KeywordsPhylogenetics Applications Teaching
In this special issue of Evolution: Education and Outreach, many authors (notably Brooks 2010) argue for the importance of helping students understand phylogenetics and outline innovative ways of introducing key concepts regarding tree reading (Mclennan 2010a) and tree building (Kumala 2010b). As argued by (Brooks 2010) and Kumala (2010a, c), evolutionary relationships (represented in phylogenies) can serve as the basic structure on which students hang their understanding of the biological world, providing a meaningful way to organize and remember facts, as well as serve as a constant reminder of the processes that have shaped biodiversity.
And of course, phylogenetics is important to understand in its own right. Biology has experienced something of a phylogenetic revolution in the last few decades (Losos 1996). Technology has advanced in several fields, making genetic sequences cheaper and faster to obtain and vastly improving our ability to analyze those data through increased computing power and new analytic methods. All of this has made phylogenies based on DNA easier to build and helped to highlight the importance of a phylogenetic perspective even when molecular data are unavailable (e.g., for most, but not all, fossil organisms). There’s a simple reason that phylogenies have become increasingly prevalent in textbooks and now even appear in middle school texts (Catley and Novick 2008): phylogenies have become increasingly important in biological research and in shaping how scientists look at the natural world. To grasp modern biology, students must understand the basics of phylogenetics.
Textbooks have responded to this need, as have the educators and scientists who develop supporting educational resources. For example, a typical high school textbook might use a phylogeny to illustrate the diversity of animal life, marking the evolution of key traits such as radial symmetry or the coelom. The same text might introduce the basics of reading phylogenies by explaining the concepts of common ancestry, clades, and shared derived characters. But how can students be motivated to learn and retain this material (i.e., not hit the delete button, which Mclennan (2010a) notes so frequently happens)? Using innovative and engaging teaching activities (e.g., Kumala 2010a) and narratives can help. In addition, instructors can incorporate examples of practical applications of phylogenetic reasoning that are compelling to students and relevant to their lives and basic social issues.
Here, we will focus on practical applications of phylogenetics, expanding on one example referenced in another article in this issue (Wiley 2010) and introducing selected additional examples ripe for deployment in classrooms. So what exactly can you do with a phylogeny? Lots...
Catch a Killer
Perhaps the most widely circulated (and most tabloid-worthy) example of phylogenetics in action is the case of the State of Louisiana versus Richard J. Schmidt (Vogel 1996). As summarized by Wiley (2010), in 1995, Schmidt (a medical doctor) was accused of injecting his former mistress (Janet Allen, a nurse) with HIV-positive blood from one of his patients. Allen and Schmidt had been romantically involved for a decade, and Schmidt had been giving her regular vitamin injections. After threatening to break off the affair, Allen found that she was HIV positive and accused Schmidt of substituting tainted blood for one of her injections.
Turn Back Time
Just as phylogenetic evidence can be used to convict a killer, it can also be used to exonerate the innocent—at least in theory. In 2004, six medical workers from Bulgaria were condemned to death in Libya where they had been working, convicted of deliberately infecting hundreds of hospitalized Libyan children with HIV (Butler 2006). Did they do it? Circumstances suggested that the Libyan authorities might have had the story wrong: many of the HIV-positive children were also infected with various hepatitis strains (suggesting repeated infection via dirty needles), and the hospital in question seemed to have unsafe medical practices.
Unfortunately, even after this evidence was introduced in a retrial, the death sentence was upheld (Bohannon 2005). Finally, in 2007, after more than eight years of imprisonment, the medical workers were released and returned home (Bohannon 2007). However, their release did not come through the Libyan court system, which had repeatedly ignored scientific evidence supporting the medics’ innocence, but through political maneuvering and incentives: promises of aid, trade, debt write-offs, and payments to the infected children’s families.
Identify Mystery Meat
While phylogenetic methods may indeed help your students identify the school cafeteria’s lunch special, the same techniques can also be used to tackle more pressing environmental issues. In Japan, whale meat is considered a delicacy—one that has become harder to find since global declines in whale populations spurred international agreements placing tight restrictions on which whales can be hunted, how they can be brought to market, and whether their meat can be imported and exported. Does the market for whale meat in Japan encourage illegal whaling and trading of whale products? The answer is hard to figure out simply by visiting Japanese fish markets. In these markets, purported whale is often simply labeled “whale” without specifying the meat’s species or provenance. Scott Baker and Steve Palumbi realized that phylogenetic analysis could help solve the problem.
Choose Your Animal Companions Wisely
In 2002 and 2003, when the airborne SARS virus caused 774 deaths, more than 8,000 cases of illness, and widespread panic, scientists and health workers alike wondered where it had come from (Normile 2005). In 2003, attention focused on cat-like mammals called civets because infected civets were discovered at a live animal market in southern China (where they are occasionally eaten and where SARS was a problem). However, further searches failed to turn up more tainted civets, suggesting that these animals were not the original source of the virus. Then in 2005, two teams of researchers independently discovered large reservoirs of a SARS-like virus in Chinese horseshoe bats. Could bats have been the original source of SARS? Figuring out the answer required reconstructing the evolutionary history of the virus.
Viruses make the jump from bats to human hosts frequently. In fact, they appear to be the natural reservoirs for many human viruses, including the Ebola, Hendra, and Nipah viruses as well as SARS. What is it about bats that makes them such a breeding ground for human viruses? Biologists aren’t sure, but they have some ideas. Bats’ tendency to roost in tightly packed caves with other bat species might encourage the transmission of viruses between species and provide opportunities for viruses to evolve and recombine with each other. Some of the new viral strains that result may be poised to move to other animals, including us!
Save the Earth
In another article in this issue, Brooks and Mclennan (2010) argue convincingly that our conservation goals should be broad—to save as many species and habitats as we possibly can, in circumstances that will allow the organisms to continue to evolve. Unfortunately, though we may aim to maintain this goal, we can’t save everything. Resources to direct towards conservation efforts are limited, and sometimes, difficult decisions must be made. But how do we make those choices? Many biologists have suggested that phylogenetic analysis can help in this process (e.g., Vane-Wright et al. 1991; Crozier 1997).
Biologists recently put some of these ideas to the test (Cadotte et al. 2008). They wondered if some plants might be more important than others in preserving a functional ecosystem. They reasoned that the biomass produced by plants might be a particularly important indicator of a diverse, functioning ecosystem. After all, more biomass translates into more plant mass providing food for animals, producing oxygen, and absorbing the greenhouse gas carbon dioxide. Furthermore, the scientists suspected that the evolutionary relationships among an ecosystem’s plants help determine the amount of biomass they can produce. An ecosystem based on distantly related plants might be more productive than one based on closely related plants, they reasoned, since the distant relatives are more likely to have evolved to occupy distinct niches.
Here, we’ve outlined and illustrated just a few of the more engaging examples of phylogenetics in action in the real world. But there are many more examples of practical and scientific applications of phylogenetics—for example, in classification (as discussed in Mclennan 2010a; Wiley 2010; and Thanukos 2009) and in testing hypotheses about evolution (e.g., see Mclennan 2010b for examples of testing hypotheses about human behavior). Incorporating examples such as these into instruction on evolution can help students view phylogenetics as more than a complicated method of analysis practiced by biologists. It can encourage them to see phylogenetics and evolutionary relationships as a useful lens through which any biological problem—from the mundane, to the sensational, to the weighty—can be viewed.
Give Me an Example of That
Using trees. Find out how scientists use trees to make predictions about fossils, to learn about the evolution of complex features, to make predictions about poorly studied species, to learn about the order of evolution, and to learn about the evolution of diversity. Read it at: http://evolution.berkeley.edu/evolibrary/article/_0_0/phylogenetics_09
Using trees to understand plants—a research profile that follows scientist Chelsea Specht as she pieces together the evolutionary history of tropical plants and their pollinators—and in the process, tries to figure out how to conserve endangered species. http://evolution.berkeley.edu/evolibrary/article/specht_01
Using trees for classification—a brief tutorial that reviews the basics of phylogenetic classification. http://evolution.berkeley.edu/evolibrary/article/phylogenetics_04
The new shrew that’s not—a news brief that describes scientists’ discovery of a new mammal species, a giant elephant shrew, and how this animal was classified. http://evolution.berkeley.edu/evolibrary/news/080301_elephantshrew
A name by any other tree—an article on phylogenetic classification from a previous issue of this journal. http://www.springerlink.com/content/k176638503p63017/
Evolutionary evidence takes the stand. This news brief describes the role of phylogenetic evidence in a Libyan court case. Six medical workers have been convicted of injecting children with HIV-tainted blood—but the evolutionary history of the virus paints a different picture. http://evolution.berkeley.edu/evolibrary/news/070101_libya
Tracking SARS back to its source. This news brief traces the source of the SARS virus. Using phylogenetics, biologists have come up with a plausible path of transmission which may help us prevent future outbreaks of diseases such as HIV, SARS, and West Nile virus. http://evolution.berkeley.edu/evolibrary/news/060101_batsars
Tough conservation choices? Ask evolution. The Earth is facing a biodiversity crisis. Nearly 50% of animal and plant species could disappear within our lifetime. To stem this rapid loss of biodiversity, we’ll need to act quickly, but where should we begin? This news brief explains how evolutionary history can help us set conservation priorities. http://evolution.berkeley.edu/evolibrary/news/081201_phylogeneticconservation
In the Classroom
What did T. Rex taste like? In this web-based module for grades 6–12 from the UC Museum of Paleontology, students are introduced to cladistics, which organizes living things by common ancestry and evolutionary relationships. http://www.ucmp.berkeley.edu/education/explorations/tours/Trex/index.html
Nuts and bolts classification: arbitrary or not? In this lesson for grades 6–12 from the Evolution and the Nature of Science Institute, students working in teams classify furniture, share their categories and rationales, then note how their different schemes are perfectly logical and useful, but they vary and are completely arbitrary. They then see how living organisms are classified, and note how these natural groupings reflect the same ancestral relationships in the same nested hierarchies, regardless of the different criteria used. This concept is exemplified using primate phylogenetic trees. http://www.indiana.edu/~ensiweb/lessons/cl.intro.html
Classification and Evolution. In this lesson for grades 9–12 from Robert Gendron, students construct an evolutionary tree of imaginary animals (Caminalcules) to illustrate how modern classification schemes attempt to reflect evolutionary history. http://nsm1.nsm.iup.edu/rgendron/labs.shtml
Ask students to compare and contrast the phylogenetic reasoning used in the Catch a Killer and Mystery Meat examples to the phylogenetic reasoning underlying the Turn Back Time example.
Ask students to compare and contrast the phylogenetic reasoning used in the Turn Back Time example to that used in the story HIV’s Not-so-ancient History (http://evolution.berkeley.edu/evolibrary/news/081101_hivorigins).
Divide students into small groups and challenge each group to identify a case of phylogenetic reasoning in action and prepare a short presentation for the class.
The author wishes to thank Judy Scotchmoor for helpful comments on an earlier draft, as well as David Smith for help developing images.
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