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Oct 1, 2013 (4 years and 10 days ago)

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North Star Academy College Preparatory High School


Lab modified from Kim Foglia,
www.explorebiology.com



Name: ______________________________



Team_____________________

EDUCATION IS FREEDOM!






Date__________/Mr. McIntire


Determining the Evolutionary Relationships of Species

Walruses and Whales and Seals Oh My!





North Star
Academy College Preparatory High School


2


Introduction


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
beings 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 ide
ntical 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 you 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 needed.

Bioinformatics is a field that combines statistics, mathematical moldei
ng, 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 Lo
cal 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, you will use sequence information in GenBank
(the public repository of
all known DNA sequences from many species), BLAST to compare these gene sequences, and then use
the information to construct a
cladogram
. A cladogram (also called a
phylogenetic tree
) is a visualization
of the evolutionary related
ness of species.


Figure 1
: Simple cladogram representing different plant species

Note that the cladogram is treelike, with the endpoints of each branch representing a specific species.
The closer two species are located to each other, the more recently
they share a common ancestor. For
example,
Selaginella

(spikemoss) and
Isoetes

(quillwort) share a more recent common ancestor than the
common ancestor that is shared by all three oragnisms.

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Figure 2 includes additional details, such as the evolution of pa
rticular physical structures called shared
derived characters. Note that the placement of the derived characteris corresponds to when (in a
general, not a specific, sense) that character evolved; every species above the character label possesses
that struc
ture. For example, tigers and gorillas have hair, but lampreys, sharks, salamanders, and lizards
do not have hair.


Figure 2
: Cladogram of several animal species.

The cladogram above can be used to answer several questions. Which organisms have lungs?
What
three structures do all lizards possess? According to the cladogram, which structure


dry skin or hair


evolved first?

Historically, only physical structures were used to create cladograms; however, modern
-
day cladistics
relies heavily on genetic ev
idence as well. Chimpanzees and humans share 95%+ of their DNA, which
would place them closely together on a cladogram. Humans and fruit flies share approximately 60% of
their DNA, which would place them farther apart on a cladogram.

In this investigation,

you will attempting to answer the following question:
Do aquatic mammals (seals,
whales, dolphins, walruses, manatees, and sea otters) share an ancestral relationship to land mammals
?

Walruses and whales are both marine mammals. So are dolphins, seals, and manatee. They all have
streamlined bodies, legs reduced to flippers, blubber under the skin and other adaptations for survival in
the water. Although mammals evolved on land, these sp
ecies have returned to the sea.
However,
without fossil evidence the question remains as to whether
they evolve
d

from a single ancestor who
returned to the ocean, or were there different return events and parallel evolution? We can’t go back in
time to obs
erve what happened, but DNA sequences contain evidence about the relationships of living
creatures. From these relationships, we can learn about the evolutionary history of marine mammals.

We will use a protein that all mammals share: the hemoglobin beta p
rotein. Hemoglobin is a good test
molecule since it shows both conservation across species (since it performs the essential function of
carrying oxygen in the blood), and variation between species. Species with unique challenges such as
holding their break

for long underwater dives may have evolved changes in their hemoglobin which
improves their supply of oxygen. In addition, hemoglobin has been studied by many evolutionary
biologists, so sequences are available in GenBank from many different organisms.


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Academy College Preparatory High School


4


O
bjectives


1.

To create cladograms that depict evolutionary relationships.


2.

To analyze biological data with a sophisticated bioinformatics online tool.


3.

To use cladograms and bioinformatics tools to ask other questions of your own and to test your
ability to
apply concepts you know relating to genetics and evolution.

Procedure
:

In this lab we will be testing hypotheses about the evolutionary ancestry of different marine mammals.
To repeat, we are trying to answer the question: Did marine mammals evolve from a

single ancestor
who returned to the ocean, or were there distinct return events from separate ancestors? As a starting
point, let’s hypothesize that marine mammals have a single common land mammal ancestor.

Part A
: First, we will explore the relationship
of the marine mammals to each other vs. their
evolutionary relationship to land mammals. To do this, we will test whether seals and whales are more
closely related to each other than either of them are to representative land mammals: dogs (land
carnivores)

or cows (land herbivores). This exercise will mainly train you in using the bioinformatics
software.

Part B
: Second, each of you will develop a cladogram that includes a selection of marine mammals and
land mammals which represent the major mammalian orde
rs. You will then use this phylogenetic tree to
test our hypothesis that all marine mammals have a single common land mammal ancestor.



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Academy College Preparatory High School


5


Part A:
Practicing Sequence Alignment and Tree Construction


Finding Amino Acid Sequences

1.

First, we need to get the sequence data for the hemoglobin protein from our marine and land
animals: seals, whales, dogs, and cows. Go to
GenBank
, a DNA and protein sequence database
hosted by the National Center for Biotechnology Information (NCBI) in Mar
yland at:
http://www.ncbi.nlm.nih.gov/genbank

(
Note
:
You can also go to Google and search for “GenBank”
and it will always come up as the first link.)


2.

One thing that you need to know, is that the hemoglo
bin beta gene and protein is known as HBB in
GenBank. In the “Search” window, select “Protein” from the pull
-
down menu, because we want to
compare the amino acid sequence from each animal for this protein. We need to be specific about
the identify of each
animal, so we will use the harbor seal, the minke whale (a baleen whale),
Canis
familiaris

(dog) and
Bos Taurus

(cow). Type in the protein that you’re looking for and the organism.
Click “Go”.



Note: This database was developed by humans, so sometimes it

is not organized logically. Don’t get
frustrated, be patient. If your search returns several answers that you have to choose between, look
for the listing with a “P0####” Accession Number. That will be the correct protein!


3.

The search result is a page

wit
h a lot of information about the protein from this organism. To see the
actual amino acid sequence for this protein, click on the “FASTA” link near the top of the page. See
the large red circle, above.


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4.

The FASTA page presents the amino acid sequence o
f the protein in a coded format using single
letters to represent each of the 20 amino acids (A = alanine, M = methionine, P = proline, etc.). Copy
the amino acid sequence. You
must

include the header line, starting from the greater than (>
)
symbol. THIS IS IMPORTANT!




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Create a FASTA File

5.

Paste the amino acid sequence into a text file on your computer. Open up NotePad on a PC (Go to
all programs


accessories


NotePad). Save as a .txt or “text only” file. Save it in a logical location
on your computer. We will refer to this as your “FASTA text file.”


6.

Go back to GenBank and collect the amino acid sequences for the HBB gene from minke whale (a
baleen whale),
Can
is familiaris

(dog) and
Bos Taurus
(cow). Paste these amino acid sequences onto
separate lines in the same FASTA text file.


7.

Once you have all of your sequences, we will need to edit the file a bit to make our phylogenetic
tree read more clearly. Let’s look

at the
sequence header

at the top of each protein sequence that
we have copied in to the FASTA text file. The species title that will show up on your tree will be the
first line of each set
of sequence data following the “>” symbol. So right now, our tree

will say things
like “gi |122664 |sp |P09909.1”. That won’t make a lot of sense will it! This header can be edited for
clarity,
but you MUST preserve the “>” symbol.

You can use the scientific name or the common
name to identify the sequence.


For example
:

The harbor seal sequences begins like this:

>gi |122664 |sp |P09909.1 | HBB_PHOVI

RecName; Full=Hemoglobin subunit beta


This can be edited to simply say this:

>Harbor_seal


Tip: If you want to use more than one word in your label, like “harbor seal” you

must add an
underscore “_” between the words (harbor_seal) instead of a space between the words. This is the
only way that all the words will show up as labels on your tree. Do not use names longer than 30
characters


8.

Scan through your FASTA text file. It

is critically important that it is formatted correctly. There must
be a “paragraph

return” or “hard return” (created by the Enter key) only after your header and only
after the complete end of the sequence. Although it may appear that a hard return is alr
eady there,
it is good practice to add one, because the hidden characters do not always cut and paste correctly.


Align Your Sequences

9.

Open

ClustalW2 from the following website:
http://www.ebi.ac.uk/Tools/msa/clustalw2/

This is the
program that will align all of your sequences.


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10.

In the top box, “Step 1
-

Enter Your Input Sequences”, choose “Browse” to select the text
-
file that
you constructed previously. Skip to “Step 4


Submit
Your Job”, and click “Submit”.


11.

Your sequences should show up in the ClustalW2 window. Check to see that they are labeled
correctly, and that the first few letters in the ClustalW2 window correspond to the first few amino
acids of each sequence (
If not, th
en return to step 8 and make changes
)
.



Tip: If your file will not load into ClustalW2, or does not load correctly, check for the following
common problems.


a.

Your file is in .doc or .rtf format. Look at the extension after the file name. It MUST end in
.
txt. Open it in NotePad or Word and save as a plain text file.


b.

You have accidentally deleted the “>” character at the beginning of each sequence header.
Simply add “>” back to each sequence header.


c.

You are missing one or more hard returns at the end of
each header and sequence. To fix
this, place your cursor at the end of each sequence and header and consciously add a return
even it one appears to be there already.


Or alternatively, you may have too many hard returns! Make sure there aren’t any at the
e
nd of lines in the middle of the sequence of amino acids, but only at the end of the
complete sequence.

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d.

If a
-
c do not help, call me over for assistance.


12.

Choose “Show Colors” to illustrate the data visually. Each line is the amino acid sequence of the
sam
e protein (hemoglobin beta) in each of the different species.
This align process has now lined up
the amino acid sequences for each of the species vertically. It is not easy to see which parts of the
protein are well
-
conserved (unchanged) and which parts o
f the protein have experiences mutations.
It’s interesting to scan along the amino acid sequences and look how they line up


how are they the
same in the different species and how are they different? You can see the traces of evolutionary
processes here:
where amino acids have changed, where they have stayed the same, and where
amino acids have been lost! You

are looking at the record of evolutionary history!




13.

Take a screenshot of this alignment chart to use in your lab report (press the “Print Screen”

key,
typically labeled “PrtScrn” on F11 while simultaneously holding the Fn key). The picture of the
screen is now waiting to be pasted into a document. Paste the screenshot into a Word document to
use later.


14.

Before you move on to building your cladogram
, make sure that you “Download Alignment File” and
save this file to a convenient location for use in the next step.



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10


Build the Tree

15.

In the left
-
hand pane, click on “Phylogeny”
. This is the program that we will use to build the
cladogram.




16.

Launch Clust
alW2 Phylogenetic Tree Generator by clicking the button.


17.

In the top box, “Step 1
-

Enter
Your Multiple Sequence Alignment
”, choose “Browse” to select the
alignment

file that you saved during the previous step
. Skip to
“Step 3



Submit Your Job”, and click
“Submit
”. Your tree was constructed using the maximum parsimony method. A new window will
open with your phylogenetic tree.




18.

We need to add one more step to make our tree more accurate. We need to add an
outgroup

to the
mi
x of species we are analyzing. An outgroup provides a “root” to the tree by serving as an example
of an ancestral state for the traits we are comparing. This clarifies the evolutionary relationships
better. So we need to choose a species as an outgroup. We

are going to use kangaroo as our
outgroup in this investigation since it is a marsupial in contrast to all of the other mammals
in our
study, which are placental. Therefore, the kangaroo is selected to be
the most different

organism
from the other mammals

on your tree. Go back to GenBank and get the amino acid sequence for
hemoglobin for “red kangaroo.” Paste this sequence into your original FASTA text file. Save it again.
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11


Load it and align it in ClustalW2. Open the new sequences file in the Phylogenetic T
ree Generator,
and make your tree.


19.

Take a screenshot of your tree and then paste it into a Word document to be used in your lab
report.


20.

Discuss the tree with your class. What conclusions do you come to about the evolutionary
relationship among seals,
whales, dogs and cows?


Note: Phylogenetic trees built with this software can only be used to amek conclusions about
common ancestry. They cannot be used to make conclusions about the timeframe or evolution. The
length of branches is NOT a measure of evolu
tionary time. It is merely an artifact of physically
arranging the tree.



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Academy College Preparatory High School


12


Modeling Debrief and Discussion Questions


Before you answer an additional research question independently, turn and talk with your partner to
answer the following check for underst
anding questions before you continue.


1.

Did the tree support our hypothesis? Why or why not?

__________________________________________________________________________________

________________________________________________________________________________
__

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__________________________________________________________________________________

____
______________________________________________________________________________


2.

What does this phylogenetic tree suggest about the evolutionary history of marine mammals. Go
into detail here about what parts of the tree lead to what conclusions about the e
volutionary history
of the marine mammals.

__________________________________________________________________________________

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__________________________________________________________________________________

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_______
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____________________________________________________________________

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3.

If marine mammals share common morphological characteristics, what do your conclusions about
their evolutionary histor
y imply about these common characteristics?

__________________________________________________________________________________

__________________________________________________________________________________

______________________________________________
____________________________________

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_____________________________


4.

Why did you use the protein sequence from the hemoglobin beta gene?

__________________________________________________________________________________

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_______
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5.

Why do you need to align the sequences (with ClustalW2) before inputting them into the
phylogene
tic tree generator?

__________________________________________________________________________________

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______________________________________________________________________
____________

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_____


6.

What organism served as your outgroup? Why? What function does the outgroup serve?

__________________________________________________________________________________

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__________________________________________________________________________________

_______
___________________________________________________________________________



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14


Part B
:
Establishing the Ancestry of Marine and Land Mammals


Option 1:

In this exercise, we are testing the hypothesis that all marine mammals have a common land animal
ancestor.
As before, you may use the hemoglobin beta protein sequence to test this hypothesis. You will
follow the complete process used in Part A to obtain y
our amino acid sequences from GenBank, align
them in ClustalW2, and build your evolutionary tree using the Phylogenetics function of ClustalW2. Take
a screenshot of your aligned amino acid sequences and your phylogenetic tree and save them in a Word
docum
ent to be included in your lab write
-
up. Then use your phylogenetic tree to determine the
evolutionary relationships amongst marine mammals and the representative land mammals. Determine
whether your hypothesis was supported by the molecular data. If you c
hoose this option, you will be
building a tree with ALL the marine mammals and ALL the land mammals listed below:



Minke whale (baleen whale)



Dolphin (toothed whale)



Harbor seal



Walrus



Otter



Manatee



Carnivora: dog,
Canis familiaris



Rodenta: rat,
Rattus norv
egicus



Herbivore: cow,
Bos Taurus



Primates: human,
Homo sapiens



Proboscidea: African elephant,
Loxodonta africana



Marsupials: red kangaroo,
Macropus rufus


Option 2

For an extra 10% on your lab report, you may design your own research question and hypothes
is that
you wish to investigate regarding the evolutionary relationship of organisms.
For example, you may wish
to investigate the evolutionary relationship of humans and primates by examining the HBB protein from
Homo sapiens

and several species of primat
e (including the Chimpanzee). Alternatively, you may wish to
construct a phylogenetic tree using a highly co
nserved protein other than HBB. F
or example
you may
wish to investigate the same question as above (and use the same species), while examining the
s
equence of the heparin protein.
In this case, think about some of the examples of highly conserved
proteins that we have discussed in class or that came up in your summer reading assignment. Also feel
free to do some online research to facilitate this proc
ess.

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Before you begin, you must have your research question and experimental design vetted by myself. See
below:


Research Question:

_____________________________________________________________________________________

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_


Experimental Design (identify your species for analysis and outgroup).

_____________________________________________________________________________________

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_________
____________________________________________________________________________

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Anticipated Relationship (draw the cladogram that you expect to obtain).

___________________
__________________________________________________________________

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_________________
____________________________________________________________________


Rationale:

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___
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_
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