Download Phylogenetic Comparison Of Oxygen

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Phylogenetic Comparison of Oxygen-binding Proteins
In the following explorations, you will gather molecular data about the DNA,
mRNA, or proteins for the group of organisms you choose to study and then use the
differences and similarities between these molecules to establish how closely related the
taxa are to one another.
When a scientist is able to resolve a segment of DNA, RNA, or a protein,
they will often add the information they have found to constantly growing international
databases so that all of the other scientists in the world can use the data. The most
common database used to collect nucleic acid sequences from DNA or mRNA is called
GenBank, and the largest and most commonly used database for proteins is called UniProt.
However, there are several other databases with information that is accessible to the public.
All of these databases are “wikis” that have some screening process but are generally open
to input from all. All of these databases serve as a library or repository of all molecular data
that is being discovered worldwide.
You will practice using some of these databases today to compare strands of DNA,
mRNA, or proteins to analyze the phylogenetic relationships between taxa.
Demonstration of Cladistical Analysis
Purpose:
To perform an example comparison to learn how molecular phylogenetics works.
Introduction:
Protein and DNA sequences have many uses in biology—one of which is to help
scientists determine which organisms are most closely related to each other. In this
activity, you will analyze several protein sequences to examine the relationships between
related organisms.
The chart below is a fabricated data set that displays a particular protein
sequence found in the six taxa listed. This protein sequence includes only 46 amino
acids (abbreviated with the standard code), but actual sequences of proteins or DNA
would normally be much longer. You will be using these shortened, fabricated
sequences to conduct a comparison by hand that would normally be carried out by a
computer (which, of course, could process larger selections efficiently and accurately).
Follow the steps below to compare the “fraternin” protein sequences given and
determine what the data reveal.
1 Taxa Fraternin protein sequences Snake
Turtle
Chicken
Lizard
Alligator
Mouse
ACDEFGHIKLMNPQRSTPWYACDEFGHIKLMNPQSTVWYACDEFGHI
ACDENGHILLMTPQRKTQWCACEHFGHIKLMNNQSTVWGACDEFLHA
ACDENGHIALMPPQRSTPWTACFEFGHIKLMNEQSTVWGACDEFEHL
ACDEFGHIKLMNPQRSTVWYACGEFGHIKLMNPQSTVWYACDEFGHP
ACDENGHIALMPPQRSTVWCACHEFGHIKLMNEQSTVWGACDEFEHT
ACCENGHILLMPPQRKTPWCACKHFNPIKGMNSQSMAWHANDCHLHM
Chart of Differences (Note: Sometimes scientists will construct a chart
of similarities rather than differences.)
Taxa
Snake
Turtle
Chicken
Lizard
Alligator
Mouse
Snake
Turtle
Chicken
Lizard
Alligator
Mouse
Data Analysis: (Attach a separate sheet of paper for your cladogram)
Use the technique described below and your distance data (from your chart of
differences) to draw a cladogram (a tree-shaped diagram that represents the
evolutionary history of these organisms).
1. Use a highlighter or light-colored markers to note the columns where there
are differences between the sequences.
a. When the sequences are identical for all taxa in one column, the
character is called “uninformative” because it does not yield data that
reveals the evolutionary relationships between these organisms.
Ignore columns where all the sequences are identical.
b. If each sequence is completely different for all taxa, the character is
also considered uninformative because no two taxa are similar enough
to potentially support an evolutionary relationship. Eliminate columns
where each taxon group has a different amino acid at that site.
2. Compare two taxa at a time, and count the number of amino acid
differences they have between them. Write that number in the data chart
above. You will notice that the chart is repetitive, so you can just
reproduce the data for the repeated areas or place a dash in those boxes.
3. Look at your chart of amino acid sequence differences for the taxa and
find the two that are the most different. Look at the number of differences
in the chart for these two organisms to determine which of the two seems
to be the most different from the other taxa overall. This organism will be
2 your “outgroup.” Write the name of the outgroup on the far-left branch of
the tree diagram and write the name of the other organism, that is the
most different from your outgroup, on the far-right branch of the diagram.
Placing the outgroup on the lowest (farthest to the left) branch of the tree
diagram is called “rooting the tree.”
4. Using the taxon name that you’ve just written on the highest (farthest to
the right) branch of the diagram, consult the chart of differences to
determine which taxon group is most similar to this organism. Draw a
perpendicular line from the main branch of the tree up to the level where
the taxon names are written, and write the name of this taxon group on the
branch you have just drawn. The branches to the far right side of the
diagram should make a “V” shape.
5. Repeat step 2 and draw new branches from the main branch over and
over until all of the taxa have been added to the cladogram.
6. Now, look once more at the chart of differences to see if you can find any
“internal relationships” in the data listed. Internal relationships are
indicated by a low degree of differences between any taxa, indicating that
those taxa are more closely related to one another than they are to the
rest of the members of the tree. When their sequences are compared, you
can see that there is a very low number of amino acid differences between
a chicken and an alligator. These two taxa are more closely related to one
another than they are to the taxa on the rest of the tree. To indicate that
relationship, erase the line that connects “chicken” to the main branch and
draw a new line from “chicken” to the halfway point of the line that holds
“alligator” (creating a “V”-shaped branch that joins these two taxa). If you
see no other internal relationships within your data set, you are finished.
7. You now have a branching diagram that describes how evolution may
have proceeded for these taxa. Use the space below to tell the
evolutionary story of how these organisms may have diverged over
a long period of time in the past.
3 8. Class Aves (birds) was long thought to be a taxonomic group separate from
Class Reptilia (snakes, turtles, lizards, alligators, etc.). As scientists were
studying dinosaur fossils, they began to gather more and more evidence that
showed dinosaurs to be more similar to birds and alligators than they were to
snakes, turtles, or lizards. With the use of molecular sequence comparisons,
the amount of evidence grew until scientists realized that birds had long been
misclassified. When a taxonomic group is embedded in another taxonomic
group, as Class Aves is within Class Reptilia, the outer group is called
paraphyletic because the basal group (reptiles) does not contain all the
descendants (birds) of the common ancestor. In fact, the common ancestor of
reptiles is the same common ancestor not only of birds, but also of mammals.
This is because the common ancestor is thought to be a group of organisms
that used an amniotic egg.
Given this example, when do you think classification systems would need
to be revised? What type of evidence and how much evidence do you
think is necessary to support changing the classification of a group of
organisms? State and explain your response below.
This cladogram and any other that is generated will always be considered a hypothesis. That’s
because it is impossible for anyone to go back in time and watch the evolutionary divergence
of these species, to confirm the accuracy of any cladogram. However, if you use other data
sets from other sources, such as additional protein chains, sections of DNA or mRNA,
ecological data, fossil evidence, morphological characteristics, or other evidence, you may
find additional support for your hypothesis. Or, you may find alternative hypotheses that are
better supported. Cladistics is the science of using comparison data to construct evolutionary
hypotheses that can be tested with additional data.
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