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 documentation for the program is on the website - please read section 5.3. The program is executed from the command line and reads two files: mainparams and extraparams. You mainly need to edit the mainparams file – but take a look at the extraparams file as well. The analysis needs to be run several times with different values of k (use 1 – 5 typically). Ideally, for each value of k you would run the analysis multiple times.

1. Run structure with various values of k (maxpops on the file “testdata”. This file is for a sample of 5 microsatellites from 200 individuals (diploid).

a. What looks like a reasonable burn-in period for this dataset?

b. Which value of K provides the best fit to the data?

c. How many populations do you conclude are in the sample?

d. Run the analysis again but for 4X as many generations. Is there any difference in your conclusions? Do this for only one or two values of K


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?

b. Which value of K provides the best fit to the data?

c. How many populations do you conclude are in the sample?