Appendix II: Syllabus

BIO 317: Molecular Ecology & Evolution

Spring 2024

Tentative Lecture Schedule

Instructor: Andrew A. Davinack, Ph.D.
office: Mars Center for Science & Technology, room 1134
lab: Mars Center for Science and Technology, room 1118
phone: 508-286-3944
e-mail: davinack_drew@wheatoncollege.edu

MEETING TIMES

Class times:

Lecture – Tuesdays & Thursdays: 9:30 am – 10:50 am, Discovery Center 1313

Lab – Thursdays: 2:00 pm – 4:50 pm, Mars Science Center 2141

Student Hours:

Mondays 9:00 am – noon

Tuesdays: 1:30 pm – 2:30 pm (or by appointment, if none of these times work)

Student hours are designated times set aside for you to come and have a one-on-one discussion with me about anything pertaining to the class, your career goals, research or internship opportunities, coursework, classes or anything else on your mind! Furthermore, if you score a C or below on any of the exams, it is strongly advised that you meet with me within a week of receiving your grade. You can attend student hours by either dropping in to my office (SC 1134) or if you would like to lock in a specific date and time,  you can use the following link https://calendly.com/drewdavinack/office-hours (url is also available on Canvas). You can also email me directly to set up a virtual meeting if none of the above days and times work for your schedule.

Course Description: This comprehensive course in Molecular Ecology integrates both theoretical concepts and practical laboratory skills, designed for advanced undergraduates in biology or related fields. It offers an in-depth exploration of molecular tools and techniques used to understand ecological processes and patterns. The course is divided into lecture and laboratory components, each complementing the other to provide a holistic understanding of the subject. The lecture series are interspersed with discussions on scholarly articles and practical applications of molecular ecology in research and conservation. The laboratory component will be a mix of wet lab and dry lab practicals including key tools every molecular biologist needs to have in their repertoire including: DNA extraction and PCR skills, gel electrophoresis, programming skills and data analytical skills. The lecture component will culminate in the preparation and submission of an NSF-style research proposal where you must develop a novel ecological project. The lab component will culminate in the preparation of a manuscript for publication in the journal Molecular Ecology based on the data collected and analyzed in lab. Compass curriculum attribute: Natural Science.

Learning Outcomes for Lecture: At the end of the lecture component of this course, students will be able to:

• Explain the basics of molecular genetics as they apply to ecological studies.
• Analyze and interpret molecular data in the context of species and population studies.
• Critically evaluate scientific literature related to molecular ecology topics.
• Explain the principles of phylogeography and its significance in understanding species distribution and evolution.
• Explain the role of molecular techniques in conservation genetics and their application in biodiversity preservation.
• Develop the ability to formulate research questions and hypotheses in molecular ecology.

Recommended text and materials for lecture:

No textbook required for this course. We will be using an Open Educational Resource (OER) textbook specifically designed for BIO 317.

A laptop i.e., a fully functional computer with its own hard disk storage unit and full OS (e.g., Windows, Mac or Linux). NO Chromebooks, tablets or Ideapads! None of these machines have good performance capabilities for the type of analyses you will be performing. If you need a loaner laptop for the semester, please contact me ASAP. The software you will need for this course will be used in both lecture and lab (though primarily in lab) and is all free.

Lecture Grade Breakdown

Lecture Components

Exams: All exams will be open book and open note, and must be completed in class except for exam #2 which will be completed and submitted online. If you have accommodations (e.g., time and a half/double time) please email me with your official accommodations ASAP and we can arrange an alternative time for you to take your exam. Questions will be 50% multiple-choice/Mix & Match/ True or False and 50% short answer. These questions are designed to test your understanding of the basics of molecular ecology and will be based on articles covered in class in addition to material presented during lecture.

Article Discussions: For article discussions, we will be using a technique to encourage deeper reading/discussion (the material below is modified from the technique developed by Parrott & Cherry, 2011). This technique assigns roles to each group member to support a more in-depth examination of the research and shared responsibility for analysis of the work with your group.

Below is a summary of the roles and your role assignment for each paper is on the next page. For each paper, you will fulfill one of these roles and come prepared to support your group’s discussion in that capacity (as defined below). Your groups will be pre-arranged:

Discussion Leader and Concept Connector. Your job is to develop at least three possible discussion questions that you can discuss in groups to help everyone understand the main points of the assigned reading. Your task is to help people understand the theory in the papers, the purpose/objectives of the study, the methods and the main findings/conclusions. In doing so you should be facilitating the group discussion (NOT presenting the findings to the group). In addition, you should help everyone make connections to other important concepts we have covered in this course, you have learned about in previous courses or through your own experience. You should have at least three discussion questions prepared with your own brief answers. In addition, you should have least two connections prepared to facilitate discussion of concepts.

Passage Master. Your job is to locate a few special passages that are important in the reading assignment. These may give key information, back up the information given, or summarize the author’s key points. They might also be passages that inspired your interest, are particularly well written, or might be controversial or contradictory with other passages or other information learned in class. You will need to note at least two important passages per reading, including a summary of the passage in everyday terminology (in other words, how you would explain the passage to your roommate), and an explanation of why you think the passage is important.

Devil’s Advocate. Your job is to challenge the ideas/findings of the article by developing a list of critical, thoughtful questions that might be raised in terms of issues resulting from experimental design, lack of controls, conclusions that go beyond the findings, etc. If it is a review paper, your tasks will be developing a list of critiques that challenges the conclusions of the article. You should prepare at least two challenging questions or issues you have with the paper and its findings/evaluations.  

*Reporter.  Your job is to prepare a one-page report that summarizes the discussion within your group and amongst the class. The report should be emailed to me within 72 hours following the discussion. Failure of the designated reporter to submit their report will result in a one-point deduction for the ENTIRE group every day that it is late.

*Any of the three roles (Discussion Leader, Devil’s Advocate, Passage Master) may serve as reporter and this will be pre-assigned prior to the discussion.

Class Participation: As this is an upper-level course, a lot of the work must be completed on your own. This includes assignments, homework and readings. Class participation will involve attendance, discussion of material in class and in-class assignments. Please note that some points will ONLY be awarded in class and therefore it is in your best interest to attend all class sessions. Should a situation arise where you will be unable to attend due to a legitimate reason, you must contact me at least 3-5 days before that particular class. Aside from this, no in-class activities can be made up (this is non-negotiable).

Research Grant Proposal: As a capstone project for BIO 317, you will be required to develop an authentic research proposal which follows the United States’ National Science Foundation (NSF) template which emphasizes the “Intellectual Merit” and “Broader Impacts” of a proposed research plan. For this course you will be following the NSF’s Division of Environmental Biology (DEB) directorate. DEB encourages research that elucidates fundamental principles that identify and explain the unity and diversity of life and its interactions with the environment over space and time. Research may incorporate field, laboratory or collection-based approaches; observational or manipulative studies; synthesis activities; phylogenetic discovery projects; or theoretical approaches involving analytical, statistical, or computational modeling. You may focus your proposed research on one or multiple species from either an aquatic (marine, freshwater, estuarine, etc.) or a terrestrial system. DEB also encourages interdisciplinary proposals that cross conceptual boundaries and integrate over levels of biological organization or across multiple spatial and temporal scale. You may work as a group (no more than three students per group) to put together a joint proposal if you wish. Specific guidelines regarding the detailed format of your proposal will be provided separately.

Attendance Policy for Lecture: Your attendance at regular lecture meetings is an essential part of our work together. While attendance is not being tracked directly, missed in-class assignments will reflect your absences in this course. As a result, it is your responsibility to (1) let me know you will be absent in advance so you complete the in-class assignment upon your return without penalty and (2) identify/learn the material covered in class (we can meet during office to review the material that you missed). Per Wheaton’s policy, I have to report students that miss two classes without prior communication to me. If you anticipate multiple absences due to any personal circumstances, please reach out to me, Susan Friedman in Advising (friedman_susan@wheatoncollege.edu), or one of the support resources listed later in this document, so we can provide you with the necessary support.

Notification of Canvas usage: All exam and project grades will be posted to the course’s canvas page once they have been graded. In addition, all handouts, lecture slides, relevant articles and videos will be posted under the weekly modules.

BIO 317L – Molecular Ecology & Evolution Laboratory

Tentative Laboratory Schedule

Spring 2024

WL: Wet Lab Practical, DL: Dry Lab Practical

Learning Outcomes for Lab: At the end of the lab component of this course, students will be able to:

• Work collaboratively in a lab setting to conduct experiments and analyze data.
• Develop a moderate level of competency in gDNA extraction, PCR and gel electrophoresis.
• Develop proficiency in bioinformatics tools, including Python programming for DNA sequence handling and analysis.
• Prepare a scientific manuscript from inception to submission for publication.
• Conduct population genetic analyses using computational tools

Laboratory Grade Breakdown

Lab Components

Lab Notebooks: As part of the laboratory component of this course, you will be required to maintain an organized lab notebook with the genetic data that you collected. The laboratory project for this course will be written up for publication in a peer-reviewed scientific journal which means that your data must be clearly and concisely recorded in a very consistent manner.  While you will be working collaboratively on the lab project, each student must maintain their own lab notebook. The guidelines for organizing your notebook are available on Canvas. Your notebook will be checked three times during the semester (specific dates are on the lab schedule).

Research Manuscript: The data collected by each group will be collated towards the end of the semester and each lab group will be required to write a standard scientific manuscript to be submitted to the journal Molecular Ecology. As you group, you will have to decide amongst yourself who will be responsible for each component of the manuscript (Introduction, Methods, Results and Discussion) and you will all have to agree on a final version that must be submitted by the due date (see lab schedule).

Bioinformatics Practicals: During “dry lab” days you will be working directly with DNA sequence data on your computers. There will several practicals completed in lab where you will be required to exhibit your proficiency at retrieving batch sequences from the GenBank database, processing them (editing & aligning) using specific software and carrying out various types of phylogenetic and population genetic analyses using Python.

Pre-lab quizzes: There will be a total of four pre-lab quizzes throughout the semester that are front-loaded in the first half of the semester. These quizzes are short (10 questions) and are based on the theory behind the laboratory techniques/data analyses we will be covering that day. You will need to read the material posted in the lab module prior to taking the quiz. You will have unlimited attempts to complete the quiz but it will be due before lab begins on Thursday.

Attendance Policy for Laboratory: Labs are an essential component of this course because you will be applying your knowledge gained in lecture to carry out a real molecular ecology project. This project will be collaborative but you will be responsible for individual lab notebooks. Because of the way the lab has been set up along with the perishable and costly nature of the reagenets being used, there are no opportunities to make up any of the wet-lab sessions. It is the course policy that if a student has more than three absences from BIO 317 lab over the course of the semester, that student may not be able to pass the course. If you know in advance that you will have to miss a lab, please reach out to me as soon as possible. If you miss a lab due to illness, you should also contact me to let me know.

Course Policies

Honor Code: You are expected to uphold the Wheaton Honor Code throughout the course.  It will be clearly specified in the course which assignments are collaborative and which must be done on an individual basis. If in doubt, ask the instructor.

DEI Statement: At Wheaton I committed to creating a learning environment that supports a diversity of thoughts, perspectives and experiences and honors your identities (including race, gender, class, sexuality, religion, ability, etc.). To accomplish this if you have a name and/or set of pronouns that differ from those that appear in your official Wheaton records, please let me know. If you have any concerns during the course, please do not hesitate to come and talk with me and you can also submit anonymous feedback if you wish.

Accessibility Accommodations: Wheaton is committed to ensuring equitable access to programs and services and to prohibit discrimination in the recruitment, admission, and education of students with disabilities. Individuals with disabilities requiring accommodation or information on accessibility should contact Autumn Grant – Associate Director for Accessibility Services at the Filene Center for Academic Advising and Career Services: accessibility@wheatoncollege.edu or (508) 286-8215. If you already have accommodations in place, please provide the instructor with documentation during the first two weeks of the semester so that timely and appropriate arrangements can be made. All lecture slides will be published on Canvas after each class period.

Counseling and Mental Health: Your wellness is important to me. If you would benefit from mental health support, please call the Counseling Center at 508-286-3905 at any time of day or night, to schedule an appointment, or follow the voicemail prompts to be connected to a clinician.

Student Recording of Class Sessions: Wheaton College prohibits recording (as defined above) and transmission of activities (e.g. lectures, discussions) that occur as part of a classroom session by a student unless: (1) Accessibility Services has authorized recording as an academic accommodation for a qualified student with a disability and the student has notified the instructor of that authorization by presenting their accommodation letter; or (2) permission from the course instructor has otherwise been granted. In these circumstances, all students participating in the course as well as any guest speakers will be informed that audio/video recording may occur.  If a student is given authorization to record any portion of a classroom session, that student understands and agrees that the recording is for the sole use of the individual student and may not be reproduced, sold, posted online, or otherwise distributed. A student does not have permission to reproduce or post the information on any social media (e.g., YouTube, FaceBook, etc.), or other public or private forum that would infringe on the privacy rights of others represented in the recording.  Public distribution of such materials may constitute copyright infringement in violation of federal or state law, or College policy. Violation of this policy may subject a student to disciplinary action under the College’s Community Standards or other relevant policies.

Wheaton Student Support & Wellness Resources:

• The Counseling Center is the confidential and FREE mental health resource on campus for all students. To learn about services, check out the website, or give the office a call at 508-286-3905. Even when the Counseling Center is closed, or staff are unavailable, After Hours Mental Health Support is available by calling the front desk 508-286-3905 and following voicemail prompts to be connected to a clinician (24/7, available in languages other than English, and accessible from anywhere you are in the world).
• The Filene Center strives to support your learning pathway by fostering successful academic, career, and personal development. The academic advising staff will work collaboratively with you, faculty and campus resources to ensure that you have the access and guidance to become a confident and reflective learner at Wheaton and beyond. Contact us at advising@wheatoncollege.edu.
• Many other offices on campus can also help support the holistic wellness of students. For students who identify as low-income, first-gen, LGBTQ+, or have a faith or spiritual practice they adhere to, the Center for Social Justice and Community Impact and Center for Religious and Spiritual Life (the Base) are good places for support and engagement. The Marshall Center for Intercultural Learning supports BIPOC students and those working towards breaking down barriers across difference, and the Center for Global Education supports international students, and students seeking educational opportunities abroad. We encourage you to reach out to any and all of these offices for support.
• Health Services through Norton Medical Center is available to support students with a variety of physical health needs including specialty support for GYN and STI care. Contact the office at 508-286-4500 to make an appointment for care. There is no copay for visits and most services are free, with select procedures and labs billed to insurance.

Policy on Plagiarism (adopted from Prof. Robert Morris)

Rule: Cite properly all those whom you draw ideas, words, or work

Plagiarism is the unacknowledged use of another’s ideas or words with the intentional or unintentional result of presenting those ideas or words as your own. In the course, all written assignments are designed for you to explore your own ideas and thoughts however in cases where you use explicitly use published material to supplement these ideas, you will be required to cite the source of the study. Try to avoid using direct quotations and instead paraphrase as much as you can in your own words. This course adopts Wheaton College’s policy on plagiarism and affirms that “authors who fail to acknowledge their sources are, at the very least, guilty of being ignorant about the ethics governing the wider community of scholars; at the worst, they are guilty of blatant dishonesty. In any case, plagiarism in any form constitutes a serious violation of the most basic principles of scholarship and cannot be tolerated”.

In the course, examples of plagiarism include:

1. Passing of written material that is not your own: this refers to the actual wording. Copying someone’s paragraph or even a few lines of sentences word for word is considered as plagiarism even if you cite it. You must paraphrase all material coming from outside sources.
2. For the final project of the semester, you will be required to develop your own host-parasite model system which will most likely require you to mine images from online sources. Any images used in assignments must have the source either in the figure legend or provide a separate “Reference” slide with the list of sources for the images used.

Consequences of plagiarism in this course: The FIRST instance of plagiarism of any form on any portion of any assignment will result in no credit award for the entire assignment and ALL MEMBERS of the group will be penalized. The SECOND instance of plagiarism of any form on any portion of any assignment will result in no credit award for the entire assignment and ALL MEMBERS of the group will be penalized. The THIRD instance of plagiarism of any form on any portion of any assignment will result in a final grade of F for the course.

The best way to avoid plagiarism altogether is to just ask! Either meet with me or send me a draft of your work and I can give you instant answer. You will not be penalized for drafts, only final versions.

Policy on ChatGPT Usage: You may use ChatGPT to brainstorm ideas for your grant proposal. However, keep in mind that ChatGPT occasionally “hallucinates” resulting in inaccurate information, and worse yet, conjures up false references to support its conclusions. Therefore, you will need to investigate any ideas that ChatGPT comes up with yourself. You will be held liable if you proposed a project and included incorrect information and supplied references that do not exist.

ChatGPT Usage Acknowledgement: If you do choose to use ChatGPT to brainstorm ideas for your proposals, this needs to be stated in a special ChatGPT Disclaimer Section that should appear at the end of your references.

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