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 Articles on Cladistics & Phylogenies


Phylogenies & Tree-Thinking
David Baum and Susan Offner
The American Biology Teacher, April 2008, pp. 222-229

---> This article is available free to NABT members on the website archive. For issues archived since January 2000, CLICK HERE, click on Members Only (left column), enter email address and password, on Welcome page, click on American Biology Teacher, then find desired issue.

This is an excellent introduction to phylogenetic trees and their several versions. The suggested presentations would be perfect for high school biology, filling a gap in biology textbooks and providing a deeper understanding of biology. Evolutionary trees provide an excellent visual aid to understanding evolution and its relationship to classification, but there are several conventions in their use that should be explained in order to prevent or remove misconceptions.

Seeing tree diagrams as the "forest" overview of what they represent at the close-up "trees" level of resolution is most impressive. Figures show how we can "zoom out" from the mating lines between various individuals in a sample population to how this would look for many generations over time from a great distance: a fuzzy branching tree. These figures are included in the PowerPoint presentation we have posted here on the ENSI site, courtesy of author Baum and NABT.

One caution with the figures: when you go from Figure 2 to Figure 3, the trees become inverted. The "zooming out" effect is performed on lines of descent (parents at top, later generations at bottom). Then, when showing the tree diagram as an evolutionary (phylogenetic) tree, earlier generations are at the bottom, more recent generations are toward the top, matching the usual orientation of fossil patterns. This might confuse some students, so might be wise to point out what was done.

Variations of trees showing the same relationships are explained, as are the degrees of relationships reflected in the number of nodes between species on the branch tips. Cladograms encourage (require?) groups to be arranged in such a way that members demonstrated to be in a single clade (and their common ancestor) must be placed together on their own branch. Some of the more common misconceptions about phylogenetic trees are also explained.

An interesting and useful application for phylogenies is to show your class where a particular physiological or anatomical trait being studied first arose (or ask them to figure out where it arose, requiring them to recognize the groups where the structure or process occurs). This shows how evolution works as a central unifying theme.

Another value is to show how phylogenies are predictive, leading to new discoveries, as paleontologist Neil Shubin describes in his excellent book Your Inner Fish (Pantheon 2008). In a remote northern Canadian area, he was looking for better evidence of early tetrapod features in fish fossils expected in the 380 million year old rocks found in that region. And he found it! It was a fish fossil whose forelimbs have typical tetrapod bones while the hind limbs were just fins. He callled it "Tiktaalik." This find was reported in April, 2006 in the journal Nature.

Author Baum has also prepared a series of quiz questions, each with sample trees, in conjunction with a similar article in Science. This could be given as a pre/post-test process to assess misconceptions at the beginning, then measure the extent of corrected concepts at the end of the unit. Science magazine and the author makes this quiz available free in pdf format. Author Baum also makes his book available in pdf format: Tree Thinking: An Introduction to Phylogenetic Biology by Baum and Smith, 2013. Each chapter ends with quiz (keys in the Appendix, starting on p. 405).
Ch. 3 has lots of tree diagrams to analyze at the end.

Taxonomic Hierarchy and Phylogenetic Trees: One use for an evolutionary tree that was not presented, but should have, was to show how the taxonomic hierarchy relates to the recency of branching in the tree. Species, genera, families, orders, etc. are simply our recognition of different levels in the nested groups of ever-larger clades. To find a version useful for classroom instruction, go to Microevolution to Macroevolution and Classification for a PDF copy with directions for use. A slightly different version of this can also be found in the Teaching About Evolution and the Nature of Science book by the NAS, chapter 3, page 32 online. And for a pdf copy of the only diagram Darwin included in his Origin of Species, go to Darwin's Tree. This one has been enhanced to show modern taxonomic terms for branches and groups of branches. Also see Darwin's Explanation of his tree, excerpted from Ch. 4 of his Origin of Species (1859).

The authors encourage the frequent teaching of tree-thinking and a useful resource for such ideas at <http://www.tree-thinking.org/resources.htm>.l However, the link is no longer working.

PowerPoint Presentations: The illustrations used in this article are excellent,. Author David Baum and NABT have kindly given us permission to make those figures in the article directly available to you on this site. I have chosen to incorportate them in a PowerPoint presentation "Phylogenetics & Tree Thinking."

A similar PowerPoint presentation about Reading Phylogenetic Trees, with figures from another David Baum article in Nature makes a nice alternative to consider. These have some color in them.

Cartoon Approaches: As teachers, we often encounter the misconception that ancestral relationships are lineal, when in fact family trees and phylogenies are branched - like trees - or even like bushes. CLICK HERE for an interactive CARTOON you can use to discuss this.

Another Cartoon Approach to Phylogenetics: Phylogenetics With Sponge Bob.

A great book that just came out is Carol Yoon's Naming Nature; and it has a classic problem for "classification": in a diagram of a salmon, a lungfish, and a cow, how should we group them? Are they all separate? Do the salmon and lungfish form one branch, and the cow the other? Do the cow and salmon go on the same branch with the lungfish on the other? Or, do the lungfish and the cow form a branch with the salmon on the other? Turns out, that the last answer is the correct one WHEN we use modern evolutionary theory as the basis for drawing the tree. Cows have a more recent common ancestor with lungfish than either does with salmon. It is clear that overall similarity is not the most important aspect of the organism for organizing the relationships among living things.

Evolutionary Trees at ENSI:
There are several lessons on the ENSI site that involve the use of phylogenies and the proper construction of cladograms. Go to the Evolution Index at http://www.indiana.edu/~ensiweb/evol.fs.html and click on "Synopses." Then scroll down to the "Classification, Hierarchy & Relationships" section for descriptions of these excellent lessons. Trees will be found in many of the other lessons, as well. Take a look at the Chronology Lab, Classroom Cladogram and Primate Cladogram lessons (in the Human Evolution Patterns section), the new Patterns in Time lesson in the Geo-Paleo Patterns list, or the Becoming Whales lesson (Procedure #10, with a Thewissen's "Family Tree of Whales," or the newer chronological look at whale relationships in the "Provisional Phylogeny of Whales and Ungulates").

For excellent new material on "Tree Thinking (June 2009), take a look at our review of the articles in the Evolution Education & Outreach Online for June 2009. Scroll down to "A Name by Any Other Tree" and "Transcending Our Thinking About Transitional Forms" among other informative articles.

Or go directly to "A Name by Any Other Tree" by Anastasia Thanukos (use the onsite search function for that title. If you can't find it, or it requires subscription or fee, let me know.). She provides an excellent introduction to the value of tree-thinking and the use of cladogams for understanding evolution, and to realize that cladograms show realistic relationships among diverse groups. "Students need to know that the guiding principle of modern classification has to do with common ancestry and the nested hierarchy formed by the tree of life." "Memorizing the ranks is much less important than understanding the concepts of clades and common ancestry." "When classifying hardware [as many students do], all classification schemes the students come up with will be equally valid - but the same is not true in biology." [The ENSI lesson "Nuts & Bolts Classification..." nicely addresses this issue.]

And here's antother source for using TreeThinking to Teach Evolution
Using Inquiry and Tree-Thinking to "March Through the Animal Phyla": Teaching Introductory Comparative Biology in an Evolutionary Context
Evolution Education & Outreach Online Volume 2, Number 3 / September, 2009: http://link.springer.com/article/10.1007/s12052-009-0156-x
James J. Smith1, and Kendra Spence Cheruvelil 1.

Current Taxonomy in Classroom Instruction
For an excellent treatment of the multi-kingdom vs 3 domain issue - and how to teach this - see the article by Laura K. Baumgartner and Norman R. Pace in The Science Teacher, October 2007, pp. 46-51: Current Taxonomy in Classroom Instruction. Excellent diagram of the 3-Domains and a chart showing the history of taxonomy. If you are a member of NSTA, go to their site, click on High School, then scroll down to Journal Archives and search for "Current Taxonomy". Click on "Click Here to read, and you will get a pdf copy of the article.

(Announced on the "Understanding Evolution" listserve; Search for "Tree-Thinking")
We'd like to draw your attention to a new online exhibit on tree-thinking and phylogenetics produced by the Peabody Museum of Natural History at Yale University. This link includes its index, including short video "Why Study the Tee of Life?"

All links checked and updated Feb 28, 2017
Larry Flammer
ENSI webmaster