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Last Lecture

Download file "8420 week 13.pdf" Sometimes lectures are useful, sometimes you can get fired up about a topic, sometimes it sets off good discussion..... I'm not sure this one did that, but let us touch our toes into how behavioral ecology and genetic methods intersect....

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Week 9 sorry for the delay

Download file "Week9_8420.pdf"

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Phylogeography

Download file "Week7-8420 phylogeography.pdf"

So now we are covering phylogeography! Tuesday I gave my pitch for what it means in the 201x's, how we have moved away from believing the tree itself to be the primary signal and instead re-focusing on summary statistics (quantitative phylogeography), and so we revert effectively to population genetics....

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starting with Structure

Download file "Week6-8420.pdf" This was my Tuesday morning attempt to walk you through the logic of how we use basic genetic models (Hardy-Weinberg, for example) to explore how well observations fit that model, and how we can make our model more complex by adding populations. This is what underlies much of our decision-making as we make conclusions about population structure from genotypic data.

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Week 5

OK, the notes from Tuesday lecture:

Download file "week5gene8420.pdf"

The software that we played with to better understand the contributions to Gst, Rst, and Analysis of Molecular Variance was GenAlEx, a free download that plugs into your version of Microsoft Excel.

Regarding the quiz, you may find helpful the paper I sent out last week on population structure, and of course there is abundant starter information on effective population size available on Wikipedia.

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Week 4 - getting into F stats

I hope my "XIJ" approach to F-statistics is a helpful generalization. Attached is the lecture that I (mostly) got through on Tuesday, which goes along with the manuscript I sent out late last week (which I'm not allowed to share online!).
Download file "week4GENE8420.pdf"

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Week 3

As always, my estimates of the time it takes to cover topics varies wildly from the truth. We probably spent too much time on the vague experimental design side of population genetics this morning, and then that leaves some thought to give to Hill Numbers on Thursday. Attached the PDF of lecture slides for this week.

Download file "Week3GENE8420.pdf"

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Models

"All models are wrong, but some are useful." With this adage in mind, the first week was more lecture-y than I hope the rest of the semester will be. I am trying to NOT use powerpoint or similar, as the canned drone of a lecture is not a good goal in a small graduate class (if any): we should use the time to interact and gain from each other through experience (at least, that sounds good; easier said than done).

So, the wipe board "slides" from this week as we covered models of molecular evolution, ensuring that we all understand the INPUTS to analyses, inferences, etc. as well as we think about the outputs.

First, a reminder that we use molecular data as an expansion of our understanding of phenotype; the benefit as well is that we have ways of parameterizing the differences among alleles (and thus among individuals). The models we use help us infer patterns of individual movement and relatedness, and population diversity and demographics as well as the overall distribution of a class of organisms (species, lineage, population, etc.). Here we are just starting to get into basic derivation of the population mutation rate...


The next day we worked our way into the basic probability of "identity by descent", the probability that 2 sampled alleles are the same (if not, they are different, leading us to understanding of heterozygosity given the population mutation rate)...


...followed by expanding our understanding of more complex models. First, the infinite sites model (appropriate for DNA sequence data), and then a few minutes (it needs more attention, that is the students' job) on the stepwise mutation model for microsatellite data.




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Lots to Read

Well, the semester is starting. Today I'm prepping for day one. One thing that is always tricky when teaching a course with new material, is how much? There is a lot of reading I expect, so that we can discuss and interact more in our valuable class meeting times. I'm hoping I haven't assigned too much. First, we will read most of Joanna Freeland et al.'s Molecular Ecology, 2nd edition. Chapter one is kind of long but pretty much a light overview, and in fact already a fairly outdated one: the problem with using textbooks. But typically academic papers don't help bring new folks in as readily, and I just don't know that much about the crowd taking this class, so we will start with the basics and move forward! In fact, in some ways it is more important to me that students understand the basics really well: how mutations occur in different types of markers, and how often. Starting with the latest in sequencing technology is amazing to point and say, wow look at those thousands of variable loci, and everybody gets excited.... but if you don't know how to analyze those loci it doesn't matter. So, that is where we start, is understanding the variation we are hoping to use.

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