Reflection: Modeling Using Biotechnology to Classify Domains - Section 5: Teacher mini-lecture: Classification of Domains


I chose to use a computer simulation, followed by class discussion because it gave students a way to be actively involved in determining the methods and thought processes that scientists use to classify organisms by domain. It also showed students how evolutionary relationships are developed and changed by scientists. It would be impossible to do this as a wet lab because of the expense in equipment. Students would simply tune out a lecture. My next steps would be to show students how scientists further use molecular and genetic data to determine evolutionary relationships at the kingdom, phyla, and class genera. 

Until they reach high school, very few students have heard of domains let alone the criteria used for placing living things into domains. This can be a very complex subject for high schoolers. However, it is important for them to have a basic knowledge of the evidence supporting the formation of a three domain system. It is important that the teacher explain the tests that scientists use so that students understand that these classifications are not random, but based on scientific data.

To determine the evolutionary relationships among domains, gene sequences in rRNA known as signature sequences were compared to determine where there were insertions or deletions in the sequence.  Also, the proteins related to information transfer processes (translation, transcription, and replication) were compared. From this comparison, scientists concluded that because of similarities in information transfer processes Archaea is thought to be monophyletic (Gupta, 1998, Valas & Bourne, 2011). After comparing the genetic sequences of certain highly conserved proteins, scientists concluded that Archaea and gram positive bacteria are more similar than gram-negative bacteria. However, there are enough differences that scientists believe that Archaea show phylogenetic branching within the Gram-positive bacteria (Gupta, 1998; Cavalier-Smith, 2002). In addition to comparing gene and protein sequences, scientists also compare structure of cell membrane and cell wall. When looking at signature sequences in proteins, it is shown that bacteria that are low-G+C (less than 50% G+C) and are gram positive are phylogenetically distinct from high-G+C Gram-positive bacteria. Also, Gram-negative bacteria appear to have evolved from high-G+C Gram-positive bacteria. Conversely, some scientists proposed that Archaea might have been derived from Gram-positive bacteria as a response to antibiotic selection pressure (Gupta, 1998). Others propose that a combination of antibiotic warfare and viral endosymbiosis in the rod bacteria led to dramatic changes in a bacterium that resulted in the evolution of Archaea and Eukarya. (Cavalier-Smith, 2002)

For some time, taxonomists and evolutionary biologists proposed that a diverse community of cells survived and evolved as a biological unit. They gave the name progenote to this first group of cells. From the progenote, all prokaryotes arose (Woese, 1990). After comparing evidence from molecular sequences, ultrastructure (cell wall and cell membrane components), evolution of photosynthesis, envelope structure and chemistry, and motility mechanisms (specifically the protein, flagellin), many scientists concur that the progenote was probably an anaerobic green non-sulphur bacterium. The common ancestor of all life was probably rooted at the divergence between sulphur and non-sulphur green bacteria (Cavalier-Smith, 2002). However, not all agree completely with Cavalier-Smith’s hypothesis, some think the tree of life is rooted in the firmicutes, a phylum of bacteria to which Bacilli and Clostridia belong (Valas & Bourne, 2011). Finally, others looking at the evidence support that the most recent universal common ancestor (MRUCA) of eukaryotes was not a bacterium. They believe that MRUCA diverged primarily by reductive loss and duplication of certain protein sequences (Harish, et al, 2013). 


Cavalier-Smith, T. 2002.  “The neomuran orgin or archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification.” International Journal of Systemic and Evolutionary Microbiology. 52(Pt 1):7-76. Web

Gupta, Radney.  1998.  “What are archaebacteria:  life’s third domain or monoderm prokaryotes related to Gram-positive bacteria? A new proposal for the classification of prokaryotic organisms.”  Molecular Microbiology. 29(3): 695-707.  

Harish, Ajith, et al.  2013. “Rooted phylogeny of the three super kingdoms.” Biochimie. 95(8): 1593-1604. 

Valas, Ruben E. and Philip E. Bourne.  2011.  “The origin of a derived super kingdom: how a gram-positive bacterium crossed the desert to become an archaeon.” Biology Direct. Feb. 28, 2011. Web. 

Woese, Carl, et al.  1990. “Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya.” Proceedings of the National Academy of Science (USA).  87: 4576-4579. Web.

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Using Biotechnology to Classify Domains

Unit 1: Phylogeny and Taxonomy
Lesson 4 of 5

Objective: Students will use data to determine how scientists describe the lines of evolutionary descent of domains.

Big Idea: Simulations are a great way for students to understand how living things are placed into domains.

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