課程資訊
課程名稱
 分子演化
Molecular Evolution 
開課學期
 103-2 
授課對象
 生命科學院  生命科學所  
授課教師
 丁照棣 
課號
 EEB5048 
課程識別碼
 B44 U1600 
班次
  
學分
 2 
全/半年
 半年 
必/選修
 選修 
上課時間
 星期三3,4(10:20~12:10) 
上課地點
 生科419 
備註
 與胡哲明合開
總人數上限：40人 
Ceiba 課程網頁
 http://ceiba.ntu.edu.tw/1032MolEvol 
課程簡介影片
 
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課程概述

This course is to introduce the fundamentals and methodology on research of molecular evolution. We will introduce the evolutionary changes and patterns of sequences, methods for phylogenetic analyses, and inferring sites under positive selection. Topics on recent advances of molecular evolution studies will be offered at the end, on phylogenomics, horizontal gene transfer, and genome evolution. Students are highly recommended to take evolution, genetics or equivalent subjects before taking this course. Laboratory practices will offered for students to be familiar with data retrieving and analyses. Homework assignments will be distributed weekly, which require substantial extra work time.

 

課程目標
 In combination with the computer laboratory practice, we aim to help our students to understand the evolutionary processes at the molecular level.

[Laboratory practice]
We will have computers available in class, but you are welcome to bring your own laptop computer. In the later case, you should download the corresponding software before the class. Date sets will be provided for the homework assignments but you are welcome to use your own data for the final presentation project.
 
課程要求
 Biology; Evolutionary Biology; Genetics or equivalent preferred 
預期每週課後學習時數
  
Office Hours
 另約時間 備註： by appointment 
指定閱讀
 Most of the lectures are based on selected chapters from the following books. Electronic copies will be provided through the semester.
Graur, D. and W.-H. Li. 2000. Fundamentals of Molecular Evolution. 2nd ed., Sinauer Assoc., Inc., Sunderland, MA, USA. (GL)
Hall, B. G. 2011. Phylogenetic trees made easy: a how-to manual, 4th ed. Sinauer Assoc., Inc., Sunderland, MA, USA.
Higgs, P. G. and T. K. Attwood. 2005. Bioinformatics and molecular Evolution. Wiley-Blackwell. (eBook available through NTU library) (HA)
 
參考書目
 Bioinformatics and Molecular Evolution by Paul Higgs and Teresa Attwood (Wiley-Blackwell, 2005)
Computational Molecular Evolution by Ziheng Yang (Oxford University Press, 2006)
Inferring Phylogenies (Paperback) by Joseph Felsenstein (Sinauer, 2003)
Molecular Evolution and Phylogenetics by Masatoshi Nei and Sudhir Kumar (Oxford University Press, 2000)
Molecular Evolution by Wen-Hsiung Li (Sinauer Associates, 1997)
Molecular Evolution: A Phylogenetic Approach by Roderick D.M. Page and, Edward C. Holmes (1991, Wiley-Blackwell)
Phylogenetic Trees Made Easy: A How-to Manual, Third Edition by Barry G. Hall (Sinauer, 2007)
Statistical Methods in Molecular Evolution by Rasmus Nielsen (Springer, 2005)
The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny Ed. by Marco Salemi and Anne-Mieke Vandamme (Cambridge University Press, 2003)

 
評量方式
(僅供參考)
  
No.
項目
百分比
說明
1. 
 Homework 
30% 
  
2. 
 Midterm exam 
30% 
  
3. 
 Presentation 
40% 
  
 
課程進度
週次
日期
單元主題
第1週
 2/25  [Lecture] Genes, Gentic Codes, and Mutations (GL1) by CTT (LS419)  
第2週
 3/04  [Lecture] Introduction: The Revolution in Biological Information (HA1)
[Computer Lab] Sequence technologies, Data formats, sequence retrieval by HYW (S301) 
第3週
 3/11  [Lecture] Dynamics of Genes in Populations (GL2, HA3)
[Computer Lab] Introduction to DNAsp by CTT (LS419) 
第4週
 3/18  [Lecture] Evolutionary Change in Nucleotide Sequences (GL3, HA4)
[Computer Lab] Introduction to Databases (HA5) by CTT (LS419) 
第5週
 3/25  [Lecture] Evolutionary Change in Nucleotide Sequences (GL3, HA4)
[Computer Lab] Sequence retrieval, Sequence alignment (ClustalW) by CTT (LS419) 
第6週
 4/01  Spring Break  
第7週
 4/08  [Lecture] Rates and Patterns of Nucleotide Substitution (GL4)
[Computer Lab] Estimating nucleotide substitution (MEGA) by HYW (S301) 
第8週
 4/15  [Lecture] Rates and Patterns of Nucleotide Substitution (GL4)
[Computer Lab] Molecular clock and estimation of species divergence time: BEAST by HYW (S301) 
第9週
 4/22  Midterm 
第10週
 4/29  [Lecture] Molecular Signature of Positive Selection
[Computer Lab] Detecting positive selection: PAML/DNAsp by HYW (S301) 
第11週
 5/06  [Lecture] Molecular Phylogenetics (GL5, HA8)
[Computer Lab] Phylogenetic ananlysis: MEGA by JMH (LS419) 
第12週
 5/13  [Lecture] Molecular Phylogenetics (GL5, HA8)
[Computer Lab] Bayesian Inference: Practice of MrBayes by JMH (LS419) 
第13週
 5/20  [Lecture] Phylogenomics
[Computer Lab] hypothesis testing by JMH (LS419) 
第14週
 5/27  [Lecture] Horizontal gene transfer
[Computer Lab] Dealing with conflict phylogenies by JMH (LS419) 
第15週
 6/03  [Lecture] Evolution by Gene Duplication (GL6, 7) by CTT (LS419) 
第16週
 6/10  Lab practice (自我練習，418教室開放，助教在場諮詢) 
第17週
 6/17  Student Presentation