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Hello! This is where I organize resources for students in my ECOL/GENE 4530/6530 course on molecular ecology, for now taught every spring semester at UGA starting in 2022. I have worked hard to make this a no-cost course in terms of materials or textbooks, though students will need access to a computer that can run R and Java. Students who do not have this (e.g. a Chromebook can be coerced to do so, with experienced IT assistance) can borrow a laptop from Dr. Wares or use one of our campus computing resources. We will start fairly quickly using these resources, which will mean by the end of the semester you will have also gained capabilities in using code and important data resources for exploring biological diversity using genomic data.
For most of my career as a biologist, I’ve found myself wanting to know why biodiversity is where it is. That means I need to know what it is, and how they can move; rules like chess but far more complex and varied, and sometimes involving low probabilities (but loads of time for rare events). I need to know these things with varying degrees of precision given the questions being asked about those organisms, and the methods available. The ‘molecular ecology’ approaches we will learn and evaluate in here have helped a lot with this pursuit, but of course it all roots in knowing as much as you can about the organisms – life history, ecology, development and maturation – otherwise.
For most of my career as a biologist, I’ve found myself wanting to know why biodiversity is where it is. That means I need to know what it is, and how they can move; rules like chess but far more complex and varied, and sometimes involving low probabilities (but loads of time for rare events). I need to know these things with varying degrees of precision given the questions being asked about those organisms, and the methods available. The ‘molecular ecology’ approaches we will learn and evaluate in here have helped a lot with this pursuit, but of course it all roots in knowing as much as you can about the organisms – life history, ecology, development and maturation – otherwise.
So, what we will be doing is learning more about the genomic diversity found within and among populations of biodiversity of all types, and how that tells us more about movement/isolation, drift/selection, and the demographic changes that involve both sets of evolutionary dynamics.
Though it may seem a modest or narrow goal, our learning objective is sufficient fluency in the methods and terminology of molecular ecology that students are able to readily evaluate the primary literature in this field.
Requirements for the class
Requirements for the class
As noted above, some access to a computer with R/Java capabilities (any MacOS, Windows, LINUX; with effort, ChromeOS) will be necessary. Dr. Wares can help guide you to other resources if you do not have a computer that can be used for these computational skills. Also, because your backgrounds vary - please be prepared to ask questions or look for resources to help guide you with information you are less familiar with. If you ask me for help, I ask that you have first looked for a resource online to answer your question so that we have some starting points for discussion.
Lightning talks on current research in the field, using the journal Molecular Ecology or equivalent. These are 5-minute presentations (please stick to time) with 1-2 figures maximum (handout or slides) to put that research into the context of what we are learning about, and why you find it interesting. Everybody must do one of these, minimum, by end of semester [10%]
"Monte Carlo" papers will be assigned 4-5 times during semester to write a one-page inquiry report (single spaced) on your questions related to class and your understanding about those topics and how to address them, with 1-2 references from the peer-reviewed literature. When assigned, they are due in 48 hours [10% of your grade]
be sure to include a sentence or few on these self-inquiries: A) How does this information build on your prior learning and experiences? B) How does this information prepare you for your future efforts?
I will use these later in the semester as a reflection exercise... look out!
Analytical exercises are contract-graded, turn in on time for full credit so I can understand how you are engaging with the material [20%]
Draft 1 Proposal: 3 page research proposal on a topic of interest to you in the field of molecular ecology, with citations, appropriate figures, A HYPOTHESIS that results from you exploring topical research papers, methods, and background. Turning it in on time is 10% of your grade, this will be peer-reviewed [10%]
Example: You like carpenter bees; you wonder how far do offspring disperse each year, finding new wooden structures to burrow into? So, you look to find out what others have studied in terms of DNA-focused exploration of this question. Not a deep dive, but start to figure out what questions are important or unanswered for you. That is the basis of a research proposal.
Your proposal must be very specific about the use of genomic markers and analytical approaches that are appropriate for that kind of data, so in the end you will have explored those methods very thoroughly relative to your question.
This means that I want at least ONE PAGE of your proposal to reflect (a) how markers or gene regions are selected and data obtained; (b) what your hypotheses are for using these data; (c) what analytical approaches, with enough detail to easily replicate by another scientist; (d) what you think likely outcomes or alternative outcomes will be (can be a graph or other visual).
I won't count off if the whole proposal is longer, I just want to be sure that there is plenty of meat on your methods and approaches!
Be mindful that you have to be strategic with methods and resources; I'm asking you to find a way to answer your question, and defend how solid the answer could be, for $5000 or less. I will help guide you on this when I do the second peer evaluation.
Draft 1 is not expected to be in great shape, but readable and interpretable so your peers can help you put it into shape. This will be due February 24.
Peer review for another student, with guidance, is 10% of your grade [10%]
Note that at this stage, with more exposure to course material and the evaluation of a peer, and more time to evaluate data and results related to your hypothesis, you may find that it needs to be revised or changed altogether. Welcome to science!
The peer review will be returned to you within ONE week.
Draft 2 Proposal: Now you have had feedback from a peer, this one is graded by Dr. Wares [10%]
At this point it is still possible you will be returned to note 6.1, but with constructive suggestions.
Please see the updated guidelines above!
Draft 2 will be due March 29. Dr. Wares will return his evaluations by April 1 if at all possible.
Final Proposal: Putting all of your concepts and methodological understanding together towards your proposed project, and aiming for a budget of $5000 inclusive of travel, consumables, sequencing, etc. [20%]
please understand this is entirely hypothetical and Dr. Wares is not funding such research :)
The final proposal will be due April 28.
The last 10% of your grade is basically to help teach the topics of the course to others. These assignments can be turned in at any point of the semester for credit.
You might provide a 1-2 page report on edits or clarifying improvements to the "textbook" that include new exercises or resources for future classes; be gentle with the harried author! Provide rationale and/or resources to ensure it makes more sense to the next users of this text!
You might find YOUR way to communicate difficult information like estimators of Fst or other diversity metrics that you think will help others - be creative if you are an artist or designer!
You might document improvements or novel information added to a public resource like Wikipedia if you have those skills
Or find some other way to make the knowledge of this class more transparent to those who perhaps don't understand using molecular data to make biological inference. Again, be creative!
because every list this long should be a multiple of 10. No seriously, you will wonder what the rubric is for grading the above items. Each is graded on a scale from 0-4.
if you didn't turn it in, you get a zero. Everybody gets a "life happened" or two, where I won't worry about the deadline. But beyond that, it is a zero.
If I give you a 1 out of 4, that means you turned it in but perhaps missed all of the goals of the assignment. I'll let you know.
If I give you a 2 out of 4, it will come with enough feedback and opportunities to discuss that you will be able to improve on subsequent assignments.
If you get a 3 out of 4, I will be clear what you could have improved for a more robust report that includes references for the ideas or methods cited, conceptual understanding, or communication of your ideas.
If you get a 4 out of 4, rock on.
These numbers should be pretty transparently related to letter grades. A weighted average of your grades, following the percentages above, will correspond roughly as:
3.7-4.0, A
3.5-3.7, A-
3.3-3.5, B+
3.1-3.3, B
2.9-3.1, B-
2.7-2.9, C+
2.5-2.7, C
2.3-2.5, C-
If I adjust this grading scheme, it will be in favor of the students. I fully recognize the arbitrary nature of these thresholds.
For graduate students (6530)
For graduate students (6530)
In addition to the assignments above, you must identify and thoroughly (re-)analyze a data set in consultation with your instructor. You will focus on assumptions that could affect the outcome, eg. alignment/assembly, data inclusion/exclusion, and present on your findings in latter part of semester. Your presentation should include information about how the study could be done better, e.g. sampling design, data inclusion/exclusion, type of data or analysis.
Being Healthy
Being Healthy
We are still very much in a pandemic in early 2022; perhaps multiple, between SARS-Cov-2 and the influenza virus, not to mention other stressors. As such, I expect that you mask in our small classroom. There are a number of local and federal statutes that apply towards this being a requirement.
I will work to have many opportunities to go outside and discuss (where masks won't be as necessary), but not being attentive to others' health concerns is pretty inappropriate given that we know how to minimize risk. So, whenever the local COVID or Flu test positive rate is above 1%, (and in early January it is >30% in our county!) it is enough risk that we should be masked when possible in the classroom and in our buildings.
By the way, the very study of pathogens (or microbes, or whatever) in the environment is a component of molecular ecology! Methodologically and in intent, the goal is to be able to detect movement, abundance, and change. A great and relevant example is Dr. Erin Lipp's ongoing work to document the SARS-CoV-2 virus in the wastewater of Athens, GA!
(see below...)
If you feel you have caught something, given your symptoms, consider how your staying-home-and-catching-up-afterwards would be better for everybody – I will not grade your attendance or 'participation'. I'd rather you followed best advice for quick recovery at home. Your classmates and I will help you with any material you miss - and I will have an online feed every day (see Resources) so that you do not feel pressured otherwise.
Your Professor
Your Professor
Dr. John Wares is a Professor in the Department of Genetics and the Odum School of Ecology, and a Curator at the Georgia Museum of Natural History. If you need assistance, appointments are available - just email me at jpwares[at]uga.edu!
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