mtDNA Comparisons
Overview: In this activity, you will be comparing your mtDNA HVR1 sequences to the
mtDNA sequences of modern human groups and to various animals to determine levels of
relatedness.
1. Go to Dolan Learning Center’s Sequence Server Database
(http://www.bioservers.org/bioserver/index1.html). Click “enter”.
2. Add your mtDNA sequence by clicking on the “Create Sequence” button at the top
center of the page. Name your sequence and enter the sequence in the “sequence”
box. Then click “OK”.
3. Add other human sequences from the database by clicking on the “Manage Groups”
button. A new window will open – select “Modern Human mtDNA” under “Sequence
Sources,” then click on each group to select and hit “OK.” Some geographic origin
categories have more than one sequence. Choose just one sequence for each
geographic origin.
4. Use the check boxes on the left to select your sequence and one of the geographic
origin sequences. Click on the “Compare” tab to generate a pairwise alignment of the
two sequences. A new window will open showing the alignment.
5. Count the number of differences between the two sequences. A yellow box indicates
positions with a nucleotide difference. (Note that if the sequences are different
lengths, the ends will be yellow because there is no data from one of the sequences.
You can eliminate this by clicking on the “trimmed” button and hitting “Redraw”.)
6. Record the number of differences and total length of the alignment in the table
below. Calculate the percentage of differences by dividing the number of differences
by the alignment length. Repeat for all geographic origin sequences.
Sequence
Geographic Origin
# of Basepair
Differences
Alignment
Length
% Differences
(rounded)
African
African American
Native American
Asian
Australian/Pacific
Islander
European
7. To what people group are you most closely related? Does this match up with what
you know about your heritage?
8. Do the same procedure for different animals by clicking on the “Manage Groups”
button. A new window will open – select “non-Human mtDNA” under “Sequence
Sources,” then click on each group to select and hit “OK.” Some animal group
categories have more than one sequence. Choose at least one sequence for each
animal group.
Sequence
Geographic Origin
# of Basepair
Differences
Alignment
Length
% Differences
(rounded)
Worm
Crustaceae
Primate
Land Mammal
Birds
Fish
Sea Mammal
Echinodermata
9. To what animal group are humans most closely related? Least closely related?
10. Based on your data above, draw a phylogenetic tree for the animals you selected.
11. Change the setting under “Compare” to “Phylogenetic Tree” – it may take a minute
or two for the website to generate the alignment and the phylogenetic tree (be
patient). Once the tree appears in the window, compare it to your predicted tree
above. Do the trees roughly match? If not, can you hypothesize why?