Module 5: Variation in Species

Due: sexta, 20 outubro 2017, 6:00

Module 5: Variation in Species


Objective:

Use mutations to study variations between species

Script:

Exercise 1

In this exercise, you will calculate the distances among the mitochondrial DNA (mtDNA) of the mammoth, African elephant and Indian elephant. The complete mtDNA of a mammoth is available on Genbank (NC 007596), as is that of African and Indian elephants (NC 000934, NC 005129, NC 004921). 

Before computing the distance between these sequences, you must first remove the control region (Dloop) and then to do the global alignment of them. Following these steps are described:

A) Only the following nucleotides should be KEPT in the sequences:

  • mammoth:  1 to 15421 
  • African elephant:  1 to 15417 
  • Indian elephant: 1 to 15419

B) Make te global alignment of the rest of the sequences. Use the following substitution matrix (gap penalty: -5 )

C) The aligned sequences must be formatted before it is used for distance calculation.

Which of the modern elephants seems to be more closely related to mammoths?

Exercise 2

Extinct saber-tooth tigers lived until 15,000 years ago, and many parts of their mtDNA are available. The 12S ribosomal RNA gene has accession number DQ097171 and can be compared to homologous sequences from various extant felines.

Make the local alignment of the gene 12S of the ribossomic RNA (rRNA) of the saber-tooth tigers against the nucleotide Genbank database. 

  • Enter the name of the 5 organisms whose sequences are more similar to the saber-tooth tigersgene. Give E-Value and the Total Score for each one of them. What conclusions can you draw about their relations?

Exercise 3

The mtDNA sequences of blue whale, hippopotamus, and cow have accession numbers respectively: NC 001601, NC 000889 and NC 006853. Is the whale genetically closer to cows or to hippos?