Course Syllabus - Bucknell University

Conservation Genetics: Spring 2011, page‐1 

Course Syllabus: Conservation Genetics – BIOL320/620-01 

Spring 2011 (Jan 19 – May 12) 

Mon, Wed, and Fri: 1:00pm–1:52pm @ Biology Bldg 324 

Instructor: 

Dr. Mizuki Takahashi 

Office location: Biology Bldg 307 

Office phone: 577-1142 

mt027@bucknell.edu 

Textbook: 

Allendorf, F. W. and G. Luikart. 2007. Conservation and the Genetics of Populations. Blackwell 

Publishing Ltd, Malden, MA. 

Course Description: 

This seminar style course emphasizes the application of population genetics, molecular 

phylogenetic analyses, and reproductive genetics to answering biological questions in wildlife 

conservation. While student presentation and discussion will be an important part of the course, I 

will give lectures providing enough background information for student activities. 

Course Objectives: 

To provide an opportunity to understand values of biodiversity and genetic diversity, current 

conservation issues, importance of genetic information in conservation of living organisms. 

To develop an understanding of available molecular tools for conservation biology by which the 

class can learn how to choose an appropriate genetic tool for a given conservation issue. 

To provide an opportunity to read, critique, and interpret scientific papers addressing 

conservation issues using genetic data. 

To foster ability of scientific questioning, writing, and designing a study. 

Course Structure: 

The course consists of 15 weeks. In each week, I will present lectures in a Monday class and in 

the first halves of Wednesday and Friday classes unless examinations or student presentations are 

scheduled. While I will typically lead a discussion in the second half of a Wednesday class, an 

assigned student will lead a discussion in the second half of a Friday class. Class discussions will 

be based on reading assignments covering the topic that we learn a week before or during the 

week of discussion. For example, in Week 2, we will read and discuss values of biodiversity, 

which we will learn in Week 1. Email will be the primary tool for outside-of-class 

communication. Please check your Bucknell email account at least once a day. Scientific papers 

for class discussions will be provided via email and blackboard. 

Class Participation: 

Students are expected to attend every class and to participate in discussion, which will be 

evaluated as “Class Participation”. To meaningfully contribute to class discussions, students are 

expected to do reading assignments before attending lectures. The reading assignments consist of 

specific chapters of the textbook as well as scientific papers that will be provided to the class. 

Also, please turn off your cell phone during the class. Participation points may be taken off, if 

you use your cell phone during the class.


Plagiarism: 

It is academically dishonest to steal ideas, paragraphs, or sentences from existent sources and use 

them in your works. Bucknell University as an academic institute takes plagiarism seriously and 

all paper submissions by students have to go through “SafeAssignments” within Blackboard, 

which detects possible plagiarism. If you have any questions about plagiarism, please contact me 

before you submit papers. 

Conservation Issues Paper: 

Students will choose a contemporary topic in conservation genetics published within the last 24 

months in a national or regional newspaper (e.g., New York Times, Washington Post, Daily Item) 

or credited internet news sources (e.g., CNN and BBC) that are targeted for the general public. 

Please do not use articles from news sources that are geared toward people who are interested in 

science (Science Daily and Science News). Once a topic is found, students will study the 

scientific background of the topic by going through scientific literatures, which is often referred 

to in the newspaper article. The goal of this assignment is to assess how accurately and 

effectively scientific findings and knowledge are publicized. All topics and sources must be 

provided to and approved by the instructor by Feb 2. A 3-5 page paper (single-spaced, Times 

New Roman font 12, one-inch margins) will be developed that summarizes the topic, explains the 

conservation issue and how genetic tools are applied, and evaluates accuracy and effectiveness of 

the newspaper article by comparing the newspaper article with the scientific articles (Due: Mar 4). 

Students will also give 15-minute oral presentations on their papers (PowerPoint format). Scoring 

will be based on quality of paper (40 points) and oral presentation (20 points). 

Research Proposal: 

Students will choose a conservation issue whose solution and/or management would benefit from 

the application of genetic tools. This project can be an extension from the “Conservation Issue 

Paper” or a new topic can be developed from any sources. Brief summaries of research proposals 

(i.e., topics, outlines, and citations; a single page) have to be submitted to me by Mar 25. With the 

sound understanding of the chosen conservation issue, a research proposal (6-8 page, singlespaced, 

Times New Roman font 12, one-inch margins) will be developed that detail the 

conservation issue, how the issue benefits from genetic information, questions or hypotheses, and 

molecular analyses that will be carried out (Due: Apr 23). Research proposals will also be 

presented orally to the class (PowerPoint format, 15min). Scoring will be based on quality of 

paper (50 points) and oral presentation (30 points). 

Assignments and Grading: 

Class Participation and leadership of assigned discussion 80 pts (20%) 

Conservation Issue Paper and Oral Presentation 60 pts (15%) 

Quiz 1 20 pts (5%) 

Quiz 2 20 pts (5%) 

Midterm Examination 60 pts (15%) 

Research Proposal and Oral Presentation 80 pts (20%) 

Final Examination 80 pts (20%) 

Total 400 pts (100%) 

A = 400 – 360 pts (100-90%) B = 359 – 320 pts (89.9-80%) 

C = 319 – 280 pts (79.9-70%) D = 279 – 240 pts (69.9-60%) 

*Grades may be curved depending of the class performance.


COURSE SCHEDULE 

*Student activities are italicized with underlines for important dates. 

*Listed reading assignments are for students to better understand lectures within the assigned weeks. 

Additional papers will be provided for class discussions. 

Part I: Introduction 

Week 1: Jan 19W-21F 

Course Introduction 

Values of biodiversity and loss of biodiversity 

Scope of Conservation Genetics 

Reading: Allendorf & Luikart, 2007. Chapter1 (p3-14) 

Part II: Principles and Analyses of Conservation Genetics 

Week 2: Jan 24M-28F 

Population genetics I 

Hardy-Weinberg Principle 

Genetic Drift 

Reading: Allendorf & Luikart, 2007. Chapters 2, 5 & 6 

Week 3: Jan 31M-Mar 04F 

Population genetics II 

Effective Population Size 

Population subdivision 

Student-led Discussion 1 

Conservation Issue Article Due (Feb 02) 

Reading: Allendorf & Luikart, 2007. Chapters 7 & 9 

Week 4: Feb 07M-11F 

Population Genetics III 

Quantitative Genetics 


Reading: Allendorf & Luikart, 2007. Chapter 11 


Molecular Phylogenetics 

Quiz 1(Feb 16) 




Genetic Tools for Conservation 

Inbreeding Coefficients 


Reading: Allendorf & Luikart, 2007. Chapters 3, 4, 13 & 14

Part III: Genetics and Conservation 

Week 7: Feb 28M-Mar 04F 

Conservation Issue Presentation 

Conservation Issue Paper Due (Feb 28) 

Week 8: Mar 07M-11F 

Conservation Issue Presentation (only Mar 07) 

Metapopulation and Fragmentation 


Midterm Examination (Mar 11) 

 

Week 9: Mar 21M-25F 

Evolutionary Significant Units 


Research Proposal Summary Due (Mar 25) 


Week 10: Mar 28M-Apr 01F 

Conservation Breeding 



Week 11: Apr 04M- 08F 

Invasive Species I 

Quiz 2 (Apr 06) 


Reading: Allendorf & Luikart, 2007. Chapter 17 & 19 

Week 12: Apr 11M-15F 

Invasive Species II 

Student-led Discussion 8, 9 

Reading: Allendorf & Luikart, 2007. Chapter 17 & 19 


Use of Genetics in Forensics 

Student-led Discussion 10, 11 

Research Proposal Due (Apr 22) 


Research Proposal Presentation I 

Week 15: May 02M 

Research Proposal Presentation II 

May 05Th – 12Th 

Final Examination 

Conservation Genetics: Spring 2011, page‐4

Course Syllabus - Bucknell University

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