How can we use genetics to show evolutionary relationships?
Investigation 3 Learning Objectives
• The student is able to evaluate data-based evidence that describes evolutionary
changes in the genetic makeup of a population over time (1A2 & SP 5.3).
• The student is able to evaluate evidence provided by data from many scientific
disciplines that support biological evolution (1A4 & SP 5.3).
• The student is able to construct and/or justify mathematical models, diagrams, or
simulations that represent processes of biological evolution (1A4 & SP 1.1, SP 1.2).
• The student is able to create a phylogenetic tree or simple cladogram that correctly
represents evolutionary history and speciation from a provided data set (1B2 &
SP 1.1).
• The student is able to construct scientific explanations that use the structures and
mechanisms of DNA and RNA to support the claim that DNA, and in some cases
RNA, is the primary source of heritable information (3A1 & SP 6.5)
Between 1990–2003, scientists working on an international research project known as the Human
Genome Project were able to identify and map the 20,000–25,000 genes that define a human being. The
project also successfully mapped the genomes of other species, including the fruit fly, mouse, and
Escherichia coli. The location and complete sequence of the genes in each of these species are available
for anyone in the world to access via the Internet.Why is this information important? Being able to
identify the precise location and sequence of human genes will allow us to better understand genetic
diseases. In addition, learning about the sequence of genes in other species helps us understand
evolutionary relationships among organisms. Many of our genes are identical or similar to those found in
other species.Suppose you identify a single gene that is responsible for a particular disease in fruit flies. Is
that same gene found in humans? Does it cause a similar disease? It would take nearly 10 years to read
through the entire human genome to try to locate the same sequence of bases as that in fruit flies. This
definitely isn’t practical, so a sophisticated technological method is required.Bioinformatics is a field that
combines statistics, mathematical modeling, and computer science to analyze biological data. Using
bioinformatics methods, entire genomes can be quickly compared in order to detect genetic similarities
and differences. An extremely powerful bioinformatics tool is BLAST, which stands for Basic Local
Alignment Search Tool. Using BLAST, you can input a gene sequence of interest and search entire
genomic libraries for identical or similar sequences in a matter of seconds. In this laboratory
investigation, students will use BLAST to compare several genes, and then use the information to
construct a cladogram. A cladogram (also called a phylogenetic tree) is a visualization of the evolutionary
relatedness of species. Figure 1 is a simple cladogram
1. Choose a gene of interest to explore.
a. Go to the NCBI web site http://www.ncbi.nlm.nih.gov .
b. Choose Gene from the right hand column and then type the gene name at the top of the
page. Hit search.
c. Below are some suggestions:
Actin
Keratin
APOBEC1
GAPDH
Zinc finger
Viperin
Pax1
Tetherin
insulin
ATP synthase
Ubiquitin
hcg
Catalase
Myosin
2. Choose and click on the human gene you are interested in from your search.
3. You will now see a lot of information about the gene you have chosen. What you want now is
the Amino Acid sequence for the protein. You want to eventually find out who also has a similar
protein coded for in their DNA. Scroll down until you find reference sequences. Choose the
NP___ number (the P stands for protein). If there are multiple NP_ numbers choose the first
one.
4. The next page tells you about the protein, who has researched it and an accession number (ID
number). Click on FASTA in the top left corner. This gives you the Amino Acid sequence for your
protein.
5. Copy and paste the whole sequence, including the top line, into a word document and save that
document as your name_______ gene name_________. (Tanner Insulin)
6. Now take your copied sequence and paste it into blast. You can do this two ways
a. Go back to the NCBI page you were on and choose run BLAST, on the right hand side OR
b. Go back to the NCBI main page, choose BLAST from the right hand side, choose protein
BLAST, paste in the sequence for your protein
c. Press BLAST at the bottom of the page.
7. Scroll down past the colorful lines that show alignments until you get to a list of organisms that
have a similar Amino Acid sequence. There are a lot!! Now choose different kinds of organisms
to compare. This is where you will need to use your google skills to figure out what each
organism is. Try to get a good variety. Put each organisms data in the data table for question 4.
8. Once you have decided which organisms you will compare click on their name. Now click on the
hyper-link number for that organism. This will take you to their Amino Acid sequence.
9. Click on the FASTA link at the top left.
10. Just like before, copy the whole Amino Acid sequence and paste it into your word document.
Do this again for all the organisms you will compare.
11. You will need to change the first line of each sequence to >Genus_species name and delete
the rest of the information. Make sure there are no spaces between the > and the scientific
name.
>Rattus_losea
MALWMRFLPLLALLVVWEPKPAQAFVKQHLCGPHLVEALYLVCGERGFFYTPKSRREVEDPQVPQLELGG
SPEAGDLQTLALEVARQKRGIVDQCCTSICSLYQLENYCN
12.
13.
14.
15.
16.
17.
These will be the names used in the alignment and cladogram you will build. Now you have a lot
of sequences to align and compare in a new program called CLUSTALW.
Go to http://www.genome.jp/tools/clustalw/
Paste in your whole word document.
Choose Execute Multiple Aalignment. This will line up the sequences, check for differences and
tell you how closely related each organism is for that particular protein.
Scroll down and copy the clustalw multiple sequence alignment. Paste this into your word
document (you will need to change the font to 8 in order to keep the lines matching up).
Scroll back up to the top of the CLUSTALW page and choose a tree to make. What are the
different kinds of trees available? Try each out and choose the one that shows you the
evolutionary relationships the best by clicking on execute.
Download the image as a PDF, open with Adobe Reader, and save it as tree_last name_gene
name.pdf