Study Guide for midterm exam

Biol 615 Systematics and Comparative Biology, (Sikes) Fall 2012

1. Study questions and terms at end of lecture notes

I will build the midterm from the questions and terms that are at the end of each set of lecture notes. If you are 100% familiar with those then you will know the answers to more than half, possibly 3/4ths, of the questions on the midterm.

2. Review lab exercises

There will be one or more questions on nomenclature so review the nomenclature lab exercise. I've posted a key with the correct answers to the nomenclature exercise to help you study (see lecture 6). For example, I might ask "Under what circumstances would a taxonomist want to designate a neotype?" The beetle lab exercise might show up on the exam in the form of a question to compare styles of building identification keys, or features of good keys. The alignment lab will also be on the exam (but don't worry - I won't ask you to determine the secondary structure of a tRNA!). I might ask you about how secondary structure can help with aligning tRNA & rRNA and what biological information we might use for protein coding DNA (since it lacks secondary structure). Etc.

3. Readings

Be able to describe a few key points from the journal article readings. For example I might ask "What were the major arguments of Hebert et al. 2003?" I suggest you prepare a list of the readings as follows (if you haven't already): the authors, year, title (or key words of the title) and at least 2 (or more) 'most important' items for that reading. Of course stick only to the 'required' readings. Also, to make your life easier, I won't be asking you about the text book readings (eg Mayr & Ashlock, Wiley, Salemi & Vandamme, Winston). These textbook readings are valuable to expand on the material presented in lecture, but are essentially redundant with lecture material. Also, in science we typically never cite textbooks because they are secondary sources - instead we only cite primary sources (ie journal articles). So focus instead on the journal articles and what key points were made therein. Feel free to impress me with your knowledge of these journal articles - for example, if you can work citations of these papers into your short answers WHEN RELEVANT, that would strengthen your writing. [And if you want guidance on what points of each paper you should consider "key" I recommend the lecture notes. In addition to the notes, I would often make comments about the readings during lecture, so hopefully you will have caught those as well.]

4. Proportion

I will try to proportion the exam according to the lectures, ie half of the exam will be on the alpha taxonomy portion of the course because this constituted half of the lectures so far.

5. Misc. Be able to convert characters to distances

This should be intuitive but I'll provide an example just in case:

1 2 3 4 5
A 0 0 0 0 0
B 0 1 0 0 1
C 1 1 0 0 0

What fraction of the character states are shared between OTU A and OTU B? You can see that A has five zeros and B has only three zeros, thus these OTUs are 3/5 similar (and 2/5 distant), - convert 2/5 to a percent and you get 40% distance between A and B.

How about A and C? they also share only three zeros, so they also are 40% distant.

How about B and C? These OTUs share two zeros and one one for a total of 3 shared states and two unshared states. They are also 40% distant from each other.

Thus the distance matrix would look like the one below (note also that a phenogram built from these distances would be a polytomy unless ties were broken somehow - whereas the character data above would provide a single most parsimonious tree [assuming the state 0 is plesiomorphic]- try to draw the trees for these two datasets). Click to see this example picture (based on a different but similar dataset) if you need help.

A 0 0.4 0.4
B 0.4 0 0.4
C 0.4 0.4 0