課程名稱 |
親緣地理分析 Phylogeography and Phylogeny |
開課學期 |
102-2 |
授課對象 |
生命科學院 生命科學所 |
授課教師 |
王俊能 |
課號 |
EEB5079 |
課程識別碼 |
B44 U1910 |
班次 |
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學分 |
3 |
全/半年 |
半年 |
必/選修 |
選修 |
上課時間 |
星期三2,3,4(9:10~12:10) |
上課地點 |
生科3C |
備註 |
總人數上限:30人 |
Ceiba 課程網頁 |
http://ceiba.ntu.edu.tw/1022EEB5079_ |
課程簡介影片 |
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核心能力關聯 |
核心能力與課程規劃關聯圖 |
課程大綱
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為確保您我的權利,請尊重智慧財產權及不得非法影印
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課程概述 |
Phylogenetics explores how organisms, genes, and traits have evolved, and seeks to represent the history of life’s divergence through the use of phylogenetic trees. Phylogenetics has contributed to a wide variety of research especially in the fields of systematics, biogeography (phylogeography), adaptive evolution, and community structure. Lectures will emphasize the logical basis and computational details of various tree-building algorithms and associated methods of hypothesis testing, as well as application of next-generation sequencing data in phylogenetic tree building. In general, this course will focus on the use, interpretation, and methods of reconstructing evolutionary trees.
1 (Feb 19) Introduction and course organization
2 (Feb 26) Introduction to phylogenetic analysis using genotyping and DNA sequences data
3 (March 5) Molecular homology, multiple sequence alignments
4 (March 12) Distance methods: models of nucleotide and protein evolution
5 (March 19) Parsimony: tree length and other indices, molecular clock, substitution modeling testing, tree-searching algorithms, consensus trees
6 (March 26) Maximum likelihood theory and methods; Phylip and PAUP*
7 (April 2) No class
8 (April 9) Accuracy and performance of MP & ML; Assessment, Tree Confidence; Phylip and PAUP*
9 (April 16) Midterm examination
10 (April 23) Bayesian methods; Introduction to MrBayes
11 (April 30) Molecular divergence dating (1)
12 (May 7) Molecular divergence dating (2)
13 (May 14) Applications in phylogeography research (1)
14 (May 21) Applications in phylogeography research (2)
15 (May 28) Applications in adaptive evolution research (1)
16 (June 4) Applications in adaptive evolution research (2)
17 (June 11) Applications in community structure research
18 (June 18) Final examination
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課程目標 |
學生將可藉此熟習分子生態及分子演化領域當代之重要研究議題,並可應用在生物多樣性及保育生物實務工作。 |
課程要求 |
最好修過遺傳學或演化生物學
Grades for the course will be based on two in-class examinations (25% each), class participation (10%) and a phylogenetic analysis project with a written paper in standard scientific format (40%). For the phylogenetic analysis project, students are encouraged to use their own data. Additionally, as a graduate student you are expected to participate aggressively in the discussion of assigned reading materials.
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預期每週課後學習時數 |
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Office Hours |
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指定閱讀 |
待補 |
參考書目 |
There is no assigned textbook for this class. Instead reading materials will assigned and course materials will be posted on Moodle. You may also wish to consult several books listed below as background references.
Nei and Kumar (2000) Molecular Evolution and Phylogenetics,
Page and Holms (1998) Molecular Evolution: A Phylogenetic Approach.
John C. Avise (2000) Phylogeography, Harvard University Press.
Felsenstein (2003) Inferring Phylogeneties,
Salemi and Vandamme, eds (2003) .The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny
Higgs and Attwood (2005) Bioinformatics and Molecular Evolution
Joanna R. Freeland (2005) Molecular Ecology, Wiley
John M. Smith (2006) Evolutionary genetics, Oxford University Press.
Yang (2006) Computational Molecular Evolution
Barry G. Hall (2007) Phylogenetic Trees Made Easy, Sinauer.
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評量方式 (僅供參考) |
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週次 |
日期 |
單元主題 |
第1週 |
2/19 |
師大黃士穎老師系統演化學的課程網頁,學生可以用密碼D201A(以訪客身分登入);即可進入網頁下載講義與資料。
http://moodle.ntnu.edu.tw/course/enrol.php?id=37741
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第2週 |
2/26 |
學生本週起至師大分部研究大樓S201教室9:00上課
,就是公館校區進來最後一棟(理學院大樓對面)</br>
位置地圖http://www.es.ntnu.edu.tw/download/map_chinese.jpg
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第9週 |
4/16 |
Bayesian methods; Introduction to MrBayes
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第10週 |
4/23 |
Molecular divergence dating (1) |
第11週 |
4/30 |
Molecular divergence dating (2) |
第12週 |
5/07 |
Applications in phylogeography research (1) |
第13週 |
5/14 |
Applications in phylogenetic community structure research (CLH) |
第14週 |
5/21 |
Applications in phylogeography research (2) |
第15週 |
5/28 |
Applications in adaptive evolution research (1) (PCL) |
第16週 |
6/04 |
R introduction (SYH) |
第17週 |
6/11 |
Applications in adaptive evolution research (2) (PCL) |
第18週 |
06/18 |
Student assignment due |
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