Exploring Molecular Evolution

Exploring Molecular Evolution

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

1. Each line in this alignment contains 60 nucleotides. How many nucleotides are there in the beta globin gene for:

1. The chimp

1. 600

1. The human

1. 626

1. A blue asterix indicates that the nucleotides 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.

1. 99%

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

1. I would expect the protein structure between a chimp and a human to be very similar because of the 99% identical genes

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

        1. What is the percentage of sequence conservation between the beta glob in gene in chickens and humans? Work this out using the second line of nucleotides only.

                      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

1. I would expect the beta globin protein found in humans to be more similar of a chimp.

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

1. Yes because scientists can tell how close something is related to another when the two things are compared with each other.

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  Results of your multiple sequence alignment comparing the beta glob in 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.

                               - Humans and chimps based on the unrooted tree appear to be more closely related to each other. When you look at a hmans dna and a chimps dna they are 99% similar.

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

                           -Two species that are least closely related to each other are a chicken and human.

3. Comparative evolutionary distance between species is indicated by the length of the clades they are on. Give the comparative evolutionary distance by percent (by percentage similarity "score") between:

1. The mouse and human

1.  79%

1. The wallaby and the human

1. 75%

1. The chimp and the human

                         1.   99%

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

           

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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: Chicken and Wallaby
2. The mouse: Human and Chimp

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?

1. Humans and chimps

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.

1. Human and Chicken with 4 nodes

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

1. Diverged from their common ancestor most recently?

                                               1.  Wallaby

1. Diverged from their common ancestor least recently?

                                               1.    Human

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 alignm

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.

• Anatomy/structure
• Fossils
• Biogeography

Bacterial I.D Lab

Bacterial I.D Lab

1. To grow bacterial colonies in a solid medium culture dish.
2. To prepare the DNA, we got a bacterial colony, and put it in a micro centrifuge tube then got some digestive buffer and put it in the tube with the bacteria. We then let the tube sit for a while and then put it in a water bath at 100 degrees celcius for a while then it in a centrifuge for a while and put the bacteria from the micro centrifuge tube into a PCR tube.
3. PCR is used to make copies of DNA sequences by annealing the primer to the template, and the synthesis of new strands. This takes less than 2 minutes. Each step is carried out in the same vial.  At the end of a cycle, each piece of DNA in the vial has been duplicated. The cycle can be repeated 30 or more times and each newly synthesized DNA acts a new template. 
4. First set up the micro concentrator column. You add buffer to the column and then add the PCR to the column. You then place the tubes in ice, and then next into the centrifuge. Then you don't need the column anymore, so you can get rid of it. 
5. They identify you by copies/ sequences of DNA being produced. 
6. They end up stopping the sequence at a certain point and then go on to the section. They repeat this same process many, many times.
7. Blast stands for Basic Local Alignment Search Tool.
8. It was pretty easy to find the things mutated in the DNA, and yes it had Bartonella Henselae.