臺灣博碩士論文加值系統

裸子植物是種子植物的主要分支之一，其影響生態環境與人類經濟活動甚鉅。裸子植物已存活於地球超過三億年，但人們對它們的親緣演化關係仍存在爭議且尚待釐清。本研究開發Python程式，從美國國家生物技術之資訊中心的資料庫，下載與整理至少約一百種以上之裸子植物質體基因體的序列資料，並擷取其83個共有的蛋白質基因序列，經排序處理後的總長度約為105.5 Kb，大小約為12.7 Mb的二維DNA資料矩陣。執行相關的各種前置處理作業後，樣本以機器學習之自主抽樣或馬爾可夫鏈蒙地卡羅採樣的方式，進行距離法、最簡約法、最大似然估算法、貝葉斯推理法之不同權重模式的運算，在反覆且系統式演算訓練或改善後，推估相關之預測的結果，同時比較親緣演化關係的差異性。分析之結果顯示不論以何種方法，裸子植物的五大分類群（蘇鐵類、銀杏、柏類、買麻藤類及松類）都可以明顯的區分開來，且都擁有100 % 的支持度，符合對裸子植物分類的基本認知，表示本研究所開發的Python程式可準確地處理及轉換DNA資料。本研究從資料矩陣去除密碼子之第三個位置上的核苷酸，此舉除了降低分類群之演化速率，亦可減緩因演化模型因核苷酸替代飽和之現象所造成的影響。以此新的DNA矩陣所建構之親緣關係顯示，無論使用何種假說演算的分析方法，皆高度（89 – 100 %）支持蘇鐵類與銀杏的姊妹群關係，但買麻藤類與其他裸子植物分類群的關係仍待釐清，未來的研究可加入更多樣性的資料，如核基因體及粒線體基因體資料，以增加親緣關係推論的支持度。

Gymnosperms are one of the major branches of seed plants. They have a huge impact on the ecological environment and human economic activities. Gymnosperms have been living on the earth for more than 300 million years, but there is still controversy and clarification about their phylogenetic evolution. This study implemented a Python program for downloading and organizing the plastid genomes of at least 100 gymnosperm species from the database of the National Biotechnology Information Center. We extracted 83 common protein-coding9inm0omngfeddd gene sequences. After sorting, we obtained a two-dimensional DNA data matrix with a total length of about 105.5 Kb and a size of about 12.7 Mb. After performing various related preprocessing operations, these samples were subjected to the distance method, the simplest method, the maximum likelihood estimation method, and the Bayesian inference method by the machine learning or Markov Chain Monte Carlo for getting different weighing modes. After cycling and systematic training to improve the calculus, the results of the related predictions were estimated, and the differences in relationships were compared. The analysis results show that no matter what method is used, the five taxa of gymnosperms (cycads, ginkgo, cupressophytes, gnetophytes, and pine family) were distinguished with 100% support, which is in line with common knowledge of the classification. It reveals that the Python program implemented by this project can accurately process and convert DNA data. We removed the third codon positions from the data matrix to avoid the effect of the evolutionary model due to the saturation of nucleotide substitutions. All analytical methods based on this new DNA matrix congruently supported the sister relationship between cycads and ginkgo with supports ranging from 89 to 100%. However, the relationship between gnetophytes and other gymnosperms remains to be clarified. Future research can add more various data, such as nuclear and mitochondrial genome data, to enrich genetic information in phylogenetic inference of gymnosperms.

目錄
摘要………………………………………………….………………………………ⅰ
Abstract..………………………………………………………….…………………ⅱ
目錄………………………………………………………………………………ⅳ
表目錄………………………………………………………………………………ⅴ
圖目錄………………………………………………………………………………ⅵ
第一章 緒論..………………………….……………………………………………1
第一節 研究背景..………………………….………………………………………1
第二節 研究動機與目的..………………………….………………………………2
第三節 研究架構..…………………………….……………………………………3
第二章 文獻探討..………………………….…………………………………………4
第一節 機器學習..………………………….………………………………………4
第二節 裸子植物..…………………………….…………………………………12
第三節 質體基因體………………………….……………………………………15
第三章 研究方法..………………………….……………………………………18
第一節 研究樣本來源..………………………….………………………………18
第二節 研究處理及分析之流程..…………………………….…………………26
第三節 自主抽樣與馬爾可夫鏈蒙地卡羅法..…………….……………………27
第四章 結果與討論..………………………….……………………………………33
第一節 質體基因體序列之處理與分析…………………………………………33
第二節 裸子植物質體基因體親緣演化關係……………………………………41
第五章 結論與建議..………………………….……………………………………55
第一節 結論..……………………………….……………………………………55
第二節 建議..……………………………………….……………………………56
參考文獻..………………………….…………………………………………………57

表目錄
表 1. 序列資料簡表….……………….……………………………………………19
表 2. 基因名稱列表….……………….……………………………………………26
表 3. 特殊序列簡表….……………….……………………………………………34

圖目錄
圖 1. 研究架構圖……………………….………………………………………………3
圖 2. 自主抽樣法之分析步驟的範例簡圖….…………………………………………6
圖 3. 蒙地卡羅隨機模擬之積分的範例簡圖…………………………………………7
圖 4. 馬爾可夫鏈蒙地卡羅的範例簡圖………………………………………………7
圖 5. Python程式語法的範例簡圖………………………………………………8
圖 6. 估算親緣演化關係之程式語法的範例簡圖……………………………………9
圖 7. 模組區塊之程式語法的範例簡圖………………………………………………9
圖 8. GNU計劃之標誌圖………………….….…….…………………………10
圖 9. 程式開發人員最愛及最欲使用之程式語言的統計排名與百分比結果……11
圖 10. 現生之植物……………………………………………………………………13
圖 11. 受威脅物種於紅色名單中仍現存物種的比例統計結果……………………14
圖 12. 歷年來被定序與發表的質體基因體核苷酸數量之統計結果………………17
圖 13. 環境建置之編寫語言的範例…………………………………………………25
圖 14. 研究方法的流程簡介…………………………………………………………26
圖 15. 進行已撰寫檔案之執行圖示…………………………………………………27
圖 16. 家族譜的範例圖………………………………………………………………28
圖 17. 距離矩陣範例…………………………………………………………………29
圖 18. ML親緣關係分析之過程圖……………………………………………31
圖 19. 以NJ法建構之裸子植物質體基因體親緣演化的關係圖…………………41
圖 20. 以NJ法建構具演化速率之裸子植物質體基因體親緣演化的關係圖……42
圖 21. 以MP法建構之裸子植物質體基因體親緣演化的關係圖………………43
圖 22. 以MP法建構出分群之裸子植物質體基因體親緣演化的關係圖………44
圖 23. 以ML法建構之裸子植物質體基因體親緣演化的關係圖………………45
圖 24. 以ML法建構具演化速率之裸子植物質體基因體親緣演化的關係圖……46
圖 25. 以BI法建構之裸子植物質體基因體親緣演化的關係圖…………………47
圖 26. 以BI法建構具演化速率之裸子植物質體基因體親緣演化的關係圖……48
圖 27. 以NJ法建構不含第三個密碼子之質體基因體親緣演化的關係圖………50
圖 28. 以MP法建構不含第三個密碼子之質體基因體親緣演化的關係圖………51
圖 29. 以ML法建構不含第三個密碼子之質體基因體親緣演化的關係圖………52
圖 30. 以BI法建構不含第三個密碼子之質體基因體親緣演化的關係圖………53

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