課程資訊
課程名稱
 分子演化: 理論與實作
Molecular Evolution: Principles and Practice 
開課學期
 107-2 
授課對象
 生命科學院  生態學與演化生物學研究所  
授課教師
 李承叡 
課號
 EEB5087 
課程識別碼
 B44EU1990 
班次
  
學分
 3.0 
全/半年
 半年 
必/選修
 選修 
上課時間
 星期四2,3,4(9:10~12:10) 
上課地點
 生科4B 
備註
 本課程以英語授課。與王弘毅、丁照棣合授
總人數上限：40人 
課程簡介影片
 
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課程大綱
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課程概述

[Lectures]
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 practice will be offered for students to be familiar with data retrieving, analyses and interpretation. Homework assignments will be distributed weekly, which require substantial extra work time.
[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.
 

課程目標
 In combination with the computer laboratory practice, we aim to help our students to understand the evolutionary processes at the molecular level.  
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
 Molecular and Genome Evolution by Dan Graur (Sinauer, 2016)  
參考書目
 Molecular Evolution by Li W.-H. (Sinauer Associates, 1997)
Molecular Evolution: A Phylogenetic Approach by Roderick Page, D.M. and Holmes, E. C.
(1998, Wiley-Blackwell)
Fundamentals of Molecular Evolution By Graur, D. and Li, W.-H. (2nd Ed., Sinauer Associates,
2000)
Molecular Evolution and Phylogenetics by Nei, M. and Kumar, S. (Oxford University Press,
2000)
Inferring Phylogenies by Felsenstein, J. (Sinauer Associates, 2003)
The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny Ed. by
Salemi, M. and Vandamme, A. (Cambridge University Press, 2003)
Bioinformatics and Molecular Evolution by Higgs, P. and Attwood, T. (Wiley-Blackwell, 2005)
Statistical Methods in Molecular Evolution Ed. by Nielsen, R. (Springer, 2005)
Computational Molecular Evolution by Yang, Z. (Oxford University Press, 2006)
Phylogenetic Trees Made Easy: A How-to Manual by Hall, B. G. (4th Ed., Sinauer Associates,
2011)
Introduction to Evolutionary Genomics by Saitou, N. (Springer, 2013)
Molecular Evolution: A Statistical Approach by Yang, Z. (Oxford University Press, 2014)


 
評量方式
(僅供參考)
    
課程進度
週次
日期
單元主題
Week 1
 02/21  [Lecture] Introduction, The Molecular Basis of Biology and Evolution (Ch1 - Lee)
[Lecture] Sequencing Technologies 
Week 2
 02/28  Holiday 
Week 3
 03/07  [Lecture] DNA and Amino Acid Sequence Evolution (Ch3 - Lee)
[Computer Lab] Sequence alignment & Estimating nucleotide substitution (MEGA) 
Week 4
 03/14  [Lecture] Bioinformatic Database (Ting)
[Computer Lab] Sequence Retrieval from Database 
Week 5
 03/21  [Lecture] Rates and Patterns of Molecular Evolution (I) (Ch4 - Lee)
[Computer Lab] Natural selection (DnaSP, PAML) 
Week 6
 03/28  [Lecture] Rates and Patterns of Molecular Evolution (II) (Ch4 - Lee)
[Computer Lab] Natural selection (PAML) 
Week 7
 04/04  Spring Break 
Week 8
 04/11  [Lecture] Molecular Phylogenetics and Phylogenetic Trees (I) (Ch5 - Wang) 
Week 9
 04/18  Midterm, project preparation 
Week 10
 04/25  [Lecture] Molecular Phylogenetics and Phylogenetic Trees (II) (Ch5 - Wang)
[Computer Lab] Phylogenetic Inference (I) 
Week 11
 05/02  [Lecture] Reticular evolution and Phylogenic network (III) (Ch6 - Wang)
[Computer Lab] Phylogenetic Inference (II) 
Week 12
 05/09  [Lecture] Mobil Elements in Evolution (Ch9 - Wang) 
Week 13
 05/16  [Lecture] Evolution by DNA Duplication & Evolution by Molecular Tinkering (Ch7,8 - Ting) 
Week 14
 05/23  [Lecture] Eukaryotic Genome Evolution (Ch11 - Ting) 
Week 15
 05/30  [Lecture] The Evolution of Gene Regulation (Ch12 - Ting) 
Week 16
 06/06  Project preparation 
Week 17
 06/13  Final Project Presentation