DNA Sequence Comparisons

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This was another web quest type deal that introduced us to our evolution unit.  We pretty much compared the data of 6 different species beta globin gene to view the similarities.  An answer sheet along with a set of instructions was provided to us.  Below is my web quest thingy with the answers.

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EXPLORING MOLECULAR EVOLUTION

STUDENT WORKSHEET

 

Results of your pairwise alignment comparing the beta globin gene in humans and in chimps:

  1. Data about the alignment can be found below the blue/black alignment chart. How many base pairs (bp) are there in the beta globin gene for:
    1. The chimp?  There are 600 bp.

 

    1. The human?  There are 626 bp.

 

  1. A blue asterisk indicates that the nucleotides (bp) in both sequences are the same, we say they are conserved. What percentage of the beta globin sequence is conserved in chimps and humans? (Don’t include the insertion at the beginning of the human gene). This percentage is often reported as a similarity “score” below the alignment.

 

The percentage of beta globin sequence that is conserved is 99%.

 

  1. Would you expect the protein structure to be highly similar or markedly different in the chimp and the human? Explain.

 

I would expect the protein structure to be similar between the chimp and the human due to what I know about evolution.  We had always been taught that we are similar to chimps and monkeys.

 

RETURN TO BIOLOGY WORKBENCH INSTRUCTIONS

 

Results of your pairwise alignment comparing the beta globin gene in humans and in chickens:

  1. What is the percentage of sequence conservation between the beta globin gene in chickens and humans?

 

Between the chickens and humans, the conserved beta globin is 57%.

 

  1. Looking at the two pairwise alignments you have performed, would you expect the beta globin protein found in humans to be more similar to that found in chickens or that found in chimps? Explain.

 

I would expect the protein to be more similar of that of a chimp to that of human because their sequence of genes is more closely related and similar.  The chicken is only about half the same, which in gene world is very scarce.

 

  1. Do the results achieved by running these alignments support the results on evolutionary relationships determined by scientists using anatomical homology (similarities)? Explain.  

 

These results do support evolutionary relationships due to the fact that it is very much believed that we are related to monkeys.

 

RETURN TO BIOLOGY WORKBENCH INSTRUCTIONS

 

Results of your multiple sequence alignment comparing the beta globin gene in a variety of animal species:

 

  1. Examine the Unrooted Tree produced.  

Record the species at the end of each branch on the unrooted tree shown below.

 

  1. Based on the information in the unrooted tree:

 

    1. Which two species appear to be most closely related to each other? Explain your choice.

The human and the monkey appear to be most closely related because their stems are closest to each other and the shortest into comparisons to each other.

 

    1. Which two species seem to be the least closely related to each other? Explain your choice.

The human and the chicken are least closely related because the chicken has the longest stem and the human has the shortest stem and they are the most far apart from one another.

 

  1. Comparative evolutionary distance between species is indicated by the length of the clades they are on. Give the comparative evolutionary distance (by percentage similarity “score”) between:
    1. The mouse and human

79% score.  Sort of related but not by too much.

    1. The wallaby and the human

75% score.  About in the same boat as above but even more slighty less.  

    1. The chimp and the human

99% score.  Very very closely related.  Only a 1% difference.

Comment on the significance of these results given your knowledge of mammalian groups.

Due to every species being over 50% related, you know that we are even more closely related than we think.

 

RETURN TO BIOLOGY WORKBENCH INSTRUCTIONS

 

Results of your Rooted Phylogenetic Tree:

  1. Examine your Rooted Phylogenetic Tree and record the species at the end of each branch.  

 

  1. Based on this tree diagram, which species is/are most closely related to:

 

    1. The goldfish: The goldfish is most closely related to the chicken because they are on the same branch.

 

    1. The mouse:  I would say that the mouse is most closely related to the chimp because they are connected on the branch.  But, also sizewise, the length is closest together.

 

  1. Homology is a term used to refer to a feature in two or more species that is similar because of descent; it evolved from the same feature in the last common ancestor of the species. Hence, similarity in DNA or protein sequences between individuals of the same species or among different species is referred to as sequence homology. Which two species in the tree above share greatest homology with respect to the beta globin gene?

The chimp and the human easily share the greatest homology in respect to the beta globin gene because of the 99% similarity rate.  

 

  1. A node is a branch point representing a divergence event from a common ancestor. Which two species have the most ancestral nodes (divergence events) in the tree above? Explain your answer giving the number of nodes leading to these species.

The human and the chimp I would say have the most divergence because they are the farthest apart in the nodes.

 

  1. Looking at the phylogenetic tree above, which two organisms:

 

    1. Diverged from their common ancestor most recently?

The goldfish and the chicken.

 

    1. Diverged from their common ancestor least recently?

The human and the chimp.

 

  1. Draw a modified phylogenetic tree to show how the tree above might change if the beta globin gene for a kangaroo was added to the multiple sequence alignment.

 

  1. It is important to understand that the phylogenetic trees you generated using bioinformatics tools are based on sequence data alone. While sequence relatedness can be very powerful as a predictor of the relatedness of species, other methods must be used in addition to sequence homology, to determine evolutionary relationships. Briefly describe 3 other methods that you think might be used to determine evolutionary relationships.

 

  • You can use the location of fossils to see whether they come from the area or not.

 

  • You can also use fossils to study the structure of bones and time that the species lived.

 

  • They type of species and feature of species can show relationships between the two.”

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