Muriele Catam
Lourdes Montoya
Jose Villianueva
July 8, 2008
Mammal Phylogeny
Our SMASH Research Explorations project was based on the biology of life.
Unlocking the mysteries of organisms and their traits can become a hard enough
puzzle to crack that even scientists are puzzled about.
We have used a type of tool to help us come up with some relationships
between organisms that were plotted on a branch-like formation, which was called a
Phylogeny. A Phylogeny is basically a mapping of organisms in a particular order
according to traits almost like a family tree. It also shows the evolution of the
organisms over a specific period of time. A Phylogeny can't give you an exact point
of how organisms are related but a clear, and educated hypothesis. A Phylogeny can
be used to tell time from distant organisms, find out relationships between the
organisms, or even find out approximately where their traits may have evolved. A
morphological phylogeny is a type of phylogeny based on shared traits (e.g.
carnassials, placental development etc) that an organism has.
In order for us to have a better understanding of how this Morphological
Phylogeny works we had used chocolates as an example. The seven chocolates that
we have used were; Hershey's, M&M's, Kit Kat, Baby Ruth, Snickers, Dove and
Twix. In order to start a Morphological Phylogeny there must be characteristics that
you can group the items/organisms into accordingly. For this we had picked out three
characteristics for the chocolates; filling, bar and 20% DV fat. Coming up with the
traits or characteristics can lead to various possibilities so it is best to just have traits
from all areas. Then we have created a table with the three characteristics to help us
create our phylogeny. After we have plotted our data by examining our items we now
have to find our out-group. An out-group is an item/organism that can serve as a
comparison. The out-group generally doesn't fall into many of the traits because it is
used as a comparison between the other items. The out-group in this scenario would
be the M&M’s, it didn’t fall into the bar, filling, or the 20% DV fat. Now that we
have found the out-group, we have to group the items in a necessary order according
the way that we want to. In this scenario we just started with traits more general to
more specific in our opinion. Grouping the items may take a lot of work because there
is no 100% answer. You may have an item or an organism that may fall under another
trait, which may lead to confusing circumstances. When you group the items or
organisms in a branch-like formation you can look at the types of relationships that
one organism has to another.
As we have learned the basics of a Phylogeny, we can now turn to our main
focus of this project, which was to observe and create a Mammal Phylogeny. As a
group we were given nine mammals; Echidna, Elephant, bat, dog, cat, porcupine,
colugo, human, and the chimp. After our group leaders had given us the basic
knowledge of a Phylogeny we were off on our own to create this Morphological
Phylogeny using the characteristics given to us. The traits given to us were; placental
development claws or nails, large bony eye socket, carnassials (shearing teeth),
spines, and gliding membrane. As we plotted our data into our character charts and
started to work on the branching of these organisms, we as a group were unsure of our
findings. This Morphological Phylogeny was the start of our hypothesis on how to
create a close educated guess, but our group leader then introduced us to another
technique rather than the use of visual characteristics.
We have learned that DNA and protein can be used to create a phylogeny, and
both have their advantages. A DNA sequence is constantly changing; it can just be
used as a control to compare. While protein sequences change slowly, it can be more
efficient to use because you can compare the information between more subjects. In
order for us to see how this technique works we have used the software called
Geneious. In the software we used Mitochondrial Cytochrome B Oxidase Gene,
which is the Mitochondria’s specialized DNA. We also used the Hemoglobin protein
sequence, which is the protein, involved in transporting oxygen throughout the
bloodstream. And we used the sequence of 4 Nuclear Genes, which made up our
longest sequence. The key steps into creating a phylogeny tree in Genius is to first
collect and sort out molecular sequences, align the molecular sequences for
comparison, construct the tree, and finally bootstrap to check for confidence. The
first thing that we have done was get information of the DNA or protein sequences for
all 3 of the testing sequences. For all nine of the organisms, we did this by getting the
sequences online off of a website. After we have retrieved the information we went to
back to the Genius software and we uploaded the 3 DNA and protein sequences for
all of the organisms. Next step was to align the molecular sequences of each of the 3
types of sequence for all nine of the organisms. By aligning the sequences you can
compare the similarities that the organisms share in their molecular sequence. After
aligning the sequences constructing a tree is the next job. After you have clicked
construct a tree you will then see the tree, and the order of the relationships of the
animals. The next job is to bootstrap the data to check for the confidence you have
with the shown data. By bootstrapping, the software recreates the tree many times,
however many times you want. The software then checks how many times an
organism was placed on a certain point to check for confidence. For example if the
computer recreates the tree 100 times and out of those 100 recreations two organisms
are placed together, you can have much confidence in their relationship.
Once our three trees were generated we had to compare. Two out of the three
trees gave us the same exact result. The least credible tree was the Tree made from
the Mitochondrial sequence. This is because the tree turned out to be polytomy,
which is a situation where the software was not able to give a fully resolved answer.
This is shown when there are many organisms arising from one single point. This is
incorrect because it is saying that all these organisms evolved at the same time. On
the other hand, our protein and gene sequences gave the same result. These were both
credible trees because the 4 genes had a long sequence to compare the organisms.
Also the fact that we used two different sequences and had the same turn out means
that we can be very confident in our results. We chose the tree made from the 4
nuclear genes as our final tree.
Our final tree demonstrated many accounts of convergence. Convergence is
when traits from an organisms evolved more than once in a time period. Convergence
can vary on the Morphological traits or the molecular sequence of an organism, it is a
situation where different organisms can evolve similar traits. For example, elephants
and humans are very different animals but they have evolved similar traits, like nails.
A phylogeny can have importance in determining how far organisms are, it can also
answer greater questions that can help others understand the evolution of traits.