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Monthly Archives: November 2011
Yaniv back from Vienna.
Yaniv is back from trip to see Nick Barton and others in Vienna. You can read more about his trip here. I’m surprised they let him back into the country as he didn’t bring a present for the lab ;).
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Population genetics course resources: Modeling a serial bottleneck out of Africa.
The decreasing level heterozygosity as a function of distance from Africa in human populations is one of the pieces of evidence for the (mainly) out-of-Africa model, see here for a review. This observation is consistent with a serial population bottleneck … Continue reading
Posted in popgen teaching, Programming exercises, teaching
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journal tea: Nov. 22nd
For Tuesday let’s read Beaumont and Balding’s paper: Identifying adaptive genetic divergence among populations from genome scans
Population genetics course resources: Coding up the coalescent time distribution.
A homework exercise coding up a coalescent model in a constant population of size N. There’s a variety of ways this could be done, the code is setup to guide a person through one of those. The code is applied … Continue reading
Posted in popgen teaching, Programming exercises, teaching
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Population genetics course resources: Exercise coding a wright-fisher model of selection and drift
A homework exercise coding a wright-fisher model of selection and drift. There’s a variety of ways this could be done, the code is setup to guide a person through one of those. If you do use these scripts and figures, … Continue reading
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journal tea: 8th Nov.
For tuesday let’s read Deep Human Genealogies Reveal a Selective Advantage to Be on an Expanding Wave Front. Moreau et al.
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Population genetics course resources: Code to simulate individuals for F statistics analysis
This code simulates inbred individuals with a particular FIS or a first generation admixed individual. The code simulates four individuals used to create the simulated individuals used in the homework exercise on F statistics. The code needs the file combined.YRICEU.out, … Continue reading
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Population genetics course resources: F statistics
Some code to demonstrate FST, FIT, and FIS as a homework assignment in R using HapMap data from YRI Africans and CEU Europeans, and simulated individuals. The file combined.YRICEU.out contains ~10,000 SNPs (less a few, due to removing some monomorphic … Continue reading
Posted in popgen teaching, Programming exercises, teaching
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gcbias 