|
課程名稱 |
親緣地理分析
Phylogeography and Phylogeny |
|
開課學期 |
105-1 |
|
授課對象 |
生命科學院 生命科學系 |
|
授課教師 |
王俊能 |
|
課號 |
EEB5079 |
|
課程識別碼 |
B44 U1910 |
|
班次 |
|
|
學分 |
3 |
|
全/半年 |
半年 |
|
必/選修 |
選修 |
|
上課時間 |
星期一2,3,4(9:10~12:10) |
|
上課地點 |
生科1217 |
|
備註 |
應有演化生物學或分子演化基礎
總人數上限：10人 |
|
Ceiba 課程網頁 |
http://ceiba.ntu.edu.tw/1051EEB5079_ |
|
課程簡介影片 |
|
|
核心能力關聯 |
核心能力與課程規劃關聯圖 |
|
課程大綱
|
|
為確保您我的權利,請尊重智慧財產權及不得非法影印
|
|
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.
Course outline
1 Course organization and phylogenetic analysis using genotyping and morphological data (SYH)
2 Phylogenetic analysis using genotyping and DNA sequences data (SYH)
3 Phylogenomics, Phylip and PAUP* for AFLP, Molecular homology, multiple sequence alignments (SYH)
4 Substitution models, Model test, Building phylogenies using distance methods, Phylip and PAUP* NJ tree reconstruction (SYH)
5 Building phylogenies using Parsimony: tree-searching algorithms, Accuracy and performance, Phylip and PAUP* parsimony tree reconstruction (SYH)
6 Maximum likelihood theory and methods; Phylml, Garli, RAxML, FastTree (1) (PCL)
7 Maximum likelihood theory and methods; Phylml, Garli, RAxML, FastTree (2) (PCL)
8 Topology testing (PCL)
9 PAML analysis for adaptive evolution (PCL)
10 Application in molecular adaptation (PCL)
11. Bayesian methods; Introduction to MrBayes (CNW)
12 Molecular divergence dating: testing global clock (PAUP); local clock (PAML); Bayesian Inference of time (BEAST) (CNW)
13 Phylogeography: Geographic range evolution, ancestral state reconstruction: Lagrange, RASP (CNW)
14 Coalescent approaches to phylogeography: Migrate, Ima2 (CNW)
15 Genetic diversity, structure and gene flow in phylogeography: haplotype network, DNAsp, Arleguin (CNW)
16 Applications in phylogeography research (CNW)
本課程由台師大黃世穎老師(SYH)、廖培鈞老師(PCL)及台大王俊能老師(CNW)合授 |
|
課程目標 |
1. 學生將可藉此熟習分子生態及分子演化領域當代之重要分析方法，直接應用在研究文章期刊發表，並可應用在生物多樣性及保育遺傳生物實務工作。
2. 所有上課所學分析，修課學生均須配合作業實作，教師群引介這些分析方法都是當代研究發表最新趨勢概念，學生若無強烈決心想學習數據的實際應用及分析，請選擇其他親緣演化、系統分類相關的基礎與理論課程。 |
|
課程要求 |
最好修過遺傳學(特別是族群遺傳部分)及演化生物學
Grading 評分方式：
1. Grades for the course will be based on homework assignments.
2. These homeworks will be separately graded by comparisons across students’ performance on each assignment on a scale of 1 to 10.
3. Final grade will be the average of assignments scale to the 100 point system. |
|
預期每週課後學習時數 |
|
|
Office Hours |
|
|
指定閱讀 |
Textbook
There is no assigned textbook for this class. Instead reading materials will be assigned and posted on the Ceiba. You may also wish to consult several books listed below as background references. However, two books which are quite good for beginners can be helpful:
1.Barry Hall (2011) Phylogenetic Trees Made Easy, Fourth Edition. Sinauer Associates.
2. Lemey et al. (2009) The Phylogenetic Handbook, Second Edition. Cambridge University Press. |
|
參考書目 |
Background reading materials
Inferring Phylogeneties, Felsenstein (2003)
Molecular Evolution and Phylogenetics, Nei and Kumar (2000)
Molecular Evolution: A Phylogenetic Approach, Page and Holms (1998)
The Phylogenetic Handbook: A Practical Approach to DNA and Protein
Phylogeny, Salemi and Vandamme, eds (2003)
Bioinformatics and Molecular Evolution, Higgs and Attwood (2005)
Computational Molecular Evolution, Yang (2006) |
|
評量方式
(僅供參考) |
|
|
週次 |
日期 |
單元主題 |
|
第1週 |
09/12 |
Course Introduction and phylogenetic analysis using genotyping and morphological data (SYH) |
|
第2週 |
09/19 |
上課教室本週起更改至理學院大樓C007大教室；從靠近學七餐廳樓梯下到地下第一間教室。9：00上課
，就是理學院大樓C棟。位置地圖http://www.ga.ntnu.edu.tw/ntnu_map/img/ntnu03.jpg |
|
第3週 |
09/26 |
Phylip and PAUP* for AFLP, Molecular homology,
multiple sequence alignments (SYH) |
|
第4週 |
10/03 |
Substitution models, Model test, Building phylogenies
using distance methods, Phylip and PAUP* NJ tree reconstruction (SYH) |
|
第5週 |
10/10 |
National Day (No class) |
|
第6週 |
10/17 |
Building phylogenies using Parsimony: tree-searching
algorithms, Accuracy and performance, Phylip and PAUP* parsimony tree reconstruction (SYH) |
|
第7週 |
10/24 |
Maximum likelihood theory and
methods; Phylml, Garli, RAxML, FastTree (1) (PCL) |
|
第8週 |
10/31 |
Maximum likelihood theory and
methods; Phylml, Garli, RAxML, FastTree (2) (PCL) |
|
第9週 |
11/07 |
Topology testing (PCL)
|
|
第10週 |
11/14 |
PAML analysis for adaptive evolution (PCL) |
|
第11週 |
11/21 |
Application in molecular adaptation (PCL) |
|
第12週 |
11/28 |
Bayesian methods; Introduction to MrBayes (CNW) |
|
第13週 |
12/05 |
Phylogeography: Geographic range evolution,
ancestral state reconstruction: Lagrange, RASP, biogeobear (CNW) |
|
第14週 |
12/12 |
Molecular divergence dating: testing global clock
(PAUP); local clock (PAML); Bayesian Inference of time (BEAST)
(CNW) |
|
第15週 |
12/19 |
Network and Coalescence + Demography (CNW) |
|
第16週 |
12/26 |
Genetic diversity, structure and gene flow in
phylogeography: DNAsp, Arlequin (CNW)
蝙蝠種化-郭浩志 |
|
第17週 |
01/09 |
Final exam week (no class) |
|
第1-1週 |
09/12 |
師大黃士穎老師系統演化學的課程網頁，學生可以用密碼d201aphylo(以訪客身分登入）；即可進入網頁下載講義與資料。
https://moodle2.ntnu.edu.tw/enrol/index.php?id=1789
|
|
第2-1週 |
09/19 |
Phylogenetic analysis using genotyping and DNA
sequence data (SYH) |
|