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Sarah Yukelis

on 18 October 2013

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Background Context
Due to the fact that we have sequenced genomes of many organisms and species, we are now able to BLAST DNA sequences and find links between species in a matter of seconds.
Morphological evidence is useful in understanding where a species belongs on a phylogenetic tree because observations allow us to understand and see traits and characteristics about the species.
Bioinformatics is a field that combines statistics, mathematical modeling, and computer science to analyze biological data. By using this method, entire genomes can be compared to detect similarities and differences.
An extremely important bioinformatics tool knows as BLAST, basic local alignment search tool, can be used to input gene sequences and search entire genomic libraries to find any species with similar sequences in a matter of seconds.
A cladogram is a diagram used in cladistics which shows common ancestors among organisms for a common trait. A cladogram is not an evolutionary tree.
After blasting Gene 1, it was discovered that the unknown species had a common link with another species known as Gallus gallus (red jungle fowl). The common link they shared was the protein collagen. Collagen is the protein that helps the formation of tissues, teeth and bones. With this information, it could be proven that the unknown species does have a common ancestor with birds.
After blasting Gene 2, it was discovered that the unknown species had a common link with the another species known as Drosophilia melanogaster. The common name for this species is the fruit fly. The common trait that the unknown species and the fruit fly possess the same x chromosomes, which is also known as the shaker gene. This proves that fruit flies and the unknown organism share a common ancestor for the shaker gene. It also shows that the organism is closely related to flies for that one trait.
After blasting Gene 3, it was found that the unknown species shared a common link with another species known as Taeniopygia guttata, also known as the zebra finch. The common link they share is the ubiquitin-conjugating enzyme. This enzyme targets abnormal proteins for degradation. The zebra finch and the unknown species share a common ancestor for this trait. This proves that the zebra finch is closely related to the unknown species for that one trait.
After blasting Gene 4, it was discovered that the fossil shared a common ancestor with the species Alligator sinensis for common mitochondrial DNA. This DNA is important in producing ATP for eukaryotic cells. By blasting this gene, it proved that crocodiles and the unknown species do have something in common.
With all of these details brought into consideration, the decision was made that the fossil belonged on the bottom half of the crocodilia branch.
If the unknown species possesses traits that are seen in the fossil such as a vertebrae, a tail, an eye on the side of its leg, and a tail, then the species will fall on the crocdilians branch before palatal valve because the palatal valve cannot be observed on the fossil.
Primary Question
How can DNA sequences and morphological evidence of organisms be useful in making cladograms based on traits and how can this help us create a phylogenetic tree of related organisms?
1. Make accurate observations about the unknown fossil.
2. Make a hypothesis on where the fossil belongs in the cladogram based on observations.
3. Download the four gene sequences of the fossil and upload them onto the BLAST program.
4. Blast each gene individually and look for the highest percentage of similarity between the gene and the fossil.
5.Google the species that comes up as most related to the fossil, figure out the name and the similarities.
6. Next to the species, find specifically what the fossil and species have in common
7. Check the phylogenetic tree to see that the fossil and the species share a common ancestor for that particular trait.
8. Repeat this process for all for genes
9. With the new knowledge, make your best assumption on where the fossil belongs.
10. Write down your results and final conclusion.
The main purpose of this lab is to correctly place the unidentified fossil in it's correct place on the cladogram. In order to achieve this, groups had to identify four genes of the unknown fossil and BLAST their sequences in order to find similarities between the unknown fossil and species that contain the same gene. Gene 1 of the fossil showed that it shared a common protein called callogen with a species known as the red jungle fowl. Gene 2 showed that the unknown species and the fruit fly shared chromosome x. Gene 3 proved that the fossil and zebra finches share a common trait for the ubiquitin-conjugating enzyme. Gene 4 showed that the unknown species and the Chinese Alligator had a common train for mitochondrias. The unknown fossil and all of the similiar species shared a common ancestor for that specific unifying trait. Due do all of this obtained information, a conclusion was made that the fossil should be placed on the branch of crocodilia before it split into birds and crocodilia, unlike in the hypothesis where it was specifically on the crocodilia part of the branch.
Paired legs
Eye towards side of head
Has a lot of bones
Gene Number: Scientific Name: Max Score: Common Name: Name of Protein: Function of Protein
1 Gallus gallus 10288 Red Junglefowl Collagen Formation of bone, teeth, and tissues

2 Drosophilia melanogaster 1189 Fruit fly Chromosome x, shaker gene Production of k-channels

3 Taenipygia guttata 2313 Zebra-finch Unbiquitin-conjugating enzyme Targets abnormal proteins

4 Alligator Sinesis 1768 Chinese alligator Mitochondria Signaling cell cycle and growth
Final Placement of the Species
The conclusion was made that the unknown species falls on the bottom half of the crocodilia branch because it possess common ancestors with the zebra finch, fruit fly, and red junglefowl. Therefore, it would fall on the bottom half before the branch splits into birds and crocodiles since it possesses common ancestors with both of them. It does not only have things in common with the crocodile, although it does share a common ancestor for that as well.
Literature Cited
Wikipedia http://en.wikipedia.org/wiki/Collagen

Wikipedia http://en.wikipedia.org/wiki/Chromosome_x

Wikipedia http://en.wikipedia.org/wiki/Ubiquitin-conjugating_enzyme

Wikipedia http://en.wikipedia.org/wiki/Mitochondrial_DNA

Wikipedia http://en.wikipedia.org/wiki/Shaker_gene
Full transcript