Purpose The goal of this project is to compare a nucleotide

Purpose

The goal of this project is to compare a nucleotide and or protein sequence from one species with the corresponding genes/proteins in other species. This will allow us to infer the evolutionary relationship between these species.

Instructions

• This project is assigned to each individual student and is not a group work. Each student is expected to work independently while completing this assignment on her/his own effort without the assistance of others and is expected to abide by University and Eberly College of Science policies about academic integrity and academic dishonesty. 
• This assignment is divided into two parts. Each part comes with it’s specific set of instructions and rubric. 
• Students will submit a single word doc for this assignment. This document should have the evolutionary trees that will be generated  and include the response to the given prompts.
• Number of allowed attempts is 1
• Total available points 30

Part 1 It’s not a mammoth task (total points 15)

1. Using the publicly available dataset on NCBI (https://www.ncbi.nlm.nih.gov/ (Links to an external site.)) search for this accession number NC_007596
2. Using this sequence as a query, run a BLASTN analysis against the ‘refseq_genomic’ database limited to the mammalian taxon ‘Afrotheria’.
3. Generate a slanted distance tree with the results and download the tree in pdf format.
4. Take a screen shot of the tree (from the PDF) and paste it in a word doc (maximum available 4 points).
5. Read the following prompts and submit your answers in the same word doc

Prompt 1.

Identify and name the query species and state its nearest and most distant relative. (maximum 3 points)

Prompt 2. (screencast)

Compare the habitat, geographical distribution, and diet of the query species with its nearest and most distant relative. (maximum 3 points).

Query species

Nearest relative

Most distant relative

Habitat

Geographical distribution

diet

Prompt 3.

Provide a list of 4-5 species (other than those named in your response to Prompt 1 and Prompt 2) that are present in the distance tree. (maximum 5 points)

Rubric for Part 1 

1. Total available points 15
2. Generating the correct tree (maximum points 4). Points will be deducted if the tree is not presented in the correct format.
3. Maximum available point 11 for prompt1-3. For points break down for each prompt see above.
4. Use binomial nomenclature to name the species. Please use the correct format. Points will be deducted if you do not use the correct format for binomial nomenclature.

Part 2 Finding the common ancestor (total points 15)

1. Using the publicly available dataset on NCBI (https://www.ncbi.nlm.nih.gov/ (Links to an external site.)) search for protein sequences for actin-related protein Arp2/3 from Monosiga brevecollis (accession number ABB29728.1).
2. Use this sequence to run a blastp against the non-redundant protein sequence database.
3. Generate a distance tree (rectangular/circular format) and download the tree in PDF format. Copy the image to word doc and answer the following prompts on the same document.

Prompt 4.

According to the distance tree you have generated explain how it supports the theory that unicellular Choanoflagellates are the closest living relative of animals.  Your answer must be minimum of 250 words and should inform the reader how this tree helps us to understand the evolution of animals. (maximum available points 5)

Prompt 5

From the distance tree, what are the different groups within the animal kingdom can you identify? Name ALL the groups. (maximum available points 2)

Prompt 6

Birds are feathered animals that can fly and or run, whereas snakes are scaly legless animals, yet these two groups of animals are considered as close relatives. Do you support this statement? Please explain your answer (2-3 sentences) by citing examples from the tree that you have generated. (maximum available points 3)

Rubric for Part 2

1. Total available points 15
2. Generating the correct tree (maximum points 5). Points will be deducted if the tree is not presented in the correct format.
3. Maximum available points 10 for prompt4-6. For point breakdown of each prompt see above.
4. Use binomial nomenclature to name the species. Please use the correct format. Points will be deducted if you do not use the correct format for binomial nomenclature.