Category Archives: teaching

Peter and I’s European genetic genealogy paper is out.

Posted on May 10, 2013 by cooplab

Peter Ralph and I’s article on the geography of recent genetic genealogy in Europe is out in PLOS Biology. We’ve written an FAQ on the paper, that we sent out with the press release. PLOS also has a synopsis of … Continue reading →

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Hardy-Weinberg and Ask Science

Posted on March 12, 2013 by cooplab

Jeremy (one of the students in the lab) acts as a moderator at the Ask Science reddit, helping answer questions on evolution, genetics, and genomics. I thought I’d post a link to a nice response of his to the question: … Continue reading →

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Population genetics notes

Posted on March 10, 2013 by cooplab

I’m releasing my notes on popgen here. I’m release the pdf (and shortly the latex, figures, and code) under a creative common license in order to encourage reuse by as many folks as possible. I’ll be updating them somewhat regularly, … Continue reading →

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Intro. to Evolution (EVE100) Reading

Posted on April 5, 2012 by cooplab

Thought I’d quickly post our reading list from my round of teaching EVE100 intro. to evolution: Week 1. Darwin and Wallace’s 1858 letters to the Linnean Society Week 2. Scaduto et al. Source identification in two criminal cases using phylogenetic … Continue reading →

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Population genetics course resources: Demostrating the uses of coalescent simulations

Posted on December 3, 2011 by cooplab

A problem set making use of the coalescent simulations the students wrote for a previous exercise (see here). They use the code to calculate p-values for the observed number of segregating sites, this could be done under the HKA test … Continue reading →

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Population genetics course resources: Modeling a serial bottleneck out of Africa.

Posted on November 19, 2011 by cooplab

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 →

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Population genetics course resources: Coding up the coalescent time distribution.

Posted on November 12, 2011 by cooplab

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 →

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Population genetics course resources: Exercise coding a wright-fisher model of selection and drift

Posted on November 9, 2011 by cooplab

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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Population genetics course resources: Code to simulate individuals for F statistics analysis

Posted on November 5, 2011 by cooplab

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

Posted on November 5, 2011 by cooplab

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 →

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