In recent years, there has been an emphasis in evolutionary biology education on teaching students what has been called "tree-thinking" (Meisel, 2010). The goal of tree-thinking is for students to understand and critically evaluate phylogenetic trees. Phylogenetic trees are used by biologists to represent the evolutionary relationships among organisms, and the branching patterns that these trees show mirror the evolutionary process. Therefore, tree-thinking provides students with a deeper and more thorough understanding of the evolution of biodiversity.
A logical extension of tree-thinking is its application to teaching taxonomy, the process of classification and identification of organisms. Taxonomy uses phylogenetics to construct classification systems that are essentially hypotheses about the evolutionary relationships among life forms (Case, 2008). With new molecular information being generated every day, taxonomy has become an extremely dynamic science. However, it is often taught as an exercise in memorization or as a "march through the kingdoms" that is unpopular and unsuccessful with students. Providing an evolutionary context through phylogenetics can give students a more meaningful experience and better retention of information (Smith & Cheruvelil, 2009).
One example in which the interaction between phylogenetics and taxonomy has been especially interesting is the current debate about how life should be categorized into kingdoms and domains. The five-kingdom system (Kingdoms Monera, Protista, Fungi, Plantae, Animalia) has been the dominant system taught in schools since the 1960s, when it was developed by R. H. Whittaker, and is still often presented today. With the advent of molecular technology, Woese et al. (1990) used ribosomal RNA sequences to generate a "universal phylogenetic tree" that clearly grouped living organisms into three clusters, which he used to propose his three-domain system (Domains Archaea, Bacteria, Eukarya). Although this new system has gained wide acceptance in the scientific community, its transfer to the classroom has been slower (Peirce, 1999; Offner, 2001; Blackwell, 2004; Case, 2008). Despite the inclusion of the three-domain system in newer state standards for middle school and high school (Case, 2008), at the undergraduate level we often encounter students who are unfamiliar with the domain system or are confused with how domains and kingdoms fit together. One reason may be that the three-domain system requires a re-evaluation of how many kingdoms there actually are and how they fit in the domain structure (Blackwell, 2004). For example, in the five-kingdom system, all prokaryotes are grouped into kingdom Monera. In Woese et al. (1990) system, prokaryotes are divided into two different domains, Archaea and Eubacteria, so kingdom Monera no longer exists in that form (Campbell & Reece, 2008). This is particularly confusing to students who have already learned the five-kingdom system and persist in trying to place it within the newer system or who equate the terms prokaryotes and bacteria. Many newer textbooks present a six-kingdom system (for example, the newest edition of Biology, Indiana Edition by Nowicki, 2012) in which prokaryotes are divided into Kingdom Archaea and Bacteria, so that there is a single kingdom in each of the Archaea and Eubacteria domains. Using this system, students often confound the terms kingdom and domain. Furthermore, this system ignores the debate in the scientific community about the number of kingdoms represented among the prokaryotes, minimizing the diversity represented in these groups.
Here, I present an active-learning exercise to introduce the three-domain system to students. The transition to the three-domain system from the five-kingdom system and from Linnaeus's original two-kingdom system provides students an opportunity to explore taxonomy as a scientific process in which hypotheses are proposed and then altered as new information is made available. …