Subscribe to our newsletter. Email Facebook Twitter. Phylogenetic systematics evolutionary trees. Choose the taxa whose evolutionary relationships interest you. These taxa will be the tips of your tree and must themselves be clades. For example, you might choose 20 species of beetle that all fall within the same genus.
Alternately, you might choose to reconstruct the relationships among the major clades of insects beetles, flies, moths and butterflies, true bugs, dragonflies, etc. Determine the characters and examine each taxon to determine the character states.
For example, you might select a suite of anatomical traits as your characters e. Alternately, you might select the bases in a particular gene as your characters, and your character states would then be A, T, G, or C for each of the characters.
Note that it is important to select characters that seem to be homologies , that is, characters that are similar because they were inherited from a common ancestor. Analogies , characters that evolved through convergent evolution in two separate lineages like the dorsal fins of sharks and dolphins , are not useful for reconstructing phylogenies. Determine the polarity of characters — in other words, figure out the order of evolution for each character.
For example, did the beetle species under consideration all evolve from an ancestor with five antennal segments — and only later did six evolve, or was it the other way around? Did a lineage with six antennal segments evolve into a lineage with five? Figuring out the polarity of a character can take some work. In some situations, it is reasonable to assume that the character states in the outgroup are the ancestral states for the taxa of interest.
In other situations, paleontologists may have fossil evidence that indicates the probable ancestral state of the character. Many different methods may be used to reason about character polarity. Note that for some types of cladistic analysis, determination of character polarity is not absolutely necessary. Group taxa by synapomorphies , not by symplesiomorphies. Symplesiomorphies are original character states shared by two taxa.
Character states and character state changes are inherited. Branching occurs, and is the predominant pattern i. Consequently, similarity in a derived character state is more likely to be due to a common ancestry homology than through random or non-random assimilation of the same feature in two different lineages homoplasy.
This follows Okkham's razor in saying that the simplest solution is the most probable. As you are no doubt realizing, the cladistic method is not entirely objective. The systematist still has to make interpretations about homology, choose characters and make decisions about weighting and ordering characters for analysis. However, the cladistic paradigm does force the systematist to state explicitly why he or she believes characters are homologous or should be ordered in a certain way.
This provides bases for falsifying hypotheses and promotes testing of alternatives. This transforms the subjectivity into science. Interpreting results The result of a cladistic analysis is a cladogram, a branching diagram of nested synapomorphies that defines relationships in a relative way.
These synapomorphies are used to recognize monophyletic clades monophyletic groups of organisms of any taxonomic rank , arranged in a hierarchical manner. Note that a cladogram does not have a time axis, and does not make any statements as to the mechanism of evolution other than it occurs by splitting of ancestral lineages. It is merely a hypothesis of character change and relationships. As such it can be carefully compared-character by character-to competing hypotheses, tested, and refuted with additional data.
What if I get more than one most parsimonious tree? If you have a lot of characters and OTUs, there are often a number of ways in which the algorithm can organize a most parsimonious tree. As a result, you might end up with more than one most parsimonious hypothesis of relationships. In order to choose the most likely cladogram, you might try adding more characters.
You might use character weighting, letting some characters have a larger influence on how the phylogeny comes out. Many scientists are conservative and only report those relationships that show up in all the most parsimonious solutions.
This is called strict consensus. As noted above, cladograms aren't evolutionary trees. They do not show ancestor-descendent relationships. Rather, they present a graphical hypothesis of branching relationships based on the distribution of synapomorphies.
To help you better understand this point, we will be looking at a make-believe example. The advantage of this example is that the evolutionary history will be known. Therefore, after you have completed the analysis, you can compare your cladogram to the actual evolutionary tree.
Meet the Ovids. Ovids are mythical creatures. You don't need to know too much about their ecology and life history because your phylogeny will focus only on morphological characters. Ovids have evolved by branching of lineages, with new traits acquired at the branching events. Thus, they are good candidates for cladistic analysis. I have already selected OTUs and examples of each are presented on your handout.
Identify characters. First you must identify morphological characters. If you can think of more characters, include them.
That will make your analysis stronger. Consider the rules for identifying good characters discussed above.
For each character identify two character states. One of the states will be coded "0" in the data matrix. By convention, the zero state is the state possessed by the outgroup.
The alternative derived state will be coded "1". Describe the characters and the character states for each on your Ovids worksheet.
Complete the data matrix. For each character, note the character state possessed by each OTU, thus completing the data matrix. Now enter your data into MacClade. Start MacClade by double-clicking on the MacClade icon. Select "new" when asked what file you want to open. Use your cursor to drag the number of columns to match the characters you have, and the rows to seven. Enter your data.
Save your matrix with a unique file name and place it in the class folder. Analyze your data. When asked which file to execute, choose you named file and click "execute". In the "analysis" menu, choose "exhaustive search". Click "search". The search should only take a moment. Now, root your tree by telling PAUP which taxon is the outgroup.
In the "tree" menu, select "root trees". Click the "rooting options" in the dialogue box that appears. Click the "define outgroup" button in the dialogue box that appears. Select your outgroup from the ingroup box and move it to the outgroup box. Click "ok"; click "ok" again; click "root".
Save your tree. In the "tree" menu, select "save trees to file? Study your trees. Return to MacClade. Open your data file again. In the "display" menu, select "go to tree window".
Select "open tree file" and choose your saved tree. Click "open"; click "get tree". Your tree should now be displayed. Copy the tree topology branching pattern into your notebook and then onto the blackboard.
When everyone is finished, we'll have a look at the real evolutionary relationships among the Ovids and compare that to our phylogenies.
Phylogenetic Exercise - Toucan Barbet Phylogeny. In this exercise we will be working with a real example, where the true relationships are not known. For this analysis, your characters will focus on the color and markings of 13 species of tropical birds, the toucan barbets.
Plumage color in birds evolves very easily and can become very complex. Because birds have excellent color vision, color can be very important to them. Thus, color and color patterns make good evolutionary characters. Meet the toucan barbets. Toucan barbets are a group of Neotropical birds. They live in forested habitats in both lowland and montane environments. They eat a variety of fruit, seeds and insects.
Your OTUs will be the established species of toucan barbets shown on the sheet. Identify at least two morphological characters for each OTU. Of course, your analysis will be stronger if you have more characters. For each character identify two character states 0, 1. Describe the characters and the character states for each on your toucan barbet worksheet. The pictures from which you will be developing and scoring your characters are cartoons.
They are designed to steer you to three types of characters: beak shape, color and markings. Consider only these types of characters in your analysis. Now enter your data into MacClade as before. Type your data. Save your matrix with a unique file name and place it in the appropriate class folder. In the "analysis" menu, choose "heuristic search".
The search should not take too long, however, the amount of time required for the search will depend on the number of characters you have generated. We will not be rooting trees in this exercise. Copy the tree topology branching pattern into your notebook, note the file name of your tree on the "stickie" on the computer desktop.
Arens will collect these and print them out on Monday morning so that you may include the tree in your report. Write up your results. A short report on your analysis will be due in lecture on Monday 18 February. Your report should be co-authored by the members of the group, typed, and contain the following elements.
Consider the following questions in your discussion:. What monophyletic clades did you identify? Are named genera monophyletic? How might you change the classification taxonomy of the toucan barbets to reflect natural groups? If you are interested in learning more about how phylogenies are constructed or how they can be used to answer evolutionary questions, some of these resources may help. Brooks, D. Phylogeny, Ecology, and Behavior.
University of Chicago Press, Chicago. Donoghue, M. Doyle, J. Gauthier, A. Kluge, and T. Rowe The importance of fossils in phylogeny reconstruction. Annual Review of Ecology and Systematics Eldredge, N. Columbia University Press, New York. Harvey, P. The Comparative Method in Evolutionary Biology. Oxford University Press, Oxford, England. Maddison, W. Mishler, B. Transition to a land flora: phylogenetic relationships of the green algae and bryophytes. Cladistics Ridley, M. Evolution and Classification: The Reformation of Cladism.
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