General Plan


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    Week One: Markers and Models

    January 12, 14
    1. HELLO Basic class greetings/mechanics
    2. READ chapters 1,2 of Molecular Ecology (Freeland) on markers and models and diversity
    3. WRITE one-page comparison of models of molecular evolution: IAM, ISM, SMM, other key variants (with refs) due next Tuesday
    4. NO discussion this week but most weeks there will be
    5. Lecture: the goal of molecular ecology; and basics on models of molecular evolution

    Week Two: Molecular Diversity and Populations

    January 19, 21

    1. READ chapter 3 Freeland
    2. DO activities from Freeland chapter 2, due next Tuesday (should not take long, n.b. you do not have to use the same software, I highly recommend using Genious, which has a UGA site license)
    3. DISCUSS your one-page paper findings; as you discuss, annotate your printed copy (turn in end of Tuesday)
    4. GROUP-WRITING: your group should put together a synthesis of your individual model descriptions
    4. INSTALL ms/sumstats on your computer (probably also FigTree or similar), get to point where you can run coalescent simulations, view summary statistics, and view the resultant genealogies. at that point, spend 15 minutes designing an experiment to understand how population diversity, sampling, or structure influence the output of such a study, write a one-page report due next Tuesday (not assigned now)
    5. SIGN up on the Course WikiEdu site - this is or will be your Wikipedia login if you already have one. Read up on how editing is done (it is a short, colorful brochure on the site) and familiarize yourself with the site. Should only take about 10 minutes.
    6. DISCUSS (unless I think of something better) Download file "Turner_ea_02.pdf" (yes, I'm a co-author, no, that's not why I want you to read this...) THANK YOU KAREN

    note: 2 things due next week!

    Week Three: Diversity Measurements and Generality

    January 26, 28

    1. READ from Magurran and McGill, chapter 15 (genetic methods) is short and complements what we have read. Part 1 (36 pages) of Magurran and McGill opens this topic up further.
    2. DISCUSS the other team's initial write-up on their model, annotate with what may be missing and what is confusing, what could be clarified, give back to group (10-15 minutes end of Tuesday)
    3. GROUP-WRITING: work together to clarify your understanding and presentation of your model of molecular evolution
    4. START analyses in R: R: http://grunwaldlab.github.io/Population_Genetics_in_R/index.html work through chapters 1 and 2
    5. DISCUSS Mark Vellend's paper: (led by Amanda Shaver)

    Download file "Vellend2010.pdf"
    and focus on the predictions of his work given the connectivity of an ecosystem/habitat.

    Week Four: Population Differentiation

    February 2, 4

    1. READ Freeland chapter 4
    2. Lecture: basics on population differentiation metrics
    3. DISCUSS your improvements on model papers and deficiencies in entry on IAM
    4. DO analyses in R: http://grunwaldlab.github.io/Population_Genetics_in_R/index.html work through chapters 3 and 4
    5. DISCUSS http://www.molecularecologist.com/2011/03/should-i-use-fst-gst-or-d-2/ and the readings therein. This will involve each of us reading at least 1-2 of these papers as well as the blog post and coming together for an informed group discussion, e.g. some of us will have gained different sets of expertise.

    Week Five: The Blurry Lines of Molecular Ecology

    February 9, 11

    1. READ Freeland chapter 4 continues, Magurran & McGill chaps 4-6
    2. LECTURE/PRESENT more on data and pairwise differentiation statistics for samples, underlying assumptions
    3. DISCUSS paper by Hairston et al Download file "Hairston.pdf" in terms of whether a system is "evolving" or changing ecologically, and the blurry lines between alleles, multilocus genotypes, lineages, and species
    NEW 3. I think we need to hold off on Hairston for right now and keep thinking about how our organisms move, how the environment influences the fitness of organisms, and our ability to separate the ecological and evolutionary dynamics from observed allele/genotype data. So I would like us instead to read/discuss the attached paper by Meirmans:

    Download file "MEIRMANS-2012-Molecular_Ecology.pdf"

    4. CATCH UP on exercises and activities assigned: Online activities from Freeland Ch. 4 and Review Questions and finishing POPPR chapters 3 and 4.
    5. POST initial model entries to Wikipedia (sandbox or "live"?)

    Week Six: Structure

    February 16-18

    1. We are finishing up dealing with individual-based structure assessments in lecture and in reading.
    2. to DISCUSS on Thursday (Sara Heisel): Pritchard et al. 2000

    Download file "Pritchard 2000.pdf"

    3. Exercises: should be completed through Freeland Chapter 4, POPPR through Chapter 4
    4. continue work on Wikipedia entry as groups

    Week Seven: Phylogeography

    February 23, 25

    1. READ Freeland Chapter 6 on phylogeography
    2. DISCUSS SOUSA AND HEY PAPER (led by Kelly Petersen) http://www.nature.com/nrg/journal/v14/n6/full/nrg3446.html on markers and inference and LD, and how SNPs become genealogical... think back to our discussion of Hairston.
    3. POST final entries to Wikipedia!
    4. EXERCISES you should continue with POPPR chapters 5-7; Online Activities and Review Questions for Chapter 6 in Freeland et al.

    Week Eight: Phylogeography

    March 1, 3

    1. Finish the wikipedia submission this week; write 1-page description of the process of how you focused on key points, how you see these models playing into your understanding of the stats and approaches we have discussed so far.
    2. Turn in POPPR chapters 5-7, Freeland Chapter 6.
    3. I will catch up with homework turned in and let you know if I think you've missed anything
    4. LECTURE on comparative phylogeography and identifying common times for divergence
    5. READ/DISCUSS Download file "nature13687.pdf" "Drivers of Tropical Speciation" Thursday (Ben Gochnour)
    6. NEXT WEEK IS SPRING BREAK, but by week after please come to class with example from lit (or calculated from data) of Tajima's D statistic with info on locus and on species and what paper suggests about result....


    Download file "donkey in hammock.mp4"

    Week Nine: Selection Changes Everything

    March 15, 17

    1. What did you find re: Tajima's D?
    2. LECTURE: selection changes the speed at which diversity is lost (by drift), how do we detect?
    3. Turn in POPPR chapters 5-7, Freeland Chapter 6.
    4. Start work on POPPR chapter 9, should be analytically new but methodologically review
    5. READ M&M chapter 12 for more background on Mantel Testing and phylogeography
    6. READ DISCUSS : Thursday: For discussion (led by Marisa), we study how adaptation and gene flow set species range distributions...

    Download file "Eckhart Geber Morris Fabio Tiffin and Moeller 2011 .pdf"

    7. We will also discuss the timeline for your proposals that are due at end of semester.
    a. outline of proposal idea is DUE March 29
    b. April 12 or 14 we will use class time for peer review of proposal: clarity, concepts, appropriate methods and budgeting?
    c. proposal is due to JW on 5/5/16, no later!!!!

    Week Ten: Adaptation Continued

    March 22, 24

    n.b. unforeseen conflict, NO CLASS ON TUESDAY MARCH 22.
    M&M chapter 14 on phylogenetic diversity
    POPPR chapter 10
    For discussion, we follow up the Eckhart paper with the related pop gen paper: IT ALL COMES TOGETHER!
    (discussion led by Clesson)
    Download file "661783.pdf"

    Week Eleven: What are we doing now?

    March 29, 31

    1. Turn in proposal draft - your brouillon
    2. Lecture: wrapping up details on the coalescent, barcoding as a mechanism of thinking about species diversity
    3. exercises: POPPR chapters 11, 12
    4. reading: M&M chapters 15, 16 on DNA barcoding and microbial ecology
    5. for discussion on Thursday (Carly):

    Download file "Syst Biol-2006-Hickerson-729-39.pdf"

    Week Twelve:

    April 5,7
    For this week, you are encouraged to read chapter 13 MM trait and functional diversity, chapter 5 FreeLand on QTLs and ecological diversity. However, both are fairly nuts-and-bolts chapters that will probably be of greater use once you are trying to use metrics associated with trait diversity or identification of QTLs. No new exercises associated with this week - we are all inundated.

    What we will talk about Tuesday April 5: Our focus continues to be on the assumption of molecular ecology, that diversity at all scales has a functional/ecological correlate. As a fun break from me talking, we've got a film on "community genetics" - so bring coffee...

    For Thursday, April 7: read/scan this report from NSF:
    Download file "nsf15030.pdf"
    Find a project that resonates with you, read a paper related to that work (presumably by that research group) and come to class ready to discuss your view of how genetic, taxonomic, and functional diversity mesh for your group - and how that may differ from taxon/lineage/clade to another.

    Week Thirteen:

    April 12,14

    1. Peer review of proposals on Thursday 4/14
    2. Lecture on Tuesday 4/12 - kinship analysis, paternity, source-sink diversity identification, behavior
    Freeland 7 on behavior stands on its own
    kinship analyses, paternity

    Week Fourteen:

    April 19,21

    Lots of reading, no homework exercises - focus on your grant proposal.

    (Freeland Chapter 8): Note that we have already discussed barcoding and species concepts somewhat; you are all well aware of the biodiversity crisis unfolding. We have discussed introgression somewhat. There is some discussion of heterozygosity-fitness correlations (HFCs) that you may find useful, but remember that current literature treats this association cautiously!

    Magurran/McGill chapter 17 is a refresher on biodiversity statistics and how they may be used following disturbance.

    As such, this week we have three papers to discuss (continuing the "cautionary tales" thread in 8420...).

    For Tuesday: We will focus on conservation genetics, how do we manage for diversity and what factors are important from the genetics side of things? For this conversation we will first discuss a classic in conservation genetics by Phil Hedrick on the Florida Panther (Puma):

    Download file "11C - CONGEN - READING - Florida panther gene flow model.pdf"

    and then discuss this short paper by Pfrender et al where the focus is on how genetic marker diversity may/may not be a good predictor of how well a population can respond to selection. A question I ask myself often is given climate change (as opposed to specific habitat reduction for a species), which species will be able to adapt and survive?

    Download file ""

    That seems like a lot, but the Pfrender discussion will bleed into our discussion of this much more recent paper for Thursday: http://onlinelibrary.wiley.com/doi/10.1111/mec.13334/abstract?campaign=woletoc on similar topic.
    Download file "vilas.pdf"

    Week Fifteen:

    April 26; no meeting on April 28

    One last paper discussion. I feel like we are at the point in the semester where we get more done with either writing, experience, or discussion than lecture (for sure), and to wrap up the semester I've chosen this review/sythesis paper so we can ponder what is to come for our own research and the field overall!

    Download file "Andrew.etal.2013.pdf"

    Remember your proposal is due 5/5/16, after that day 10% reduction/day