Aligning sequences to create a Phylogenic tree of mammals

Mohamed Adnan
Partner: Hosni Sirhanshiraji 02/03/2012

Abstact I obtained different amino acid sequences for hemoglobin through a database and created a tree showing evolutionary pathways between those different organisms. We were able to create a phylogenic tree that compared various mammals based on their DNA sequences found in the database. Materials and Methods Computer 1. Use the bioinformatics software to determine how closely seals and whales are related to each other and to land mammals such as dogs and cows. 2. We find and copy the amino acid sequences and then we get the sequence data for the hemoglobin protein from our marine and land animals: seals, whales, dogs, and cows. 3. Then go to GenBank, a DNA and protein sequence database called NCBI at http://www.ncbi.nlm.nih.gov/Genbank. 4. Create a FASTA page which has the amino acid sequence of the protein in a coded format using single letters to represent each of the 20 amino acids A is alanine, M is methionine, P is proline. 5. Align the sequences using the program, ClustalX. 6. Build the tree then take a picture and then analyze the results. Data and Results

Analysis and Discussion There is a common ancestor and this did not differ from my expectations because in evolution, as you go back in the way that species evolve, you eventually get to a single common ancestor. The walrus, otter, and harbor seal were broken off into individual branches. There are no sources of error, there was human error. I now understand how different species can be very closely related and how the effects of evolution have changed mammals in general. The use of NCBI has allowed me to learn how to use its features when looking for sequences. The difficulties were how I could actually figure out how the different species were related and through the lab I was able to create the Phylogenic tree that showed how the mammals were

related. My data did support my hypothesis. The skills of using NCBI will help me during college and graduate school. I found it fascinating that the Clustal X program was able to map out the different species based on their sequences. I used the tree to interpret the data and I did not use spreadsheets or graphing in this lab, but I took screen shots of the tree data. Writing this report has conditioned my skills on writing formal lab reports. There were no limitations because the procedure was step by step on the computer. I did not notice any unexpected results. Conclusion The overall findings in this lab were that there is a common ancestor for the mammal species. We have predicted this by using the phylogenic tree to see how the different species mapped out. The objectives of the lab were all completed. The Phylogenic tree was successfully created and has shown the mapping of the mammal species. Questions 1. Yes because most of the amino acid sequences were similar so the different mammal species showed that they were all interconnected and had a common ancestor. 2. It suggests that mammals have evolved from one simple form of organism that evolved as it faced environmental challenges. 3. These common characteristics show that they probably have a common ancestor because of their common traits. 4. It is the one available in humans that can be used to compare to other organisms 5. Without aligning them, it would be difficults to find the similarities and it would be difficult to map the various organisms 6. An outgroup is an organism that is not part of a group on the tree but very closely similar with maybe only one difference. This would be the kangaroo.