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1. Baum DA, Smith SD, Donovan SSS. 2005. The Tree-Thinking Challenge. Science 310:  979-980. [DOI: 10.1126/science.1117727].
This paper is really the "call to arms" with respect to tree-thinking, referring to the use of phylogenetic trees to study evolution.  These authors point out that phylogenetic analysis, which is used to infer phylogenetic trees to interpret ancestor-descendent relationships, is rarely employed outside the realm of professional evolutionary biologists.  The authors would like to raise the status of tree-thinking as a major theme in our students' evolution training, arguing that phylogenetic trees are the most direct representation of ancestor-descendent relationships, which are the core concept of evolutionary theory.   I have heard anecdotally that many people have used the Tree-Thinking Quizzes that are included in this paper as supplemental material available online.

2. Gregory TR. 2008. Understanding Evolutionary Trees. Evolution Education and Outreach 1:121-137. [DOI 10.1007/s12052-008-0035-x]
This paper provide an extensive introduction to evolutionary trees with guidelines about how to read and interpret them.   The author then examines, with excellent examples, ten common misconceptions about phylogenetic trees that he claims represent "fundamental barriers to understanding how evolution operates". This paper is really nice in that it provides the reader with a reference to the tree-building quiz developed by Eli Meir et al. (contained in EvoBeaker), is well referenced, and has many useful links to online resources for understanding evolution and tree thinking.

3. Brewer S. 1996. A Problem-Solving Approach to the Teaching of Evolution.  Bioscene 22(2): 11-17.
Brewer's work with John Jungck on the computer program Phylogenetic Investigator, available through BioQuest, has inspired some of my own teaching efforts.  The goal of Phylogenetic Investigator was to have students use phylogenies in a problem-posing, problem-solving and peer-evaluation instruction model.  I used Phylogenetic Investigator with a group of Honors students one semester in my Intro Organismal course to study the evolution of HIV.  The Bioscene paper, while not particularly well focussed, has much valuable information on problem-solving as a general educational method with comments to its applicability to the teaching of evolutionary concepts.  Again, it is argued that the historical and comparative approaches, which are important for really understanding the significance of evolutionary theory, are really given short shrift compared to natural selection and the functional perspective.  This paper derives from Brewer's Ph. D. dissertation in Science Education.

4. Julius ML, Schoenfuss HL.  2006. Phylogenetic Reconstruction as a Broadly Applicable Teaching Tool in the Biology Classroom: The Value of Data in Estimating Likely Answers. Journal of College Science Teaching 35: 40-45.
This paper describes an exercise that is very similar in spirit to the one that we developed in our course.  Julius and Schoenfuss used a set of vertebrate skulls to have students develop a character matrix for phylogenetic analysis.  Julius and Schoenfuss emphasize scientific literacy, which gets to the heart of the matter with respect to why I wanted to use phylogenies in my class in the first place.  They do a really nice job of bringing in Popper's 1959 book, "The Logic of Scientific Discovery", in which the importance of using data to discern between competing hypotheses is brought out.  This is the key concept I want to teach.  Phylogenies are hypotheses of the evolutionary relationships of groups of organisms, and we have objective criteria (data and methods) that we use to decide which of two competing hypotheses is preferred.  This is the key thing that makes evolutionary biology science.  This paper also includes some assessment of student learning in summary form.  Senior level students who had completed this laboratory performed better on the evolution section of a summative exam (65% vs. 34%), while students in lower level courses who had completed this laboratory were found to perform an average of 11% better in an exam covering systematics and evolution.  Unfortunately none of the actual data were included in the paper.  .

5. Singer F, Hagen JB, Sheehy RR. 2001. The comparative method, hypothesis testing & phylogenetic analysis – An Introductory Laboratory. The American Biology Teacher 63: 518 – 523.

The paper by Singer et al. is one of two papers (the other is: Giese AR. 2005. Using inquiry and phylogeny to teach comparative morphology.The American Biology Teacher 67: 412 – 417.) whose methods we merged to create our own laboratory stream.  One goal of this work was to have students learn that phylogenetic trees are graphical representations of hypotheses about evolution.  The authors also point out that practicing phylogenetic analysis provides practice in critical thinking, strengthening students' logical and mathematical abilities, and their problem-posing and problem-solving skills.  Singer et al. provided skeletons of five animals (opossum, dog, cat, rat and rabbit) to their students, who were then asked to generate a character matrix based on observations of these skeletons.  Using this matrix, and other information on the anatomy, physiology, behavior and ecology of these animals, students were asked to propose a hypothesis of evolutionary relationship, using the extinct Megazostrodon as an outgroup (there are 105 possible hypotheses).  Students then tested this "tentative statement" using DNA sequence data to infer a phylogeny of these five animal group, showing the students that hypothesis are tentative statements that are open to testing and revision using additional data or data from a different source.  In our own work, we have used the opossum as outgroup, and then show the students that there are only 15 possible phylogenies.  Our students are given two of these 15 trees, and then asked to develop an explanation of why one is better than the other by mapping individual characters onto their trees and applying the principle of parsimony.


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