[Laboratory II -- Phylogenetics -- The Science of Who's Related to Who]

Phylogenetics Exercise

In this exercise, you will work in groups. The Mesozoic Garden outside the Herbaria (opposite the T. rex) in the VLSB Atrium houses living plants that are descended from lineages common during the Cretaceous. We have given you a head start by defining your six OTUs:

  1. Moss
  2. Osmunda regalis (a fern)
  3. Zamia pumila (a cycad)
  4. Araucaria heterophylla (Norfolk Island pine)
  5. Annona sp. (a flowering plant)
  6. Chloranthus spicatus (a flowering plant)

Your job will be to develop a phylogenetic interpretation (cladogram) for these six taxa.

In the week BEFORE this lab, you will work with the other members of your group to identify characters and score character states. You should have at least ten (10) independent characters identified and scored when you come to your lab section. Talk with your team members about how to work together most efficiently (teamwork is important in science!). One suggestion would be for each of you to think of four or five characters and then meet together to discuss them before deciding on those to score and use for your analysis.

Once you have identified your characters, you will need to score the states of each for all six taxa. For some characters, examining the plants in the Atrium planters will be sufficient. However, you may need to do some additional research to score some characters.

Some Useful Hints and Resources

Here are some hints on characters to look for in your OTU's for this exercise. Try to generate a number of ideas for plausible characters while you are studying the plants in the Wallace Atrium. Don't worry if you can't observe all of the characters on the plants themselves; you may need to consult literature to examine them in more detail. The BioSciences Library is close at hand!

Remember that ten useful characters (characters that have gone through a careful character analysis to show that they are independent and define nodes etc.) will be more useful than twenty not-so-well-thought-out characters. This is NOT phenetics!

An EXAMPLE of how you might score your character states is given in parenthesis after each character listed below. You should follow this example in your written lab report on this exercise. However, just because we have written out three possible character states as an example does not mean that you are going to find all three states in the plants you study or that you couldn't perhaps find more character variation. Also, don't take for granted that "0" represents the primitive state for a character. That is part of your job to figure out. However, in your data matrix, "0" should represent your hypothesis of the primitive character state.

If a character has too many character states, things can sometimes be simplified by dividing the character into several few-state characters. For example, the character "leaf-type" has an infinite number of states, but if you break it down into a number of characters describing the leaves, like "compound or non-compound", "leaf-venation: net-like or not", "petiolate/non-petiolate" etc. it becomes more manageable. Note, though, that the characters must still be independent!

First, think about features describing the life cycles of your OTU's.

  • The gametophyte free-living? (yes=0; no=1)
  • The sporophyte free-living or dependent of the gametophyte? (yes=1; no=0)
  • Which phase is dominant, the haploid generation or the diploid? (haploid=0; diploid=1)
Now, look at the sporophyte vegetative structure (remember NOT to mix oranges and apples-don't compare features of the gametophyte with those of the sporophyte!). Leaves:
  • Are they present? (yes=1; no=0)
  • Are they compound or simple? (compound=0; simple=1)
  • What kind of venation do they have (open, reticulate)? (open=0; reticulate=1)
Vascular system:
  • Is it a vascular plant, i.e. are tracheids present? (yes=1; no=0)
  • Are sieve cells present? (yes=1; no=0)
  • Are vessel elements present? (yes=1; no=0)
  • Are sieve tube cells present? (yes=1; no=0)
  • What is the manner of protoxylem maturation? (exarch=0; endarch=1; mesarch=2) Stele type? (protostele=0; siphonostele=1; eustele=2)
  • Is it woody, that is, is secondary xylem produced?/Does a vascular cambium exist? (yes=1; no=0)
  • Are they present? ? (yes=1; no=0)
  • What is the position of roots -- do they come off all along a rhizome/stem (homorrhizy), or are they confined to the zone at the basal part of the stem, well separated from the rest of the shoot system (allorrhizy)? (allorrhizy=1; homorrhizy=0)
Reproductive features of the sporophyte are of course quite useful. Here are a few:
  • Does it have sporangia giving rise to two different types of spores, i.e. it heterosporous or homosporous? (homosporous=0; heterosporous=1)
  • Does it have seeds? (yes=1; no=0)
  • How many megaspores per megasporangium? (many=0; few=1)
  • Where on the plant are the reproductive structures borne? (on leaves=0; on axes=1)
  • Are the reproductive structures terminal? (yes=1; no=0)
  • How are they borne? In a strobilus or singly? (singly=0; in cone=1)
  • Is there a second integument around the ovule? (yes=1; no=0)
  • Are they monoecious/dioecious? (yes=1; no=0)
  • Are their reproductive structures bisexual or not? (yes=1; no=0)

Your course materials list the books on reserve in the BioSciences Library for IB181. Many of them will be invaluable in scoring these and other characters for your OTU's. Here are some particularly good references:

Bierhorst, D.W. 1971. Morphology of Vascular Plants. MacMillan, New York.

Foster, A. and E.M. Gifford. 1974. Comparative Morphology of Vascular Plants. Freeman, San Francisco.

Raven, P.H., R.F. Evert, and H. Curtis. 1981. Biology of Plants, third edition. Worth, New York.

Stewart, W.N. and G.W. Rothwell. 1993: Paleobotany and the evolution of plants. 2nd edition. Cambridge University Press.

Some characters are not going to be present in all taxa, but that is OK. Just write "0" ("not present") for that character state. You will have a week to assemble a data matrix, using your own observations, literature, and clues available on the Virtual Laboratory. During the lab section this week, you will enter your completed data matrix onto the computer and run the analysis. Remember that the character analysis is the absolutely most important and time consuming part of reconstructing a phylogeny; once the data are assembled in the computer, the algorithm finds the most parsimonious tree(s) within less than a second (at least for the size data set we are examining -- some research data sets may take days or weeks to run). Once each group in your section has developed a phylogeny, you will have a chance to discuss your results.

A short report on your phylogeny will be due at the beginning of lab next week (week of 14 September). Plan to submit one report per group. The report should include (1) a character analysis section that describes all the characters you used and how they were scored; (2) your results including your cladogram; and (3) a brief discussion interpreting your cladogram.

What if I get more than one most parsimonious tree?

If you have a lot of characters and taxa (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 use character weighting discussed above, to let some characters have a larger influence on how the phylogeny comes out. Many scientists try to be conservative and only report those clades that show up in all the most parsimonious solutions. This is called strict consensus. However, there are a number of methods to help you decide what phylogeny to pick. Taslk with your GSI, the instructor, and your colleagues in class to decide how to choose between or resolve among competing cladograms.

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