Phylogenetic Tree Project Directions PDF

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Guide for completing phylogenetic tree project ...

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Assignment: Reconstructing Evolution Background Information Reconstructing the evolution of organisms allows us to construct a classification. Classification is one of the fundamental concerns of science. Facts and objects must be arranged in an orderly fashion before their unifying principles can be discovered and used as a basis for prediction. A classification provides the framework for storing information in a condensed and easily retrievable form. In biology, organisms are grouped according to the similarities they share. The groups into which organisms are placed are referred to as taxa (singular, taxon). The taxa are arranged in a hierarchy or graded series. The broadest taxa contain a large number of organisms that share very fundamental characteristics. Each broad taxon includes many smaller, more inclusive taxa (each of which contains organisms that share increasingly more specific characteristics). The levels in the hierarchy are: Kingdom Phylum (plural, phyla) Class Order Family Genus (plural, genera) Species The basic taxon of classification is the species. Each species includes organisms that share genes through inbreeding. Closely related species are grouped within a genus. Related genera are grouped together within a family; related families within orders; orders within classes; and classes within phyla. A biological classification should (1) summarize the characteristics of organisms efficiently (in other words, have high information content), and (2) reflect real groups (in other words, reflect evolutionary relatedness or phylogeny). The purpose of this assignment is to teach you how classifications are constructed so that they reflect both information and phylogeny. In constructing a classification, a biologist goes through four basic steps: 1. Taxa to work on are chosen. 2. Characteristics of the organisms are chosen for comparison. 3. The characteristics are analyzed to a scheme of relationships among the organisms. 4. The scheme of relationships is converted into a classification.

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In this project, you will go through all four basic steps. The group you will be working on has been sent to you in an email. All of these organisms are on display at the Smithsonian’s Natural History Museum. Part I – Selecting Taxa You have been given seven taxa and one outgroup for your project. All of these are on display in the Hall of Osteology on the second floor. Most of them are also on display on the first floor in the Hall of Mammals as well. The exhibits on the first floor can give you some good ideas for characters so make sure you look at both exhibits. On the first page of the assignment, list your seven taxa and outgroup by common and scientific name (use correct scientific nomenclature).

Part II - Selecting Characters

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To recognize how closely organisms are related, their relative degree of common ancestry is judged by the similarities among them. Organisms are compared by the presence of homologous characters. Each character has different forms called character states. For example, the number of teeth on the mandible i s a character and 12 teeth o r 17 teeth a re examples of character states. In simple terms, when we compare organisms, we are ascertaining whether or not they have the same state for a character. For This Assignment In order to complete this project in the time we have in this course, I recommend that you limit the characters you examine in the following way: (1) The characters and character states should be features that you can easily observe on the specimens or find in the written descriptions next to the display. Don’t attempt to do a lot of research on these animals. The point is not to get the “correct” phylogeny but to learn how to convert your own observations in to hypotheses about phylogeny. (2) Limit your characters to those that have just two states. Multistate characters greatly add to the length of time it will take to complete the assignment. On the second page of the assignment, list 10 characters with character states, for your seven animals and the outgroup. No two animals may have the same states for all ten characters. Example: Character 1: Adults are: (a) tailess; (b) have tails. Character 2: Skin color: (a) brown; (b) green. Character 3: Raised tubercles (“warts”): (a) absent; (b) present. (… Etc. for 10 characters) Next create a chart showing the distribution of the character states for your seven organisms. No two organisms may have the same states for all ten characters. Example:

Part III – Analysis of the Characters 3

In the lecture notes, I argued that the best way to reconstruct evolution was with cladistics analysis. Is that going to be true for your animals? Let’s try two different analyses: 1. Phenetic clustering 2. Cladistics

Phenetic Clustering Phenetics was developed in an attempt to make classification more objective and quantitative. Pheneticists classify organisms exclusively according to their overall similarity. This approach is simple. Character states of different organisms are compared and the number of characters in which the two organisms have identical character states are noted. A percent similarity is calculated for each pair of taxa. Taxa with highest similarity are grouped most closely together. These taxa groups are, in turn, eventually grouped with the taxa with whom they share a lower degree of similarity. Calculation of Similarity There are many ways of measuring similarity, but usually the simple matching coefficient is used. This coefficient treats all characters the same and measures the similarity with the formula: Sm =

sij/p = a

Where, Sij is the simple matching coefficient for two taxa (i and j); a is the number of characters i and j have in common, and p is the total number of characters. The similarity coefficient is often multiplied by 100 and expressed as a percent similarity. 1. The first step in constructing a phenogram is to calculate the matching coefficient between all taxa. For example, by looking at the character distribution chart I put on page 2 above, we can see that taxa A and B are the same for characters 1, 2, 3, 4,5, 7, 8, 9 and 10:

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Thus, they share 9 out of 10 characters. The simple matching coefficient is: SAB = 9/10 = 0.90 In other words, A and B share 90% of the characters. All of the similarities for these taxa are found in the table below (the outgroup is only used in cladistics, so it is not on the similarity chart):

Construct a similarity table for your organisms. Turning the Similarity Table into a Tree (a Phenogram) Once the similarity among all the organisms is known, they can be grouped on the basis of this similarity. The steps are: 1. Draw a vertical axis divided into 10 parts. Each part represents 10% similarity. Therefore the top of the axis is marked 100% and the bottom is marked 0%:

2. Find the two most similar animals and link them.

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From the similarity table for the example, we can see that A and B are the most similar they are the same for 90% of the characters. So they are linked first at 90%:

3. Link the next most similar taxa. From the similarity table for the example, we can see that E and D have the next highest similarity - they are the same for 80% of the characters. They are linked next at 80%:

4. In the example, B and C share 70% of the characters, but B is already joined to A. Therefore C must be linked to the A-B cluster. This is done by finding the average similarity between C and A, and C and B: C-A 60% C-B 70% 60% + 70% = 130 average 130 ÷ 2 = 65 (average similarity is 65%) Then C is linked to the A-B cluster at 65%: 6

5. Finally the A-B-C cluster is linked to the E-D cluster. The average similarity between the example taxa in the A-B-C cluster to the E-D cluster is: A-E = 30 A-D = 30 B-E = 30 B-D = 40 C-E = 50 C-D = 50 total = 230 average = 230 ÷ 6 = 38.3% Then the A-B-C cluster and E-D cluster are linked at 38.3% and the phenogram is complete:

Using the similarity matrix created for your animals, construct a phenogram.

Cladistics Analysis 7

Cladistic analysis was developed in an attempt to make phylogenetic analysis more objective and quantitative. No theories of evolutionary processes are assumed before the animals are classified. However, the resulting classification may be interpreted to reflect the evolution of the group. The cladist groups organisms by shared derived characters. The phylogeny is constructed such that the number of changes from one character state to the next are minimized. Each change is called an evolutionary step. The principle behind this is the rule of parsimony – any hypothesis that requires fewer assumptions is a more defensible hypothesis. Cladistic analysis is covered in detail in the lecture notes. I am going to briefly go over the steps here with the example datachart. Refer to the lecture notes for more detail. 1. It is common practice to designate the primitive states as 0 (zero) and the derived states as 1 (one). The information from the outgroup is used to determine primitive (plesiomorphic) and advanced (apomorphic) states:

For your taxa, score the characters as primitive or derived and list them in the chart. 2. Going one character at a time, put organisms together that share apomorphic (advanced features). See the lecture notes for more detail. Here it is for the example taxa:

Build a cladogram for your taxa.

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Part IV – Final Questions Answer the following questions: 1. Compare the two classifications you have made. Describe the similarities and differences in the ways the organisms are related to each other in the different trees (if there are any differences).

2. What question did I ask you to test? What is your answer?

3. For each phylogeny reconstructed, create a formal classification using the Linnaean categories (species, genus, family, etc.). You can make up names or can just tell me which “Taxon A, B and E are in the same genus” … etc).

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