January 11 - 1st day of class, we meet in Ecology 12 on Zoom (see Resources) at 1420-1535 EST. Our first meeting is online because (a) COVID positive rates are sky-high (see the Home page); (b) I will have had a knee procedure earlier that day; (c) many of you will likely have been up late watching Georgia in the title game!
If at all possible, before class you should have installed R, RStudio, and Geneious on your personally-available computer (see Resources). This may involve asking IT or other expert users for help. Our meeting will be short and organizational, your job today is...
A one-hour movie for us to all start thinking?! This is a nice film about thinking how climate has been/is selecting on genomic diversity at the same time demographic responses are changing where that diversity can be found. The point is to start thinking about how molecular data may be our quickest way of understanding the distribution of diverse traits in biodiversity. I'm hoping this puts us all on the same page for this semester.
One way or the other you will have access to the 'textbook' document (Resources) that will guide us the rest of the semester - I will post a static version of chapters 0/1 here - and we will discuss the assigned readings (1) Travis 2020, (2) Marmeisse et al 2013, on Thursday!
Please pay attention to announcements/emails about class mode!
January 13 [ z o o m ] - given the film day on Day 1, we introduce ourselves to talk about goals now with a bit of shared insight from the film, continue working on installation issues, but we discuss the assigned papers to get our heads into the game, this is covering Chapter 1.
Software Installation Query please fill this out A.S.A.P.!
In-class exercises: we will work in groups to discuss life history traits, referring to the cottonwoods and other organisms noted in Genes to Ecosystems; take notes as you talk with your group as this is part of your weekend homework. This is where your insights from the Travis 2020 and Marmeisse et al 2013 papers should come into play in thinking about how life history traits bridge questions in ecology and evolution, and the extent to which we need to quickly gain insight into these traits for generating smarter hypotheses.
Over the weekend you will read Chapter 2 and you have two (2) assignments.
Your first Monte Carlo writing is due on Tuesday. Use your reflections from discussions today (and those resources) as a baseline, and identify an element from the "Genes to Ecosystems" film that is of particular interest to you - seed dispersal? Fecundity? Drought tolerance? Spatial distribution? - and find and read ONE MORE article from a peer-reviewed journal that expands on your understanding or follows the material in that film. Follow the directions for the Monte Carlo assignments (Home), ensuring that you provide citations for what resources you use.
Your first Analytical exercise is due next Thursday. This is a modified/simplified version of the exercise in the green box under Figure 2.5b (yes, the numbering of many things in the 'text' is wonky; writing a book has all sorts of challenges!) where I want you to have Geneious running on your computer, take 10-15 minutes to do the Tutorial (see the ? Help button in upper right), and download some "barcode-appropriate" DNA sequence data for organisms you are interested in. No, you don't have enough information to do this today, there will be more discussion and tutorial on Tuesday but I want you to do this legwork first!
I would also like somebody - perhaps one of my 6530 students! - to step up and do their Lightning Talk next week so we get those rolling. Remember, everybody needs to do one!
January 18 [ v i d e o ]
Note this class will be on Zoom as announced on eLC; Dr. Wares family has a positive COVID test.
Today we will use to get some familiarity with the software Geneious and specifically some elements of using it for the homework assignment (which is now due one week, January 25).
SLIDES FOR TODAY'S INTERACTION ARE HERE
For Thursday, read this paper by Karen Bell et al. on metabarcoding the pollen picked up by bees in their daily foraging.
Don't forget to turn in your first Monte Carlo paper using the eLC dropbox by midnight tonight!
January 20 [ v i d e o ]
Today we will finish our "Tour de Geneious" and take some time to discuss the assigned Bell et al paper.
On the resources page I have posted some R code (open the .R file in RStudio) that will help with the 'barcode gap' exercise that is due on January 25. Some additional steps are listed there as well. This weekend, I'm not giving any other assignment!*
*other than, you should now have R/RStudio working on your computer, and you should have downloaded the interactive textbook directory (whole directory) to your computer. You should be able to open May5_MolEcol.Rmd in RStudio, and click "Run Document" and in a few minutes have the text ready on your screen! If you cannot do this by Sunday, email Dr. Wares so we can figure out the problem.
January 25 [ v i d e o ]
Today we will work on fixing remaining issues with the software we will be using in this class, and have a short introduction to marker types -- and how they all come from the same basic genomic information.
Special Note: ECOL seminar today (online at 4pm) by Dr. Randall Hughes, one of my favorite colleagues - contact me if you want access!
January 27 [ v i d e o ]
argh I got flustered by computer issues on Tuesday - I think we are homing in on the solutions!
For today, you will finish your barcode exercise and turn it in by tonight. Who will do a Lightning Talk next week??
I also asked you to read Chapter 3, but we are not quite done with Chapter 2 issues yet. For the weekend, there are two papers to read for discussion on Tuesday.
Hebert paper - finding probable species that are most easily detected using DNA barcode data. This paper is a good example of finding high levels genomic divergence of individuals within what is thought to be a species, and learning more about how that pattern emerged. This is analogous to the work shown in Chapter 2 , Example 3 - where new species aren't declared, but the pattern of deep divergence guides us to environmental shifts.
Smith et al 2016 - an example of looking at the very beginnings of temporal/environmental isolation. As we finish talking about the diversity of marker types and how they are interpreted (Chapter 2, Box B), I wanted an example that helped us see that the right choice or technique in finding molecular diversity can open up all sorts of questions about isolation and environmental divergence. This one came to me thanks to your classmate who mentioned epigenetic modifications as affecting restriction enzyme cut sites - good point!
Finally, we will use our class time today to finish setting up our R/RStudio capacity and working with textbook so we have a straight path towards doing some of the other exercises and analyses. This weekend you will also read Chapter 3 up through the first exercise.
The Github page for the text has been updated; if everything works for you, don't worry about it. Otherwise, it now has:
Jan22_MolEcol.Rmd - complete (though still flawed!) textbook
Jan22_MolEcolstatic.Rmd - has no Shiny apps embedded, thus can easily create a cleaner 'static' version of the textbook, Jan22_MolEcolstatic.html (but it only is readable if you download it - otherwise this website thinks it is html code!)
Jan22_ShinyEx1.Rmd - in case the image files end up being a problem, this is the Shiny app isolated
So, one way or the other, this weekend read Chapter 3 and do the first exercise so that we can all feel more comfortable thinking about the effects of genetic drift on population diversity. With email and peer assistance, I know we can do it :)
February 1 (happy lunar new year!)
SLIDES for today [ v i d e o ]
Discussing marker diversity and the techniques/pros/cons of different kinds.
Assessing genetic drift and how it works to remove diversity from populations over time.
Discussing two papers we read over weekend about genomic diversity, species and speciation
Planning: first draft of your research proposal due late this month! WHO will give the next lightning talk?
Read rest of Chapter 3 and do exercises, we will work together to understand the coalescent effect more on Thursday! Also read Rosenberg & Nordbord 2002 as an introduction to coalescent theory and thinking.
February 3 (slides for today, same link as Feb 1) [ v i d e o ]
Lightning Talk (Anna Marie, doi: 10.1111/MEC.16377)
Discussion of our weekend reading
What is the problem with drift simulations?
Over the weekend, you will finish reading Chapter 3. You also will read this overview paper by Luikart et al (2010). You will start to see a convergence of our study of drift, coalescent theory, and our need to understand population size. A warning that the Luikart paper is a functional review; it is a bit dry and covers material pretty thoroughly for biologists who need to estimate the size of a population. You aren't being tested, you're being exposed :)
You will write your second Monte Carlo paper to be turned in on Tuesday. Again, find another paper or resource that is relevant for your musings and observations about how effective population size works and what it means for understanding the genomic diversity of a sample as well as the biology of the organisms involved.
February 8 (slides for today) [ v i d e o ]
Today our goal is to de-obfuscate how genetic drift and coalescent theory are used to establish a "null hypothesis" for evolution so that we can start to understand better how clearly deviations from this null expectation lead us to finding new evolved lineages, patterns of selection and migration, and interpretation of behavioral effects on the diversity we find in the DNA of wild populations.
I know that this material is tough - prior to 2020 this was a grad-only class - and I appreciate y'all being willing to speak up so I can see how to present it most effectively!
Over the weekend you had readings on population size, coalescent theory, and a Monte Carlo assignment to provide your first 'take' or understanding of these concepts. Revisit these readings as appropriate this week to improve your clarity, no homework for Thursday.
February 10 (slides for today) [ v i d e o ]
Lightning Talk (Skye)
Today we will delve into effective population size and THETA and all that it can tell us (and why it is so difficult to really grasp).
Over the weekend, prep for our discussion on topics to consider for your grant proposal writing this semester, and read this paper by Roman & Palumbi on estimating early whale population sizes.
February 15 (slides for today) [ v i d e o ]
Today we will start with a workshop/discussion on topics to consider for your grant proposal writing this semester.
We will also discuss the effective population size of whales!
This week we will start moving ahead with more complexity in analysis, so go ahead and follow instructions at beginning of Chapter 4 to add some packages to your R environment. In fact, now is also an important time to download the latest version of the textbook as I have updated Chapter 4 considerably.
February 17 (slides) [ v i d e o ]
Lightning Talk: Ben Frick
Discussion of Beta-diversity moving forwards!
Over weekend read Wares (2016) and do F-statistics exercise:
Work on proposal draft for next Thursday!
February 22 World Bivalve Day :)
Dr. Lotterhos Fst exercise n.b. for future years - 30-35 minutes is good, could do 45
Remember your first proposal draft is due by midnight on Thursday, after they are in I will assign peer review partners.
You have a lot of other work to do by next Tuesday, March 1:
Start POPPR exercises in Part II (1-5) - this will guide your next MC paper, I want to know what you do and do NOT understand
Chapter 5, read that AND Cancellare et al 2021 we will discuss on Tuesday 3/1
sorry if it seems I am shouting, I was just copying from the slides... anyway, start working in that R training series and I will formalize the assignment later this week. You should also read Chapter 5 in the text, and this paper by Cancellare et al 2021 to think about as we start talking about organism movement models.
Summary of WHAT YOU NEED TO TURN IN, and WHEN, as AGREED UPON BY THE DEMOCRATIC CAUCUS OF ROOM 12, ODUM SCHOOL OF ECOLOGY:
Tonight (2/22/22!) turn in your F-stats simulation/power exercise to eLC
Thursday (2/24) your grant proposal DRAFT ONE is due and you should start on the POPPR exercise up above, the report for which - not yet specified - is due a week later on 3/3
Tuesday (3/1) you should have read Chapter 5 and the paper by Cancellare for discussion; by today you will have your peer assignment for reviewing somebody else's grant proposal
Thursday (3/3) your peer evaluation of the proposal assigned to you.
After spring break (3/15) your Monte Carlo response paper to the POPPR exercises is due today, as well as
If this works out the way we think it will, we will arrive at Spring Break with some good feedback on our proposal, and some good groundwork on population movement and how genomic data help quantify movement vs. isolation.
February 24 - your DRAFT ONE of your proposal is due today
SLIDES [ v i d e o ] yes, today was a little hand-wavy what with being outside and all.....
Today you turn in your draft proposal (2/24).
This weekend, you will read Imogene Cancellare’s paper and my Chapter 5 of the textbook. You will also begin the POPPR exercise listed on our class calendar.
Tuesday, we discuss the Cancellare paper and spatial models of movement. I will assign a peer proposal evaluation that is due BEFORE SPRING BREAK. There will be other reading for Thursday.
Tuesday after spring break, MC3: assignment detailed in lecture notes, requires you use R.
March 1
today we will start talking about movement of individuals among populations in a more formal way (Chapter 5), and take time to discuss Dr. Cancellare's work on bobcats that was assigned.
For Thursday, you should finish your peer evaluation of a proposal, and begin the R analytical work for your next Monte Carlo paper - this will have you actually analyzing molecular data to understand diversity, richness, and divergence more effectively.
March 3 - your PEER REVIEW of another's proposal is due today
(slides)
Spring Break March 7-11
Okay welcome back - to a slightly different class :)
A frighteningly complex war in Ukraine, and state-level political assaults on Black history, LGBTQ, and voting access in this state are just the environment in which I learned of something that will likely prevent me from teaching this class again because I will be needed for a different class. However, I think we pushed hard enough in the first half of the semester that you are going to feel more confident and competent in exploring this field more through the literature now.
March 15 (slides) [ v i d e o ]
Lightning Talk: CJ Hannan!
We will go over some more basic R skills today to help you finish up the next MC exercise using the POPPR tutorial. This assignment will still be due, but not today rather on March 22 so you can complete it and absorb what these analyses are providing in terms of basic diversity statistics relevant to molecular as well as organismal diversity.
nb TWO WEEKS to turn in second draft of proposal, following new guidelines
I will spend a little bit more time talking about how now that we understand diversity, population size, and movement - and all that portends for spatial patterns of genomic diversity - that selection or adaptation can only be inferred by how it generates patterns that deviate from that underlying selectively neutral diversity across a landscape.
For Thursday, read Chapter 6 and you should complete the next analytical exercise in section 6.2.1 as written in the green box. As before, you are being asked to set up a small simulation experiment that helps you understand better how population size and movement rate (m) interact over time to lead to low levels of divergence (Fst < 0.1 consistently). We will build on this exercise for next week. You won't turn this in until we do the second component.
March 17 ( v i d e o )
Lightning talk:
I will walk us through the originally-planned exercise using available data in BalanusPopGen.Rmd so we start to see these analyses playing out with typical SNP data.
Over the weekend, you have two tasks:
reading and planning for class discussion of Nunez et al 2020.
Using the same R simulation as before, I now ask that you do the same simulations but add in very slight levels of natural selection (fitness AA 1.0, Aa 0.99, aa 0.98) - what happens to the outcome of your previous simulation? If you do 100 simulations with no selection, how often does this tweak lead to a more extreme shift than in any of the neutral simulations? For this homework #4 you will provide a ~1 page report on how you see modest selection affecting the results from the previous simulation work.
March 22 (SLIDES) [ v i d e o ]
Lightning talk: Maddy Lawson
Turn in Exercise 5, assigned on Thursday, as well as the Monte Carlo #3!
We will discuss the paper by Nunez et al 2020 thoroughly as a case study of very local adaptation
for next Tuesday, please read this paper by Zerebecki et al on phenotypic divergence of Spartina for discussion.
n.b. you have ONE week until DRAFT TWO is due!
March 24 NO CLASS - RESEARCH COLLEAGUE IN TOWN TO LEARN NEW LAB SKILLZ
You are ALSO requested to read this kick-ass paper that just came out. This is one of many reasons knowing these patterns of biodiversity can be so mission critical!
March 29 - your DRAFT TWO of your proposal is due today
Lightning talk:
Lecture/interaction on the cool mosquito paper I assigned last week...
Quantitative traits, fitness, and molecular diversity -- it is at this point that the unfinished textbook starts to show its gaps pretty badly! But, in class I will go over the Shiny app in Chapter 8 so we can think more clearly about the genes that contribute to traits and marker density in a genome.
Discussion of Spartina phenotypic diversity and genotypic diversity (Zerebecki et al)., part 1.
Questions assigned to you during class, for Thursday!
March 31 (slides) [ v i d e o ]
we will finish discussion of the Spartina paper
For Tuesday April 12, we will read and discuss this paper by Mikko Koskinen et al on a simultaneous evaluation of molecular divergence and quantitative trait divergence. This is going to get us into thinking about yet another weird version of XST!
No class April 4-8, use this time to advance your class proposal following Dr. Wares' review!
April 12 (slides) [ v i d e o ]
Lightning talk: Ally Whiteis
Discussion of molecular data in questions of 'adaptability' - learning Q_st statistic
Discuss the Koskinen et al paper
For Thursday let's read Vilas et al on how molecular markers predict quantitative variation
April 14
Lightning talk: Stephen Eastin
Discuss Vilas paper, thinking about trait/diversity linkages
For Tuesday read Teixeira and Huber on drawbacks to molecular diversity for conservation questions
Over the weekend, you should also listen to this podcast: https://www.kuow.org/stories/in-the-footsteps-of-wolverines
April 19 (slides) [ v i d e o ]
lightning talk: Natalie Dietz
we will discuss the Vilas paper and Teixera and Huber, and then start talking about studies in conservation and management for the rest of the week:
Thursday is International Wolverines Day, I think. Your readings and assignment will be explained, and the links to the PDFs are in the slides from today.
Note that there is a FINAL MONTE CARLO PAPER ASSOCIATED WITH INTERNATIONAL WOLVERINES DAY
April 21 - WOLVERINES DAY!
Lightning Talk: Stephen Eastin
Discussion in the courtyard
Monte Carlo paper no. 4: International Wolverines Day reflection
Same length as previous MC papers. I'd like you to reflect on your knowledge from the class overall, from your readings, and from our discussion. The question to consider: we know that more sampling and more genomic markers leads to more detailed insights relevant to fine-scale movement and the potential for adaptive responses. Would you advocate for more detailed sampling (of the genome, or of animals) for wolverines to understand how best to manage and recover their populations? What is "enough data" for management purposes -- is there a level that is too little to be helpful, or too much to be cost effective given many conservation concerns?
Remember to include references to support your arguments.
April 26 - we will use today to give "lightning talks" - either talk, visual presentation, interpretive dance, or sing us a song - on what you proposed and what you found difficult about trying to identify a "fundable" question!
MC4 is due today!
Tentative order of presentations:
Bartlett, Sierra
Saeed, Marya
Shirazi, Sherwin
Smith, Kimani
Smith, Reagan
Solis, Zianya
Tarranum, Anika
Verma, Shikhar
Zempel, Bella
Ahmed, Shamir
Goberdhan, Govinda
obviously talks are likely to carry over into Thursday!
April 28 - your FINAL PROPOSAL is due today, and we will use today to give "lightning talks" - either talk, visual presentation, interpretive dance, or sing us a song - on what you proposed and what you found difficult about trying to identify a "fundable" question!
May 3 last day of class - we will end with another film to wrap up the creative process, thinking now how molecular tools can be useful in studying aquatic biodiversity, movement, isolation, and speciation :)