For this exercise, you will use the program Arlequin 3.0
(available at
http://anthro.unige.ch/arlequin/). The two data files are available at the
course page on myASU.
- Examine the genetic structure of the populations in the
file (NAmMtDNA.arp) where the populations are
grouped (into 3 groups) based on geography. This file mtDNA HVI sequence data
from 15 populations in North American. Choose the “open project” button to
select this file. Next choose the ‘settings” tab, and then on the page, click
on AMOVA. Put a check in the box for AMOVA computations. Since these are HVI
sequences, set the distance measure to “Tamura-Nei” and the gamma a value to
0.2. (the default is “pairwise distance”). To run the analysis, click on the
“start” button in the upper right corner. What is the percentage of variation
that is within populations? Is this similar to that found by Lewontin (1972)
in the article that you read for the second week of class? Is the percentage
of variation among groups larger than the percentage of variation among
populations within groups (and what values for each of these did you get?)?
- Next, under settings, choose “molecular diversity
indices” and click on the “molecular diversities indices” box on that page.
Start the analysis. Which population has the highest nucleotide diversity and
which has the lowest (what are these values?)? Within each group defined in
the previous question, do there appear to be any outliers (i.e. a population
that has a nucleotide diversity that is clearly above or below the others in
that group)? (the results for this analysis will be at the end of the Arlequin
results file).
- Examine the genetic structure of the populations in the
file (NAmMtDNA2.arp) where the populations are
grouped (into 3 groups) based on language. What are the percentages of
variation among groups, among populations within groups, and within
populations? Compare these values to those in question 1. Does language or
geography seem to be a better way to group these populations? (explain your
choice).