Fish/Biol 340: Introduction to Genetics and Molecular Ecology
An overview of the fundamentals of molecular genetics and the application of genetic techniques to problems in ecology, evolution and natural resource management
Autumn Quarter 2022, 5 Credits
Course Description
Rationale
In the past few decades, molecular genetics has become one of the fastest growing fields in the life sciences. The application of molecular methods has spread to virtually all fields of modern biology, including ecology, conservation, breeding and natural resource management, leading to the establishment of a new discipline, Molecular Ecology. With the expansion of the application of molecular tools, it has become crucial that all biologists have a basic understanding of genetics and molecular biology, and the application of molecular tools to the detection of kin, the identification of populations, the reconstruction of phylogenetic relationships, and more recently, to the understanding of local adaptation and evolution. Rather than providing an overview of classical genetics, the aim of the course is to provide an understanding of the genetic principles underpinning these applications, thus allowing an assessment of the potential and limitations of molecular approaches to specific questions in ecology, evolution and resource management.
The course will be important to students for the following main reasons:
- Basic understanding: The current ubiquity of molecular genetic studies in virtually all fields of biology requires some basic understanding of the genetic principles underpinning molecular methods. Continuing developments in molecular technology, statistical analyses and computer power will further widen potential applications. Thus, even if students do not envisage using genetics in their own research, some genetic knowledge will be necessary in almost any career track.
- Practical application: If molecular genetic methods are to be applied effectively in ecology, evolution and general biology, they have to be carefully chosen according to the ecological and biological circumstances, assumptions of the methods and the specific aims of the study. Furthermore, an understanding of the evolutionary dynamics of molecular markers in the context of the biological question of the research is a crucial prerequisite for the interpretation of genetic data. It is thus necessary that students have a good overview of available methods, their appropriate application and potential shortcomings.
- Communication: Many of the current problems in the application of genetic data are founded in conceptual misunderstandings between scientists applying genetic methods and the end users of their research (fisheries managers, breeders, forest managers, conservationists). It is therefore important that students are aware of these misunderstandings and are able to understand and explain genetic research.
Aim and Objectives
To provide students with a fundamental understanding of genetic principles underlying the application of molecular genetic techniques.
Students will be able:
- To understand basic principles of molecular genetics
- To apply such principles to ecological, environmental and conservation research
- To interpret genetic data in an applied context
- To communicate and disseminate the results of their research
Basic Approach
We will achieve the above aim and objectives by the following means
- Lecture Videos: Most basic material will be delivered as short videos by subject. Watch those videos, and take notes! Most videos also contain one or two quiz questions, which will contribute to your grade. Make sure you watch these videos before class sessions, because I will not repeat them in class.
- Class sessions: Class sessions on Tuesday and Thursday will be in person in FSH107 and will be used to go over examples and past exam questions. Some of these exercises will be graded. Make sure to use these sessions to ask questions if you don't understand something, and come prepared. Class sessions will use PollEverywhere, so make sure you are registered.
- Textbook: there is no required textbook for this class, but one is highly recommended (see Readings page).
- Primary literature: There are links to primary literature in the field on the Readings page as well as in the specific week under Modules. All these papers are fairly brief and easy. Don't worry too much about details of the methods, but consider the problem, the approach the authors took, their general results and their interpretation of the results. You should read these papers - although they won't be on the exam per se, they may be used as examples in exam questions aiming at lecture material. Furthermore, they will help you deciding on style and detail needed for your project report.
- Laboratories:
- Molecular Labs (Wet Labs, FTR 113): The first three weeks and one of the later labs will be used to introduce you to molecular methods such as DNA extraction, PCR and electrophoresis. These methods usually involve a lot of waiting, so we will use these labs also to deepen your theoretical understanding of molecular methods. Most of these labs will contribute data to your lab project.
- Computer Labs (FSH 136) will be used to improve and deepen your understanding of concepts from lecture and textbook (see also the lab sections on the Modules page). We will use simulation programs to learn about genetic processes and analysis programs to analyze sample data sets. The software we will use is freely downloadable, and it may be an idea to install them on your own machine.
- Project Report: As part of the laboratories, we will conduct a study on the population structure of Pacific cod in the Bering Sea and the Gulf of Alaska (see lab project). Students will submit a 2500 word (about 8-10 double spaced pages) project report, which aims at integrating lecture material, laboratory experiments and literature and also will help to improve communication skills. The project report will be structured like a scientific paper (Introduction, Methods, Results, Discussion), and we will write sections for this report as the quarter progresses. These draft sections will be reviewed by class mates, using an online peer review system (Peerceptiv). See the Lab Project page for more details and specific instructions.
See the 'Pages' (Front Page) link for more information about the course, lecture notes and lab handouts.
Technology
Although the class will be held in person, we will use a lot of technology, and here are a few pointers:
- If you are off-campus and you want to access on-campus resources, the best way is to install Husky-OnNet. This software will allow you to access library and other resources, though you will still have to sign on to Canvas.
- Communication: Please use Ed Discussion for any questions - our response time is likely much shorter there than by e-mail. Make sure to read replies on Piazza before asking questions. Also, feel free to reply to questions - instructors will monitor traffic and approve correct answers. Students who consistently answer questions correctly will receive extra points.
- Clickers: As a classroom response system, we will use PollEverywhere, which is free for students. You are already registered, so make sure you login with your UWNetID to receive credit. Have your device handy, and respond under www,pollev.com/lorenz.
- Peer Review: we will use Peerceptiv to peer review sections of the project report throughout the quarter (see Project Report for details). This tool is now integrated with Canvas, so you only have to click on the assignment (in Modules) to access it. Importantly, if there are any hiccups, let me know straight away so I can deal with them. The good news is that SAFS will pay the charges for Peerceptiv, so don't pay anything.
- Video calls: Although most contact will be in person, we may have some sessions that are held via Zoom (for example, if instructors get sick). Because some students may not be able to attend, these Zoom class sessions will be recorded. The recording will capture the presenter’s audio, video and computer screen. Student audio and video will be recorded if they share their computer audio and video during the recorded session. The recordings will only be accessible to students enrolled in the course to review materials. These recordings will not be shared with or accessible to the public, and will be deleted after the course ends. By enrolling in this class, all students agree to not upload the recordings to other platforms - this is also true for any recordings made in person in the classroom. The University and Zoom have FERPA compliant agreements in place to protect the security and privacy of UW Zoom accounts. Students who do not wish to give consent to being recorded should:
- Choose a Zoom profile name that does not include any personal identifying information like their name or UW Net ID and do not upload a profile picture
- Not share their computer audio or video during their Zoom sessions
- Nettiquette: See also the CoE Covid-19 resources for undergraduates.
Strategies for success
The most important thing in this class is to be an active participant, and be prepared for lectures and laboratories. Make sure you stay up to date with the lecture material, and ask if anything is unclear. Make sure to watch videos and complete quizzes before synchronous class sessions. DO NOT leave revisions until the day before the exam. Also, make sure to read lab handouts before lab, and submit your lab reports in time. Be aware that the project report (together with the drafts) counts for 35% of the class grade - you won't pass this class without submitting a final project report. Make sure to submit your drafts and reviews on time (Wednesdays, 23:59), and most importantly, keep on revising your drafts throughout the quarter.
Time table
This is a very rough timetable by week. More specific details will be provided under Modules
|
Week |
Date (T) |
Lecture Topic |
Lab |
|---|---|---|---|
|
1 |
9/29 |
Introduction, Project |
DNA extraction, notebook, pipetting, Project |
|
2 |
10/4 |
DNA, replication; PCR & sequencing |
PCR, qPCR |
|
3 |
10/11 |
Sequencing, Mendel, Relatedness |
Gel electrophoresis |
| 4 |
10/18 |
Hardy-Weinberg equilibrium |
Relatedness |
|
5 |
10/25 |
Fixation indices |
Project Data Analysis |
| 6 |
11/1 |
Microevolutionary forces: mutation, drift |
Population Genetics Simulations |
|
7 |
11/8 |
Microevolutionary forces: selection, migration |
Veteran's Day |
| 8 |
11/15 |
Phylogeography, Phylogeny |
Phylogenetic trees |
|
9 |
11/22 |
Genomics |
Thanksgiving |
| 10 |
11/29 |
Gene expression |
Scientific figure interpretation |
|
11 |
12/6 |
Phenotypic Traits |
Review Session |
|
12/12 (M) |
Final Exam |
Grading and Course Policies
Covid-19
We recognize that the circumstances presented by the COVID-19 pandemic are challenging and that there is some degree of uncertainty associated with the return to in-person learning this quarter. We also understand that each person has a life outside of this course that can impact their education. Your physical well-being and mental health are the top priorities for this (and every) quarter. Please treat your peers, your instructor and laboratory leaders, and yourselves with the utmost care; we are all human and we are all in this together.
The class is conducted in-person, and students are expected to participate in class to fully benefit from course activities and meet the course’s learning objectives. Students should only register for this class if they are able to attend in-person. Students are required to wear a mask over their nose and mouth in class, labs and field trips. To protect their fellow students, faculty and staff, students who feel ill or exhibit possible COVID symptoms should not come to class. To allow for these absences, there is an assignment drop policy for prelab quizzes and in-class assignments, to allow you flexibility and to accommodate illness/absence/quarantine with no questions asked. Limited additional allowances can be negotiated if they are justified. For chronic absences, the instructor may negotiate an incomplete grade after the 8th week, or recommend the student contact their academic adviser to consider a hardship withdrawal (known as a Registrar Drop).
To reiterate the two major rules to keep everybody safe:
- The University recommends wearing a high-quality mask inside UW facilities where they aren’t otherwise required.
-
If you are sick with any illness, you must stay home, even if you are fully vaccinated. Here is a useful site for the UW Covid response and Covid-19 FAQ.
Grading
Assessment will mainly be aimed at problem solving abilities rather than regurgitation of read material. All aspects of the assessment, from laboratory participation to the final exam will thus involve worked examples, many of which will have been discussed in lectures.
We do not mark on a curve, but set the grade based on equal categories between the top grade and the passing grade. This means that your grade is only affected by the top grade. You do need 50% of the final research paper grade, 50% of the exam grade, and 50% of the marks overall to pass this class.
Percentage grades (PG) can be transformed to approximate decimal grades (DG) on the 4.0 scale using the following equation:
DG = 0.063*PG - 1.7
Breakdown of percentage score
- Video quizzes - 5%
- Panopto videos contain fairly easy quizzes to make sure that you haven't fallen asleep.
- In class assignments - 10%
- In each class session there will be some clicker questions and sometimes other assignments. These will be graded, but the lowest two scores will be automatically dropped to allow you to stay home if you feel sick. If you need more dropped scores, let us know in advance.
- Pre-lab quizzes - 5%
- We will distribute a lab handout at the beginning of each week, and there will be a quiz that has to be completed by the beginning of the lab.
- Laboratory reports - 15%
- There will be some form of report after each lab. This reporting may have several forms, ranging from short answers to questions in the lab handout to short lab reports. We will also give points for in-lab participation. The exact form of the report will be explained in each lab, so make sure to take notes. Be aware that the material will also be on the exams and is the basis for your project reports. You should be able to complete these reports in the lab, but if you need more time, lab reports are due at the beginning of the next Tuesday's lecture.
- Lab Notebook - 5%
- You should keep a lab notebook for the molecular labs. Specific instructions will be provided during the first lab. The lab notebooks will be graded by TAs during the midterm. Lab notebooks are not required for computer labs.
- Project Report - 30%
- Students will write a ~2500 word report on the results of the laboratory project. This report will be prepared in sections which will be submitted to an online peer review system allowing feedback from classmates. The final report is due at the end of quarter.
Project Report Drafts, reviews and back evaluations - 15%: There will be four project report drafts, one each for introduction, methods and results. These will be submitted online and graded by four of your classmates. You will review four of your classmates drafts and provide comments. See the Syllabus and the Project report pages for more details.
Final Project Report - 15%. The final report will be submitted to Canvas and will be graded by instructors. - Mid term exam - 10%
- The mid term exam serves to give a first insight into teacher and student performance and to identify problem areas. Here are midterm questions from past years.
- Final exam - 20%
- The final exam will cover the material of the entire class, including required reading material and labs (i.e. the exams are cumulative).
Course Policies
Make-up labs
All laboratories take considerable time to prepare. Therefore, we cannot offer make-up labs. If you cannot come to a lab, let us know at least a week in advance. If the absence is justified, we will try to accommodate you in one of the other sections or try to find other solutions. Note that lab material may be on the exam, that lab reports will be graded, and that many labs are needed to complete the project report.
Late work
We have designed this course to maximize your learning of the subject matter and advance your skills through a variety of activities. Therefore, our attendance policy is aimed at supporting our educational goals.
Assignments designed to help you prepare for class (e.g. online quizzes, discussions or homework due in class or section) will not be accepted after the due time (i.e., the night before the class by 11:59 pm).
Work scheduled to be presented or performed in class (e.g., in class worksheets, discussions and hands-on simulations) will not be accepted after the due time (i.e., 24h after the beginning of each lecture: T, Th, Sat 9:30 am)
Writing and lab assignments that are submitted late will incur a 10% deduction for every day that the work is overdue, starting from the deadline given in class. In other words, if you are given a deadline of 5:00 pm, and you hand in the assignment at 6:00 pm, you will lose 10%.
Assignments and lab reports are due at the beginning of the class period on the due date. After that, 10% of the mark will be subtracted for each day late, and after three days we won't grade it anymore.
Exams
Missed Exams: Exams are only offered on the scheduled dates and time, and “make up” exams will not be offered. Acceptable reasons to miss an exam are listed in the University handbook (Links to an external site.) Make-Up exams may be provided after the exam - these make-up exams will consist of questions different from the scheduled exam, and may therefore be more difficult. No make-up exams will be provided before the class exams, so make sure that you stay in town until the final exam.
Regrading: regrading requests must be submitted in writing together with the exam no earlier than three days and no later than a week after publishing grades. We will regrade the entire exam, and so your grade may go down as well as up.
Plagiarism and Cheating
Please check out the University Policies on Cheating and Plagiarism (Links to an external site.). Both are serious offenses, and may have severe consequences ranging from unreported grades to dismissal.If you have any doubt about plagiarism, feel free to ask. Additional resources are offered on the Project report page.
Instances of cheating during an exam will be awarded a zero on that exam, quiz or test. Entering responses on a clicker other than the one registered to you will result in a zero clicker score up to the day of the event, both for you and for the person whose clicker you use.
Accommodations
Religious Accommodation
Washington state law requires that UW develop a policy for accommodation of student absences or significant hardship due to reasons of faith or conscience, or for organized religious activities. The UW’s policy, including more information about how to request an accommodation, is available at Religious Accommodations Policy (https://registrar.washington.edu/staffandfaculty/religious-accommodations-policy/) (Links to an external site.). Accommodations must be requested within the first two weeks of this course using the Religious Accommodations Request form (https://registrar.washington.edu/students/religious-accommodations-request/) (Links to an external site.)
Disability Accommodation
It is crucial that all students in this class have access to the full range of learning experiences. At the University of Washington, it is the policy and practice to create inclusive and accessible learning environments consistent with federal and state law. Full participation in this course requires the following types of engagement:
|
Course component |
Requirements |
|---|---|
|
Videos |
The ability to watch short videos (up to 30 min), take notes and answer a few quiz questions. This can happen in your own time. |
|
Lectures |
The ability to attend weekly online lectures of 80 minutes with 60 other students. The ability to collaborate in teams; includes worksheets, short discussions of data, the ability to conduct short exercises. |
|
Molecular Labs |
The ability to operate lab equipment, in particular pipettes; includes repetitive motions, use of microscopes and standing for extended periods of time. The ability to collaborate in teams |
|
Computer Labs |
The ability to spend 3 hours in computer labs with 20 other students to analyze data. The ability to collaborate in teams; may include 10-15 minute data presentations and discussions |
|
Research project |
The ability to collaboratively analyze and interpret data and primary literature; involves computer work, creating text, uploading assignments. The ability to comment on other student's writing, to provide back-evaluations on such comments and to consider constructive criticism of your work. |
|
Exams and Quizzes |
The ability to complete multiple choice, short-answer questions or other questions within a limited amount of time. |
If you anticipate or experience barriers to your learning or full participation in this course based on a physical, learning, or mental health disability, please immediately contact the instructor to discuss possible accommodation(s). A more complete description of the disability policy of the College of the Environment can be found here. If you have, or think you have, a temporary or permanent disability that impacts your participation in any course, please also contact Disability Resources for Students (DRS) at: 206-543-8924 206-543-8925 V / TDD / uwdss@uw.edu e-mail / http://www.uw.edu/students/drs.
Roles & Responsibilities
Student: inform the instructor no later than the first week of the quarter of any accommodation(s) you will or may potentially require.
Instructor and TA: maintain strict confidentiality of any student’s disability and accommodation(s); help all students meet the learning objectives of this course.