2.4 Molecular dating and historical demography ...................................................... 6
3. Results ........................................................................................................................ 8
3.1 Genetic diversity and genealogy .......................................................................... 8
3.2 Population differentiations within lineages ......................................................... 9
3.3 Molecular dating and historical demography .................................................... 10
4. Discussions .............................................................................................................. 11
4.1 Phylogeographic pattern within T. barbatus ..................................................... 11
4.2 Population differentiation within southern lineage ........................................... 12
4.3 Divergence and historical demography ............................................................. 13
Reference ..................................................................................................................... 16

List of Figures
Fig 1. Sampling sites and summer hydrographical conditions. . ................................. 27
Fig 2. TCS haplotype networks. . ................................................................................ 28
Fig 3. Distributions of southern lineage and northern lineage. ................................... 29
Fig 4. Bayesian trees of concatenated haplotypes. ...................................................... 30
Fig 5. Bayesian trees of cyt b haplotypes. . ................................................................. 31
Fig 6. Bayesian trees of RAG1 and Rh haplotypes. . .................................................. 32
Fig 7. Pairwise Fst matrices of southern lineage and northern lineage. . .................... 33
Fig 8. Isolation by distance. ........................................................................................ 34
Fig 9. Bayesian skyline plot. ....................................................................................... 35

List of Tables
Table 1. Primers. ......................................................................................................... 36
Table 2. Diveristy indexes of southern lineage and northern lineage. ......................... 37
Table 3. Pairwise Fst matrices of southern lineage and northern lineage. .................. 38
Table 4. AMOVA. ....................................................................................................... 39
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