Biol375 2014

Molecular Evolution (BIOL 375.00/790.64/793.03, Fall 2014) Instructor: Dr Weigang Qiu, Associate Professor, Department of Biological Sciences Teaching Assistant: Ms Saymon Akther <saymon.akther@gmail.com> Room: 926 HN (Seminar Room, North Building) Hours: Mon. & Thur 4:10-5:25 pm Office Hours: Room 839 HN; Wed 5-7 pm or by appointment Course Website: http://diverge.hunter.cuny.edu/labwiki/Biol375_2014

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Course Description

Molecular evolution is the study of the change of DNA and protein sequences through time. Theories and techniques of molecular evolution are widely used in species classification, biodiversity studies, comparative genomics, and molecular epidemiology. Contents of the course include:

• Population genetics, which is a framework of understanding mechanisms of sequence evolution through mutation, recombination, gene duplication, genetic drift, and natural selection.
• Molecular systematics, which introduces statistical models of sequence evolution and methods of reconstructing species phylogeny.
• Bioinformatics, which provides hands-on training on data acquisition and the use of software tools for phylogenetic analyses.

This 3-credit course is designed for upper-level biology-major undergraduates. Hunter pre-requisites are BIOL203, and MATH150 or STAT113.

Textbooks

• (Required) Roderic M. Page and Edward C. Holmes,1998, Molecular Evolution: A phylogenetic Approach, Blackwell Science Ltd.
• (Recommended) Baum & Smith, 2013. Tree Thinking: an Introduction to Phylogenetic Biology, Roberts & Company Publishers, Inc.

Learning Goals

• Understand mechanisms of DNA sequence evolution
• Be able to describe evolutionary relationships using phylogenetic trees
• Understand the computational algorithms for building phylogenetic trees
• Be able to use web-based as well as stand-alone software to infer phylogenetic trees

Links for phylogenetic tools

• NCBI sequence databases
• A Molecular Phylogeny Web Server
• EvolView: an online tree viewer

Exams & Grading

• Assignments. All assignments should be handed in as hard copies only. Email submission will not be accepted. Late submissions will receive 10% deduction (of the total grade) per day.
• Three Mid-term Exams (30 pts each)
• Comprehensive Final Exam (50 pts)

Bonus for active participation in classroom discussions

Academic Honesty

While students may work in groups and help each other for assignments, duplicated answers in assignments will be flagged and investigated as possible acts of academic dishonesty. To avoid being investigated as such, do NOT copy anyone else's work, or let others copy your work. At the least, rephrase using your own words. Note that the same rule applies regarding the use of textbook and online resources: copied sentences are not acceptable and will be considered plagiarism.

Hunter College regards acts of academic dishonesty (e.g., plagiarism, cheating on examinations, obtaining unfair advantage, and falsification of records and official documents) as serious offenses against the values of intellectual honesty. The College is committed to enforcing the CUNY Policy on Academic Integrity and will pursue cases of academic dishonesty according to the Hunter College Academic Integrity Procedures.

Course Schedule

Part 1. Tree Thinking

• 8/28 (TH). Overview & Introduction. Lecture slides:
  File:Intro.pdf

Assignment 1 (10 pts; Due: 9/4, Thursday)
File:Pretest.pdf

• 9/1 (M). Labor Day. No class
• 9/4 (TH). 1.1. Introduction (Continued). In-class exercise 1.
  File:In-class-1.pdf

Assignment 2 (5 pts; Due: 9/8, Monday)
Watch Origin of Species: Lizards in an Evolutionary Tree. Provide short answer (1-3 sentences) to each of the following three questions. What are the two hypotheses explaining the origin of different ecomorphs of lizards on Caribbean Islands? What is the expected phylogeny under each hypothesis? Which hypothesis is supported by the phylogeny of actual DNA sequences?

• 9/8 (M). 2.1. Intro to trees
• 9/11 (TH). 2.2 & 2.3. Tree Distance. In-class exercise 2.
  File:In-class-2.pdf

Assignment 3 (5 pts; Due: 9/15, Monday)

Computer exercise. Obtain an account on EvolView. Once logged in, under the "Basic" tab, click the first icon & copy and paste the following NEWICK string: "(monkey:0.09672,((tarsier:0.18996,lemur:0.14790)0.999:0.09005,(macaque:0.18524,(gibbon:0.10388,(orang-utan:0.09481,(human:0.03391,(gorilla:0.06135,chimpanzee:0.05141):0.01580)0.316:0.05381)1.000:0.03019)0.978:0.05616)0.997:0.05042)0.965:0.09672);". Name your project as "Assignment 3" and the tree as "primate". Render the tree in all five available formats. Using the "Export" tab to download all tree graphs (in "jpeg" or "png" format). Copy and Paste your tree graphs into a single page of Microsoft Word or PowerPoint. Turn in a printed hard copy.

• 9/15 (M). 2.4 & 2.5. Species Tree & Lineage Sorting
• 9/18 (TH). 2.5. Consensus Tree & Review. Chapter 2 Slides:File:Part-1-tree-thinking.pdf. In-class Exercise 3:
  File:In-class-3.pdf
• 9/22 (M). Midterm Exam I

Part 2. Trait Evolution

• 9/25 (TH). Holiday Recess. No Class
• 9/29 (M). Traits & trait matrix

Assignment #4 (5 pts; Due 10/6)
Based on the lizard card, construct a character-state matrix for all lizard species. For each species, list its character state for each of the following two characters (as columns): (1) Geographic origin, and (2) Habitat. Re-watch the video may help this assignment. Hint: use Excel & hand in a printout of your Excel sheet.

• 10/2 (TH). Homoplasy & consistency
• 10/6 (M). Parsimony reconstruction (Chapter 5)

Assignment #5 (5 pts; Due 10/9)

Use EvolView to display the following tree of Caribbean lizards: "((Anolis_chlorocyanus:0.15297,(Anolis_evermanni:0.09207,(Anolis_cristatellus:0.14363,Anolis_pulchellus:0.07962)0.931:0.02884)0.997:0.04280)0.897:0.02232,(Anolis_cybotes:0.17149,Anolis_olssoni:0.12747)0.974:0.03034,(((Anolis_ophiolepis:0.06969,Anolis_sagrei:0.06284)1.000:0.09480,(Anolis_valencienni:0.10249,(Anolis_grahami:0.10016,Anolis_lineatopus:0.10064)0.613:0.01700)0.999:0.04077)0.997:0.04169,((Leiocephalus_barahonensis:0.24783,Anolis_occultus:0.15489)0.978:0.05261,(Anolis_alutaceus:0.14271,(Anolis_porcatus:0.10377,(Anolis_sheplani:0.15083,Anolis_angusticeps:0.12285)0.943:0.02748)0.898:0.01870)0.989:0.03278)0.514:0.01385)0.404:0.01061);" Note: Show the "rectangular phylogram" format (2nd tree option). Show species names (aligned, use the button "align/unalign leaf node labels"), scale bar and bootstrap values. Mouse over the branch "Leiocephalus_barahonensis" and click "reroot here" Make a printout of the tree & then hand-draw a tree without un-supported (support value < 0.8) branches (i.e., making polytomies).

• 10/9 (TH). Genome & gene structure (Chapter 3)
• 10/13 (M). No Class
• 10/16 (TH). Homology search with BLAST

Assignment #6 (TBD, Due 10/20)
TBD

• 10/20 (M). Review & Practices
• 10/23 (TH). Midterm Exam 2

Part 3. Tree Algorithms

• 10/27 (M). Alignments (Chapter 5)
• 10/30 (TH). Genetic distances (Chapter 5)
• 11/3 (M). Distance methods (Chapter 6)
• 11/6 (TH). Parsimony reconstruction (Chapter 6)
• 11/10 (M). Likelihood methods (Chapter 6)
• 11/13 (TH). Tree-testing (Chapter 6)
• 11/17 (M). Midterm Exam 3

Part 4. Mechanisms of Evolution

• 11/20 (TH). Instructor traveling. No class
• 11/24 (M). TBD
• 12/1 (M). Instructor traveling. No class
• 12/4 (TH). TBD
• 12/8 (M). TBD
• 12/11 (TH). TBD
• 12/15 (M). Review
• 12/19 (TH) Comprehensive Final Exam (Regular class hours & Room)
• 12/31 (Wed). Grades Submitted to Registrar Offices (Hunter and Graduate Center)