Molecular Ecology 2022

Day 12: Where do we go from here?

How many whales are there? How many were there?

What is the premise of this paper?

Discuss - take turns throughout - and answer these questions:

1. Why is it important to know how many whales there are now?
2. Does the method presented - based on what we learned quickly last week - tell you about how many whales there are now?
3. If not, what does it tell you and why is THAT important?

2 minutes in small groups.

What are the mathematics?

OK, so now we know why they did this study.

1. What data did they collect, and how did they measure diversity?
2. That measurement of diversity, what name do we give it? What is it estimating?
3. How on earth is that number converted into units of “whales”?

Different groups, 3 minutes.

What questions do you have about how its done?

Who, in particular, might have argued the most about the validity of this paper? Does it seem like an over-reach or do you believe the results? Why or why not?

That’s directed to all of us together.

​

Are there ways in which you can think of applying the same methodology to another biological/ecological question of interest?

Types of Ne estimation (genomic)

What kind was just used?

Inbreeding, or coalescent - typically useful for a time span in the past, over roughly 1/µ years - literally integrating across mutational time

Drawbacks?

Doesn’t tell you what Ne is *currently*, and requires decent estimate of µ

How do we estimate µ?

Mutation Accumulation studies, or biogeographic dating

​

Everybody likes whales, what organisms intrigue you?

So what do you want to know?

How far do the spores from a moss disperse? Are all the jumping spiders in Athens closely related, or has the Loop highway isolated them in anyway from Oconee county? Are the corals in the keys largely spreading by asexual or sexual reproduction? Is there population structure in salt marsh grasshoppers? Why do many marine invertebrates show a genomic transition among populations near Delaware? How much diversity do long-lived vertebrates like gopher tortoises harbor? Does gene flow interact with selection in the garter snakes that eat poisonous newts? Why do birds suddenly appear every time you are near? Are there ‘trailing edge’ diversity patterns in neotropical migratory birds, for that matter? Do ebony jewelwing damselflies show divergence across watersheds?

If you want to test a big idea, what organism is most useful?

What big ideas?

What trade-offs are involved in mixed-sex mating models? Are invasive species typically lower in genomic diversity in their introduced range than home range? Does passive rafting boost gene flow? If there is polymorphism in egg provisioning how does that affect population structure? Do common bird flyways predict subspecies? Can species arise through hybridization? A rose, by any other name, would disperse just as easily. How do we best protect large mammal populations from extirpation? Is climate change more likely to change the distribution of species or their genomic diversity? How do state and international borders influence species management efforts? Does mating type affect gene flow? Can seeds disperse in rivers? What is the rate of erosional capture of neighboring watersheds? How large can the disparity between Ne and Nc be in a stable population?

Small group sharing again - then conversation

Your assignment, should you choose to accept it…

1. 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%]
1. 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.
2. 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. 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.
3. 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.

​

For Thursday

We will finally start dealing with samples across space and time

1. Download latest version of textbook and start using new - lots of recent edits esp. Ch4
2. At begin of Ch4 see note on the poppr training website, install some additional R packages as it explains (and read, not long)
3. Read through section 4.2, note you have a new shiny simulator…you will have an exercise using it soon