NAME: ____________________________________ DATE: ______________ BLOCK: ____
Are polar bears closely related to American brown bears? Do you think the giant panda is
more closely related to the American brown bear or the polar bear? Is the giant panda a bear
at all? What about the red panda – is it a giant panda relative? What does the evolutionary
history of bears look like? In this activity you will use real gene sequences to figure out which
animals are more closely related. You will create a family tree for bears and help to solve the
mystery of bear history!
TABLE 1: Accession numbers and scientific names different species
1.
Organism
Accession Number
American black bear
Y08520
American brown bear
L21889
Spectacled bear
L21883
Asiatic bear
L21890
Polar bear
L22164
Giant panda
Y08521
Red Panda
S80939
Northern raccoon
U78345
Leopard seal
AY377288
Scientific Name
Go to NCBI (National Center for Biotechnology Information) www.ncbi.nlm.nih.gov.
To the left of the Search button are (1) a list Drop-down List box and (2) an Edit box.
In the drop-down List box, select Nucleotide. In the center Edit box, paste the
Accession Number (from Table 1 above) for the American Black bear.
Click the Search button.
2.
When the entry pops up, you’ll see the following: U. americanus mitochondrial 12S
rRNA gene. U. americanus is the scientific name for the American black bear. The
search found a partial gene sequence for this species’ mitochondrial DNA that makes up
part of each ribosome. Enter the scientific name in the 3rd column of Table 1.
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3.
Click the FASTA link near the top of the page to view the DNA sequence.
Highlight and copy the entire sequence including the title (everything from the > onward).
>gi|1871572|emb|Y08520.1| U.americanus mitochondrial 12S rRNA gene
CAAAGGTTTGGTCCTGGCCTTCCTATTAGCTGCTAACAAGATTACACATGTAAGTCTCCGCGCCCCAGTG
AAAATGCCCTTTGGATCTTAAAGCGGTTCGAAGGAGCGGGCATCAAGCACACCTCTCCCCGGTAGCTTAT
AACGCCTTGCTTAGCCACACCCCCACGGGATACAGCAGTGATAAAAATTAAGCTATGAACGAAAGTTTGA
CTAAGCTATGTTGATCAAAGGGTTGGTTAATTTCGTGCCAGCCACCGCGGTTATACGATTGACCCAAGTT
AATAGGCCCACGGCGTAAAGCGTGTGAAAGAAAAATTTTTTCCCCACTAAAGTTAAAGTTTAACCAAGCT
GTAAAAAGCTATCGGTAACACTAAAATAAACTACGAAAGTGACTTTAATACTCTCAACCACACGACAGCT
AAGATCCAAACTGGGATTAGATACCCCACTATGCTTAGCCTTAAACATAAGTAATTTATTAAACAAAATT
ATTCGCCGGAGAACTACTAGCAACAGCTTAAAACTCAAAGGACTTGGCGGTGCTTTAAACCCCCCTAGAG
GAGCCTGTTCTATAATCGATAAACCCCGATAGACCTCACCACCTCTTGCTAATCCAGTCTATATACCGCC
ATCTTCAGCTAACCCTTAAAAGGAGTAAAAGTAAGCACAATCATCCCACATAAAAAAGTTAGGTCAAGGT
GTAACCCATGGGGTGGGAAGAAATGGGCTACATTTTCTATTCAAGAACAACCTACGAAAGTTTTTATGAA
ACTAAAAACTAAAGGTGGATTTAGCAGTAAACCAAGAATAGAGAGCTTGGTTGAATAGGGCAATGGAGCA
TGCACACACCGCCCGTCACCCTCCTCAAGTGGCACAAGTCAAATATAACCTATTGAAATTAAATAAAACG
CAAGAGGAGACAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGATAAAC
4.
Open an MS-Word document and call it Fasta.docx. Paste the sequence into the
document. Change the Title line (the first line, it begins with >) to:
>American-black-bear-Y08520. There should be NO SPACES anywhere on the line.
5.
Collect the DNA sequences for all 9 species, and change the title lines in a similar
fashion.
6.
In a 2nd browser tab, go to the Next Generation
Biology Workbench page (http://www.ngbw.org/)
User: ______________________
7.
Click Use the Workbench now.
PW: _______________________
Click on Create an account.
Fill out the 7 required fields, and click Register.
Enter your password and user name in the box above so that you do not forget it.
8.
Log in to your account.
Click Create New Folder, call it Bears, and click on Save.
Two subfolders are automatically created: Data and Tasks.
Click on Data.
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9.
Click on Upload Files.
You will not be Uploading files – rather you'll be pasting your data into the browser, as
follows:
In the Label field, paste the Title (without the >), e.g.:
American-black-bear-Y08520
In the box where it says: Enter your data, paste in the entire record, including the title
line, e.g.:
>American-black-bear-Y08520
CAAAGGTTTGGTCCTGGCCTTCCTATTAGCTGCTAACAAGATTACACATGTAAGTCTCCGCGCCCCAGTGAAAATGCCC
TTTGGATCTTAAAGCGGTTCGAAGGAGCGGGCATCAAGCACACCTCTCCCCGGTAGCTTATAACGCCTTGCTTAGCCAC
ACCCCCACGGGATACAGCAGTGATAAAAATTAAGCTATGAACGAAAGTTTGACTAAGCTATGTTGATCAAAGGGTTGGT
TAATTTCGTGCCAGCCACCGCGGTTATACGATTGACCCAAGTTAATAGGCCCACGGCGTAAAGCGTGTGAAAGAAAAAT
TTTTTCCCCACTAAAGTTAAAGTTTAACCAAGCTGTAAAAAGCTATCGGTAACACTAAAATAAACTACGAAAGTGACTT
TAATACTCTCAACCACACGACAGCTAAGATCCAAACTGGGATTAGATACCCCACTATGCTTAGCCTTAAACATAAGTAA
TTTATTAAACAAAATTATTCGCCGGAGAACTACTAGCAACAGCTTAAAACTCAAAGGACTTGGCGGTGCTTTAAACCCC
CCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGATAGACCTCACCACCTCTTGCTAATCCAGTCTATATACCGCCAT
CTTCAGCTAACCCTTAAAAGGAGTAAAAGTAAGCACAATCATCCCACATAAAAAAGTTAGGTCAAGGTGTAACCCATGG
GGTGGGAAGAAATGGGCTACATTTTCTATTCAAGAACAACCTACGAAAGTTTTTATGAAACTAAAAACTAAAGGTGGAT
TTAGCAGTAAACCAAGAATAGAGAGCTTGGTTGAATAGGGCAATGGAGCATGCACACACCGCCCGTCACCCTCCTCAAG
TGGCACAAGTCAAATATAACCTATTGAAATTAAATAAAACGCAAGAGGAGACAAGTCGTAACAAGGTAAGCATACTGGA
AAGTGTGCTTGGATAAAC
Configure the Data Type fields as follows:
Entity Type: Nucleic Acid (RNA or DNA)
Data Type: Sequence
Data Format: FASTA (.fsa, .fasta, .fst)
Click Save.
Click Return to Data List.
Enter all 9 DNA sequences in a similar way.
10. Click on the Tasks subfolder.
Click Create New Task.
Name the task: Bears-Tree. Click Set Description.
11. Click Select Input Data.
Click Select all to check all 9 DNA sequences.
Click Add Selected to Task.
12. Click Select Tool.
Select / click ClustalW-N.
13. Click Save and Run Task.
14. Wait until View Status turns into View Output.
Click View Output
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15. To see how the sequences aligned (lined up), click View File for either outfile.aln entry.
.
16. To see the Phylogenetic Tree, click View File for either newtree.dnd entry.
Click Save to Current Folder.
Select the Type of Data parameters as follows:
Entity Type: Taxon
Data Type: Phylogenetic Tree
Data Format: Newick (Phylip) Tree (.dnd)
Click Save.
Click on the Data folder.
Click on the tab Phylogenetic Tree.
Click on the Label: newtree.dnd.
Click Draw Tree.
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