Download Using 16S rRNA to Construct Evolutionary Relationships Figure 1

Using 16S rRNA to Construct Evolutionary Relationships
Figure 1 & Sketch of Cladogram – ___________
Final Poster & Analysis – ____________
Purpose: Students will
1) Choose four species, one bacterial, to compare DNA sequences with humans
2) Find the DNA that codes for the small subunit in ribosomes (rRNA) for up to six
species, including Homo sapiens (5 is needed for an A, 4 for a B)
3) Align the gene for small subunit rRNA from one species with the other species.
4) Create a cladogram using the alignment data from all the species.
Websites to Use
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=gene: This website
allows you to search through copious amounts of genetic information. First of all, make
sure you select Gene in the search box. Then you can type in a name, abbreviation or
description of the gene you are interested in. You will be searching for the same gene
in all species. This gene codes for rRNA that will be used in the small subunit of
ribosomes within the organism. You should type the following in the search box
“rRNA[title] AND 16S”. The 16S refers to the size of the rRNA molecule. The AND is
a Boolean descriptor that tells the computer to search for both things; rRNA and 16S.
You can add descriptors to help you find genes for specific organismal groups. For
example, rRNA[title] AND 16S AND Amphibia will give a list of amphibian links.
When you complete a search and click on a choice you should scroll down until you
reach a portion of your screen that looks like this:
Click on FASTA to get the DNA sequence of this RNA gene. This is the sequence you
will use for your project.
It is these displayed sequences that you can copy and paste into the SDSC website for
alignment and other types of analyses. Whenever you copy a sequence take note of what
species it comes from. You will need this information later. Information about the
species and its lineage can be found in the summary section at the top of your search.
http://workbench.sdsc.edu/: This website allows you to create a free account to use the
San Diego supercomputer. This computer can align the DNA of different species with
each other to determine the % homology (the percentage of bases that are the same)
between the same gene from different species.
1) Before you can perform alignments you have to import your nucleotide sequences
by selecting nucleic tools. The sequences you get will come from the first
website, described earlier in this document.
2) Click the Add button on the nucleic tools page
3) You can copy the DNA sequence from the first site and paste it into the large
white text box on the workbench. Make sure you include a label in the small text
field above the large field. Be sure to type in the species name in the small text
field so you know where the sequence is from
4) After pasting your sequence, click SAVE. Repeat these steps for each sequence.
Once you have imported all of the sequences you want to work with:
1) select two sequences (unfortunately that is the max) and then select ALIGN –
optimal global sequence alignment.
2) Click run and another page will come up displaying parameters - keep the
parameters as they are set and click Submit.
3) Now you will get a page displaying where your two sequences line up. You will
also see a % homology figure that shows how similar the two sequences are to
each other (the percentage of bases that match). You can scan through each page
looking for alignment to get an idea of what matches and what does not.
4) Record your results in Figure 1.
Paper/Project requirements
1) Align the DNA of the rRNA genes from each of your species with each other.
Record the % homology between the species in Figure 1.
2) Create a cladogram using the information obtained through your searches and
alignments.
a. Homo sapiens should be farthest to the right on your cladogram.
b. The distances between each species should correspond to the percent
difference between their 16S rRNA.
c. Hints:
i. Create a scale. For example: 1% difference = 1 mile. This would
be a big cladogram, but use this logic to make an appropriate scale.
ii. Points where lines intersect on a cladogram show a common
ancestor to all the species that connect to that point
iii. The same amount of time has passed since a common ancestor and
all its descendant species.
iv. Data is not perfect. 23.4% and 23.5% might be different by 0.1,
by 0.06 or, they might even be the same. It depends on where the
percentages came from. Some things are up to your judgment. Try
to minimize error as much as possible
v. Think big picture: you are trying to show how closely things are
related to each other AND how long ago they shared a common
ancestor.
d. Be creative! Display your cladogram in an attractive/creative way while
maintaining the integrity of your data. Try to represent your species in an
artistic manner (not just simply writing the species name)
3) Analysis Questions:
a. What is the premise behind this approach to understanding evolution (in
other words, describe how this approach can be useful for determining the
evolutionary relationship between two species)?
b. Why did we use genes for small subunit rRNA rather than a gene for an
actual protein when trying to determine common ancestry between
species?
c. How would this cladogram, constructed using genetic homology, compare
with what you would expect from simply looking at the organisms?
Explain
Figure 1: Percent homologies of 16S rRNA genes for five different species
Species A
Species B
%Homology
% Difference
Product : A poster of your cladogram that includes figure 1 and your analysis
(questions a, b, and c above)
See rubric for expectations and how your work will be assessed