GENOME 561, Spring 2010
Molecular Population Genetics and Evolution

Structure lab

1.Download structure2.3.3.mac.tar to desktop from http://pritch.bsd.uchicago.edu/structure.html.

The documentation for the program is on the website (under structure data) - please read section 4.3

GENOME 561, Spring 2010
Molecular Population Genetics and Evolution

Structure lab

The purpose of this lab is to become familiar with the structure program for inferring population subdivision, in particular for determining the number of populations (k). The analysis needs to be run several times with different values of k (use 1 - 6 typically). Ideally, for each value of k you would run the analysis multiple times using different number of generations. 



1. Run structure with various values of k (maxpops) on the testdata. This file is for a sample of 5 microsatellites from 200 individuals (diploid). Use "dataplot" to see likelihood versus generation. a. What looks like a reasonable burn-in period for this dataset (can be different for each k)?
b. Which value of K provides the best fit to the data?
c. How many populations do you conclude are in the sample?
 Use "Bar Plot" to visualize the data..


2. Run structure with various values of k (maxpops) on the file "testdatab". This dataset is for a sample of 3 microsatellites from 100 individuals (diploid).
a. What looks like a reasonable burn-in period for this dataset (can be different for each k)?
b. Which value of K provides the best fit to the data?
c. How many populations do you conclude are in the sample? Use "Bar Plot" to visualize the data. Run the analysis again but for 4X as many generations. Is there any difference in your conclusions?



3. Download the americas.zip file from the structure data folder. This was an analysis (k 1 -6) of the samples from the roseneberg data for just the samples from america. From the output provided, determine the number of populations and compare the results in the Science paper. If you want to do other populations, the entire human dataset is provided.