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研究生:沈敬家
研究生(外文):Shen, Chin-Chia
論文名稱:鬼基因滲入可能是造成斯文豪氏蛙(Odorrana swinhoana)複合群粒核不一致的潛在原因
論文名稱(外文):Ghost introgression as an underlying cause of mitonuclear discordance in Odorrana swinhoana complex
指導教授:林思民
指導教授(外文):Lin, Si-Min
口試委員:黃仁磐廖培鈞林思民
口試委員(外文):Huang, Jen-PanLiao, Pei-ChunLin, Si-Min
口試日期:2023-06-07
學位類別:碩士
校院名稱:國立臺灣師範大學
系所名稱:生命科學系
學門:生命科學學門
學類:生物學類
論文種類:學術論文
論文出版年:2023
畢業學年度:111
語文別:英文
論文頁數:104
中文關鍵詞:族群動態模型鬼基因滲入粒核不一致臭蛙屬族群基因體學親緣關係樹限制酶位點標定定序
外文關鍵詞:demographic modellingghost introgressionmitonuclear discordanceOdorranapopulation genomicsphylogenyRADseq
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由於有著不同的演化特性,粒線體和核基因有時會發生不一致的演化趨勢。這種現象稱為粒核不一致(mitonuclear discordance),並經常造成親緣關係分析過程中的矛盾。核粒不一致的現象中經常可見劇烈的粒線體基因分化(deep mtDNA divergence),目前已有數種理論解釋這樣的演化事件,例如不完全譜系分選、性別偏差的播遷、或是鬼基因滲入(ghost introgression)。若現今的物種中含有來自已滅絕物種的基因滲入即可定義為鬼基因滲入,這是近年演化學界中備受關注的議題,也可透過演化模型和特定基因組中的訊息來進行檢定。在本研究中,我利用粒線體基因和限制酶位點標定定序(RADseq)分析斯文豪氏赤蛙複合群的粒核不一致現象;這個複合群包含了斯文豪氏赤蛙、宇都宮臭蛙以及一個位在台灣東部的斯文豪氏赤蛙族群,三者有著分化差距大的粒線體基因。RADseq的資料顯示所有的斯文豪氏赤蛙間有著相近的親緣關係,然而粒線體基因則顯示台灣東部的斯文豪氏赤蛙族群位於整個複合群的最基群,代表現今的斯文豪氏赤蛙並不是一個單系群。透過演化族群動態模型和基因組中的族群分化,我們推測台灣的東部曾經存在一個擁有特殊粒線體基因的臭蛙屬物種,但西部的斯文豪氏赤蛙在向東擴散的過程中將其取代,而在分布重疊的區域中留下該物種的粒線體和少數核基因。這是兩棲類發生鬼基因滲入的第一篇研究,也顯示鬼基因滲入在自然界中的存在可能被低估。如果光靠粒線體基因進行物種界定或是親緣關係重建,可能會得到偏頗的結果,需加入一定數量的核基因才能更全面地描繪物種的演化進程。
The inconsistent evolutionary patterns between mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA), also known as mitonuclear discordance, have been reported for long time. Deep mtDNA divergence is a common phenomenon in mitonuclear discordance, which could be explained by various reasons, including speciation reversal, sex-biased dispersal, incomplete lineage sorting, or ghost introgression. Among these, ghost introgression has attracted reserch attention in recent studies and can be tested by using genomic data and demographic models. In this study, I used mtDNA and RADseq to reconstrct the evolutionary process of the Odorrana swinhoana complex (Anura: Ranidae), which comprises O. swinhoana, O. utsunomiyaorum, and a deeply divergent mitochondrial lineage recently discovered in eastern Taiwan. The RADseq data demonstrated a close relationship between all the populations in O. swinhoana, whereas the mtDNA data showed that a group of eastern populations formed an early diverging lineage, indicating that O. swinhoana is not a monophyletic group. Using demographic modeling and genome-wide SNP data, I inferred that this unique lineage might be the consequence of an eastward expansion from western O. swinhoana, which replaced an ancient, extinct Odorrana species, leaving its distinct mtDNA and small parts of nuclear genome. Our results provided the first case of ghost introgression in amphibians and demonstrated that ghost introgression is probably a widespread phenomenon in nature, which should be considered in evolutionary studies. This study also suggests that only using mtDNA to reconstruct phylogeny or species delimitation could yield erroneous results, and incorporating nuclear loci would depict the evolutionary of species more completely.
摘要 I
Abstract II
1. Introduction 1
2. Materials and Methods 6
2.1 Sample collection & Laboratory procedures 6
2.2 De novo locus assembly 7
2.3 MtDNA phylogeny & divergence time estimation 9
2.4 Phylogenetic analysis & Population structure 10
2.5 Procrustes test 12
2.6 Effective migration and landscape connectivity 13
2.7 Species tree 14
2.8 Gene flow detection 16
2.9 Demographic history 17
2.10 Loci Dxy estimation 20
2.11 Sex-biased dispersal 21
2.12 Morphological analysis 22
2.13 Acoustic analysis 23
3. Results 26
3.1. De novo locus assembly 26
3.2. MtDNA phylogeny and divergence time estimation 27
3.3. Phylogeny and population structure using RAD-seq 28
3.4. Procrustes test 30
3.5. Effective migration and landscape connectivity 30
3.6. Species tree 32
3.7. Gene flow 32
3.8. Demographic history 33
3.9. Loci Dxy estimation 34
3.10. Sex-biased dispersal 35
3.11. Morphological analysis 35
3.12. Acoustic analysis 37
4. Discussion 39
4.1 Mitonuclear discordance pattern in O. swinhoana complex 39
4.2 Complex ghost introgression in the evolutionary history of O. swinhoana complex 40
4.3 Phenotypic variation and future directions 44
5. Reference 48
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