How would deletions or insertions appear in a sequence alignment?

Include it in your assignment. Answer these questions for your lab manuals: 1 . Do the alpha sequences cluster together separately from the beta sequences? 2. Is the branching pattern among the alpha sequences similar to the branching among the beta sequences? Independent project: For (10) bonus points you may do an independent project where you align sequences from 5 different species from a gene you are interested in or you may extend the beta hemoglobin gene analysis and complete the project idea below. Print the phylogenetic tree and include it in your homework assignment to get the bonus 9 points. Bonus project idea Estimating relationships between existing mammals. In the analysis that we carried out, it was fairly easy to predict the results because we understand the relationships between humans, gorillas, mice, chickens, and frogs. The way in which other animals are related can be difficult to understand. Even among the mammals, it may be difficult to see how different organisms are related to each other. Using beta hemoglobin sequences, investigate relationships between the organisms below. Minke whale Killer Whale Harbor seal Indian Elephant White Rhinoceros Brazilian Manatee European River Otter Polar Bear Hippopotamus Before carrying out the analysis, predict the relationships between the different organisms. 1. Are whales and seals more closely related to one another than to any of these other species? 2. To which organism is the manatee most closely related? 3. To which organism is the elephant most closely related? 4. To which organism is the otter most closely related? After carrying out the analysis: 1. Are whales and seals more closely related to one another than to any of these other species? 2. To which organism is the manatee most closely related? 3. To which organism is the elephant most closely related? 4. To which organism is the otter most closely related? Would you predict that you would see the same results if you used a different protein for 1 0 the analysis, for example the cytochrome c protein? Why or why not? 10 The following review questions will help to reinforce what you’ve learned in this tutorial. Answer them for your lab manual. Questions – Review 1. Why was it necessary to carry out an alignment of the sequences we analyzed? 2. Nucleotide substitutions might lead to changes in the sequence of amino acids in a protein, which can be seen by comparing homologous positions in a sequence alignment. How would deletions or insertions appear in a sequence alignment?