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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	112-2
授課對象	學程生物多樣性學分學程
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419
備註	本課程以英語授課。生多學程演化與遺傳領域。與王弘毅、丁照棣合授總人數上限：40人

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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
指定閱讀
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	2/22	[Lecture] Introduction, The Molecular Basis of Biology and Evolution (Ch1 - Lee) [Lecture] Sequencing Technologies and Genomics
Week 2	2/29	[Lecture] DNA and Amino Acid Sequence Evolution (Ch3 - Lee) [Computer Lab] Sequence alignment & Estimating nucleotide substitution (MEGA)
Week 3	3/7	[Lecture] Rates and Patterns of Molecular Evolution (I) (Ch4 - Lee) [Computer Lab] Natural selection (PAML)
Week 4	3/14	[Lecture] Rates and Patterns of Molecular Evolution (II) (Ch4 - Lee) [Computer Lab] Natural selection (PAML)
Week 5	3/21	[Lecture] Molecular Phylogenetics and Phylogenetic Trees (I) (Ch5 - Wang)
Week 6	3/28	[Lecture] Molecular Phylogenetics and Phylogenetic Trees (II) (Ch5 - Wang) [Computer Lab] Phylogenetic Inference (I)
Week 7	4/4	National Holiday
Week 8	4/11	[Lecture] Reticular evolution and Phylogenic network (III) (Ch6 - Wang) [Computer Lab] Phylogenetic Inference (II)
Week 9	4/18	[Lecture] Mobil Elements in Evolution (Ch9 - Wang)
Week 10	4/25	Mid-term Exam
Week 11	5/2	[Lecture] Evolution by DNA Duplication (Ting)
Week 12	5/9	[Lecture] Evolution by Molecular Tinkering (Ch7 - Ting)
Week 13	5/16	[Lecture] Prokaryotic Genome Evolution (Ch10 - Ting)
Week 14	5/23	[Lecture] The Evolution of Gene Regulation (Ch12 - Ting)
Week 15	5/30	Final project preparation week
Week 16	6/6	Final project presentation