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The first paper you will look at is not a direct contribution to understanding the origin of eukaryotes but it uses phylogenetic techniques in the same way that they are used to address this problem. The other two papers provide some comments on the approach used, especially relating to the impact of HGT on prokaryotic evolution. In this assignment you will use the reading strategies we introduced in the first assignment to help you understand the paper by Ciccarelli et al. This will allow you to evaluate the quality of their evidence so you can analyse the arguments put forward in the other two papers. These types of arguments will be relevant to many of the essay topics so it is important that you are able to understand their strengths and weaknesses.
This assignment will be easiest if you read all three papers before starting to answer the questions.
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Step 1 Ciccarelli et al The procedure used to generate a phylogenetic tree is shown in Figure 1. Explain this procedure in your own words. What does bootstrap support mean? Refer to Evolution 101 and the resources on phylogenetic trees for background information but you may also need other sources. For Figure 2 in the paper by Ciccarelli et al, answer the following questions. “Official” title for this figure or table (from the caption):
My (simplified, decoded, in regular language) title for this figure or table. The specific hypothesis being tested, or specific question being asked in the experiment represented here is. What data is used to generate this figure? Overall, what we learn from this figure is: The following three issues are of concern to me: (these can be things you don’t understand, or criticisms of the method, questions for the authors, or anything else that comes to mind). Explain your concerns and then write each of your three issues as a question.
Step 2 The following questions will help you address the criticisms Dagan and Martin make about the Ciccarelli et al paper. Why do Dagan and Martin call the tree generated by Ciccarelli et al “the tree of one percent”? What do they claim about the origin of the genes used to construct the tree? Why is the origin of these genes important? What process do they claim has been neglected in the Ciccarelli et al tree? Why do they claim it is important? What does Figure 2 in Ciccarelli et al imply about the relationship between eukaryotes, eubacteria and archaea? Which model of Dagan and Martin (from their Figure 1) matches the Ciccarelli et al phylogenetic tree? Explain your choice.
Step 3 The paper by Ciccarelli et al was published in the journal Science, which means that at least two reviewers and an editor thought it was really important. In spite of this, the immediate reaction was strong criticism from Dagan and Martin. Does this mean the reviewers and editor made a mistake? Give a reason for your answer. Computer programs that generate phylogenetic trees rely on an underlying assumption that the history of life is best represented by a tree. Which of these papers question that assumption? What reasons do they give? The paper by Koonin gives a perspective from ten years after the other two. What resolution to the controversy does he suggest? Do you find his argument convincing? Why or why not?Biology Assignment: I need help writing a research paper.
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