ASCB logo LSE Logo

Teaching the Process of Molecular Phylogeny and Systematics: A Multi-Part Inquiry-Based Exercise

    Published Online:https://doi.org/10.1187/cbe.09-10-0076

    Abstract

    Three approaches to molecular phylogenetics are demonstrated to biology students as they explore molecular data from Homo sapiens and four related primates. By analyzing DNA sequences, protein sequences, and chromosomal maps, students are repeatedly challenged to develop hypotheses regarding the ancestry of the five species. Although these exercises were designed to supplement and enhance classroom instruction on phylogeny, cladistics, and systematics in the context of a postsecondary majors-level introductory biology course, the activities themselves require very little prior student exposure to these topics. Thus, they are well suited for students in a wide range of educational levels, including a biology class at the secondary level. In implementing this exercise, we have observed measurable gains, both in student comprehension of molecular phylogeny and in their acceptance of modern evolutionary theory. By engaging students in modern phylogenetic activities, these students better understood how biologists are currently using molecular data to develop a more complete picture of the shared ancestry of all living things.

    INTRODUCTION

    Teaching fundamental mechanisms of evolution by natural selection is more important than ever, both to biology students and the general student population, and fresh pedagogical approaches to accomplish this are needed at all levels (Dagher and BouJaoude, 1997; Robbins and Roy, 2007; Labov and Kline Pope, 2008). Perhaps more than any other subdiscipline of biological sciences, the study of systematics tangibly and powerfully invokes the biological results of evolution and selection. Thus, its inclusion throughout all levels of the biology curriculum has long been strongly recommended. However, as powerfully argued by Rudolph and Stewart (1998), misunderstandings about evolution are largely philosophical, rooted in a poor understanding of the scientific method and how it applies to the study of natural history. Indeed, even advanced biology students can harbor striking misconceptions regarding the fundamental basis of evolutionary history (O'Hara, 1997; Robbins and Roy, 2007).

    This lack of fundamental understanding by students is compounded by the seemingly subtle differences among different systematic approaches. Phenetics seeks to classify organisms based on observable differences regardless of evolutionary history, while cladistics, which also examines observable characteristics, has the explicit goal of inferring shared ancestry and constructing a hierarchical classification. Molecular phylogenetics is similar to cladistics, but instead of relying on primitive and derived morphological characteristics, it uses molecular sequence data and other quantifiable measures to establish data matrices to infer likely evolutionary relationships. Further, there exists a variety of possible forms for expressing the results of systematic analyses: phylogenetic trees, cladograms, phylograms, dendograms, ultrametric trees, etc. Thus, it is not surprising that students sometimes fail to grasp the larger conceptual framework amid this disciplinary complexity.

    Explicitly teaching the process and nature of scientific research results in considerable learning gains, among science majors and nonmajors alike (Lederman, 1992, 1999; Lombrozo et al., 2008). The National Academy of Science (NAS) and the National Science Foundation (NSF) have explicitly called for the teaching of the practice of science within the existing science curricula, especially in relation to evolutionary theory (Alberts and Labov, 2004; Miller et al., 2006; Ayala, 2008). However, this pedagogical approach is not trivial to implement. First, there are at least two distinct conceptual frameworks to consider: the philosophical nature of the scientific pursuit, and the true-to-life realities of the modern scientific practice, which are markedly different among disciplines (Matthews, 1994; Rudolph and Stewart, 1998; Staver, 1998; Schwartz and Lederman, 2002). Second, using real datasets that challenge students to apply scientific concepts and analysis is key to learning scientific thinking (Wise and Okey, 1983; Soloway et al., 1999). These active-learning methods are often met with student confusion and resistance, especially if they have not learned this way before (Gosser, 2003; Shetlar, 2005). Considerably more effort and thought is required of students, compared with traditional passive learning approaches involving didactic lectures and protocol-driven laboratory exercises in which students simply follow clear experimental procedures and interpret data as instructed (Hofstein and Lunetta, 2004; Hanauer et al., 2006).

    Several new educational resources have emerged that specifically give attention to the methods and practice of the modern field of systematics (Clough, 1994; Alles, 2001; Perry et al., 2008). Because the majority of biology students don't properly grasp discrete information conveyed by a simple phylogenetic tree, groups including the “tree-thinking group” (http://tree-thinking.org) have resolved to develop resources and support for biology teachers at all levels (O'Hara, 1997; Baum et al., 2005). Other tools include the Understanding Evolution resource (http://evolution.berkeley.edu) from the University of California Museum of Paleontology in Berkeley, CA, resources from the NAS (www.nationalacademies.org/evolution/index.html), the Public Broadcasting Station (www.pbs.org/wgbh/evolution), and Visionlearning (visionlearning.com), which is funded by the NSF and the U.S. Department of Education.

    In designing the educational method described herein, we aimed to develop another teaching tool for demonstrating the modern practice of molecular phylogenetics by using actual datasets and challenging students to interpret those data using their own skills in deductive reasoning. We do this by providing DNA sequences, protein sequences, and chromosomal electron density maps of five closely related species, and then asking students to make simple hypotheses regarding the phylogeny of these species. There are several unique features of this approach. First, by having students participate in the scientific process of hypothesis-making, they gain familiarity with “what scientists do” with experimental data. Second, by engaging several types of data addressing the same underlying question, we demonstrate to students how scientists use multiple lines of evidence to support or refute hypotheses. Third, by exposing students to raw data that can be used to elucidate the common evolutionary origins of related species, we may break through resistance that some students have to evolution in general (Clough, 1994; Lombrozo et al., 2008; Perry et al., 2008). In our chosen method of implementation, unbeknownst to the students, the raw data they will be handling are taken from Homo sapiens and four closely related primates, thus shedding light on the biological origin of humanity. Fourth, the method that students will use, comparative genomics, is currently used by evolutionary biologists in exactly this context (Zhu et al., 2007), thus accurately “mimicking” a relevant and cutting-edge scientific practice.

    EXPERIMENTAL METHODS

    Student Assessment Groups

    Assessment took place in spring of 2009 in the course Biology 104 (Bio104), Principles of Modern Biology II, the second semester of the majors-track introductory biology course at John Jay College, a large, urban, minority-serving institution, and part of the City University of New York (CUNY) university system. All three activities were conducted in one 2.5-h laboratory session, with students working in their normal laboratory group (pairs). The laboratory took place after the second week of the course, immediately after the course lecture on phylogeny and systematics, which follows lectures on natural selection, micro- and macroevolution, speciation, and Hardy–Weinberg equilibrium. Two laboratory sections (28 students each) meet jointly for course lectures. For the assessment, both lab sections met with the same course instructor at the same time, thus providing for a case-controlled experimental design. One lab section completed the traditional laboratory exercise [chapters 20 and 21 of the Helms biology laboratory manual (Helms et al., 1998)] and is referred to as the control section, while the experimental section completed the exercises described herein.

    Performance on Exam Questions

    The three phylogeny-related exam questions referred to in the Assessment of the Activity section were as follows:

    Q1. If two modern organisms are distantly related in an evolutionary sense, then one should expect that…

    A1. they should share fewer homologous structures than two more closely related organisms.

    Q2. In evolutionary terms, the more closely related two different organisms are, the…

    A2. more recently they shared a common ancestor.

    Q3. The theory of evolution is most accurately described as…

    A3. an overarching explanation, supported by much evidence, for how populations change over time.

    These questions were given in multiple-choice format (other answer choices are available upon request), and the results shown in the Assessment of the Activity section represent the percentage in each group that selected the correct answer.

    Surveys Regarding Perceptions of Evolution

    The surveys used in this study (results shown Assessment of the Activity section) were devised and twice validated by administration to similar student sections in previous semesters and were deemed exempt from full panel review by the John Jay College Institutional Review Board (IRB). Several “control statements” were included regarding the acceptance of the scientific validity of current understandings of geologic time, which had shown in previous validations of this survey to be relatively stable in group responses before and after learning about evolution in detail. Next, we included a series of overlapping statements about 1) evolution, 2) natural selection, and 3) how those processes contributed to the emergence of Homo sapiens, which, in previous validations, had generated responses that were subject to change as students studied the mechanisms of evolution.

    For this survey, students were asked to report their acceptance of the statements on a five-point scale: strongly agree, agree, neither agree nor disagree, disagree, strongly disagree. Importantly, similar concepts were repeated in several variations, because studies have shown that students may key in to certain “trigger words” including theory, Darwin, evolution, scientists, and descent; and different wordings can lead to different survey results, even with the same students (Evans, 2001; Scott and Branch, 2009). For most statements, a response of “strongly agree” was scored as a “1” and indicated the strongest acceptance of current scientific theory, while a response of “strongly disagree” was scored as a “5” and indicated the strongest opposition to current scientific theory. However, three statements were expressed as “inverts,” such that agreement would indicate a rejection of currently accepted scientific theory. The numerical scoring of these questions was inverted to maintain the pattern that the lowest score indicates the strongest acceptance of scientific theory. The survey questions were as follows:

    Control Questions

    C1. I agree with the scientific evidence that dates the earth to more than 4 billion years of age.

    **C2. Although some scientists claim otherwise, the earth is not more than 10,000 years old.

    C3. I agree with the theory that, over the course of time, the positions of the great land masses (continents) have undergone many dramatic changes.

    Probative Questions

    **Q1. I believe that, with only a few exceptions, the life forms that exist on the planet today are, more or less, the same that have always been here since life first began on earth.

    Q2. I believe that, over many generations, natural selection has contributed to the gradual evolution of animals and plants into their present forms.

    **Q3. I believe that evolution by natural selection is just one theory about how life on earth came to its present form and I personally don't support it.

    Q4. I feel that a large body of evidence supports the Darwinian theory of evolution by natural selection.

    Q5. I support the theory that the biological species, Homo sapiens (Human beings) evolved from an earlier species of primates.

    Q6. I agree with Charles Darwin, who first suggested that the current form of human beings was influenced through the process of evolution by natural selection.

    Q7. Because human beings are mammals, I believe that they have a shared ancestry with all other mammals.

    Q8. I believe that human beings descended to their present form through natural processes, including natural selection.

    **=inverted statements; scoring is reversed.

    Survey responses were tabulated, scores for invert statements were reversed, and group patterns were analyzed. First, responses to the control questions were analyzed to ensure that the two groups were comparable. To assess changes in perception, we scrutinized pre- and posttreatment responses to identical questions and performed the following calculation on the “average group scores” (arithmetic mean) to individual questions: 100% × (pre − post)/pre. By placing the pretest values in the denominator, this formula normalizes for beginning differences in the two student groups and expresses change relative to the initial condition. Error bars were added to indicate relative variance in survey responses, as calculated by the following formula: (SD)/(average response) multiplied by the “percent change” score for that question for proper scaling.

    DESCRIPTION OF THE ACTIVITIES

    This activity, suitable for laboratory, discussion, or any other group work setting, is broken into three parts. Although common connections are drawn at the conclusion, each individual part could be done at different times or stand entirely on its own. Further, each part could be simplified, further extended to include a quantitative parsimony analysis, or otherwise modified, as explained within each description. Thus, these exercises are flexible and can accommodate many teaching environments. The driving theme is to provide actual scientific data to students and challenge them to draw conclusions about the data in ways that lead them to propose a hypothetical phylogram describing the evolutionary relatedness of the species involved. Although it may be best if these activities follow a lecture on systematics that covers the differences between cladistics and phylogenetics, as we have done, this may not be strictly essential and a short primer on systematics (see www.ncbi.nlm.nih.gov/About/primer/phylo.html) might suffice, depending on the academic background of the students. The complete student handout for this exercise is provided as Supplemental Material 1, while the complete instructor guide is provided as Supplemental Material 2.

    Activity One: Molecular Phylogenetics Using a Pseudogene

    In the first activity, students are given four short DNA sequences (Ohta and Nishikimi, 1999), shown in Figure 1A, with a brief description.

    Figure 1.

    Figure 1. (A) Aligned genomic DNA sequences from the GULO pseudogene taken from the short arm of chromosome %8 (8p21 in humans) of the following species: %1 = Pan troglodytes, %2 = Pongo pygmaeus, %3 = Homo sapiens, and %4 = Macaca mulatta. (B) The discrete nucleotide differences among the four DNA sequences have been highlighted. The asterisks indicate key positions that help reveal ancestry. (C) The most likely phylogram indicating the ancestry and divergence of the species based on these DNA sequences.

    • Below are four gene sequences. These are taken from four animals that are believed to have “recent shared ancestry” (are closely related).

    • The gene sequences are from a so-called “broken gene” or pseudogene, the evolutionary remnant of a gene, which is now nonfunctional, in a given species or group of related species. In this case, the gene is called GULO (L-gulonolactone oxidase), which codes for the enzyme which catalyzes a key step in the synthesis of ascorbic acid (vitamin C). Along the way, some animals have lost the function of this gene (by random mutation) and must consume vitamin C in their diet.

    Procedure

    1. Examine the four gene sequences below and mark any differences among the sequences that you can find.

    2. Discuss the following questions with your lab partner: Do you notice any specific pattern? What could this pattern mean regarding the ancestry/relatedness of the four species?

    3. Together with your lab partner, make a hypothesis about the ancestry of these four species in the form of a phylogenetic tree. Draw this tree on a separate sheet of paper and make a few notes explaining why you drew it this way.

    In an effort to reduce intellectual resistance to the topic, we elect not to reveal the identity of the species until all activities are complete (Lombrozo et al., 2008). Studies have shown that many self-identified Christians in the United States have brokered a psychological compromise between science and faith by accepting the validity of geologic time and evolutionary change but maintaining that these processes had little to do with the divinely instituted emergence of Homo sapiens (Smith, 1994; Meadows et al., 2000; Miller et al., 2006). The DNA sequences are derived from a pseudogene, which opens up an interesting discussion in itself (Nishikimi and Yagi, 1991; Eyre-Walker and Keightley, 1999). As students begin to examine the DNA sequences, they have little trouble identifying the differences between the species, highlighted in Figure 1B. However, if students are then unsure what to do next, we let them wander through the initial confusion and discuss how to approach the problem with their lab partner and other classmates, reinforcing the collaborative nature of scientific research. Eventually, students focus on the differences marked with asterisk in Figure 1B, and nearly all student pairs draw a phylogram similar to that shown in Figure 1C. A quantitative analysis of parsimony might enrich this activity significantly for more advanced students. Based upon such a quantitative parsimony analysis, the phylogram shown in Figure 1C is indeed the most parsimonious relationship based on these DNA sequences (data not shown).

    Activity Two: Amino Acid Sequences of Functional Homologous Proteins

    In this activity, we present students with sequences from related species and challenge them to deduce a phylogram. However, this exercise is more complicated because there are sequences provided from five species, and students are provided with the amino acid sequences of a functional protein, chromosome-encoded SCML1 protein that functions in male embryonic development and male fertility (van de Vosse et al., 1998; Wu and Su, 2008). Because mutation and evolutionary change are more “constrained” in a protein sequence (Nachman and Crowell, 2000), these sequences utilize the “…/…” symbol to denote long stretches of protein sequence with no differences in amino acids. This opens a discussion of different silent mutations that might be present in these species, both of the wobble and intronic variety. The five sequences provided to students are shown in Figure 2A (Wu and Su, 2008).

    Figure 2.

    Figure 2. (A) Aligned amino acid sequences from the SCML1 gene product of the following species: %1 = Homo sapiens, %2 = Pan troglodytes, %3 = Gorilla gorilla, %4 = Pongo pygmaeus, and %5 = Macaca mulatta. The symbol …/… indicates a long stretch of amino acids with no differences among the species. (B) The discrete amino acid differences among the five protein sequences have been highlighted. The asterisks indicate key positions that help reveal ancestry. (C) The two most likely phylograms indicating the first (most distant) divergence of the species based on these protein sequences. (D) The two most likely complete phylograms indicating the ancestry of the species based on these protein sequences.

    The differences between the homologous sequences, highlighted in black in Figure 2B, are more numerous in this activity, but because of the practice they had in activity one, students are more prepared to “see through the noise” and ignore instances in which one species has a unique amino acid at a certain position. Another new challenge faced by students in this activity is the inclusion of data from five species, instead of just four, which will require a more complicated phylogram. Although most of the student groups will notice the early divergence of the ancestor of %1 and %2, from the ancestor of %4 and %5, these same groups are often split evenly regarding which side of the branch point includes the most recent unique ancestor of species %3. Thus, most students begin by constructing their phylograms according to one of the options shown in Figure 2C, evenly split between the two possibilities.

    The fact that two hypothetical phylograms are nearly equally likely provides a good teaching moment as this introduces the nature of scientific controversy and debate. We encourage students to present data for their position, and we have observed that some lab groups argue strongly that, using the positions marked with an asterisk in Figure 2B, there are three examples of species %3 being similar to %1 and %2, and only two examples when %3 is similar to %4 and %5. Because three is more than two, this does argue, albeit weakly, that the convergence of species %3 from %1 and %2 was more recent than its divergence from %4 and %5. This opens a discussion of “weight of evidence” and the need for much larger sets of sequence data, from many genes, to build stronger hypotheses. Further still, this provides a nice segue to the next activity, which is a wholly different method of analysis, and how scientific research relies on multiple lines of evidence from different methodologies, resulting in an inherently self-correcting march toward a more detailed understanding of the natural world.

    Activity Three: Electron Density Maps of Chromosomes

    In the final activity, students are given chromosomal maps (cytogenetic ideograms) of a few of the larger chromosomes from four different species (Murphy et al., 2005). This opens up a short discussion about euchromatin versus heterochromatin, and how and why some DNA is kept “silent” (Yunis and Prakash, 1982). The maps are shown in Figure 3A and are provided to students with the chromosomes clearly arranged by species. Students are instructed to cut each chromosome out and compare them to each other in a search for homologous chromosomes shared by all four species. After some time, most student groups identify the three sets of homologues shared by all species (Figure 3B).

    Figure 3.

    Figure 3. (A) Chromosomal maps (cytogenetic ideograms) for assorted chromosomes from the following species: %1 = Pan troglodytes, %2 = Pongo pygmaeus, %3 = Gorilla gorilla, and %4 = Homo sapiens. (B) The same chromosomes, but arranged by homologues that are shared by all four species. (C) The two most likely phylograms indicating the first (most distant) divergence of the species based on the degree of similarity among the chromosomal maps of the homologues. (D) The two most likely complete phylograms indicating the ancestry of the species based on the chromosomal maps. (E) A cladogram showing the ancestry expressed in 3D. (F) The arrangement of chromosomes showing how species %4 has one unique chromosome with two long arms, each of which shares substantial similarity with other chromosomes from the other species. This is evidence that this long chromosome in species %4 is actually the result of a chromosomal fusion of two smaller ancestral chromosomes.

    Concentrating only on the three sets of homologues, students are challenged to make qualitative comparisons about the similarities and shared features of the homologues, and in so doing, infer the relatedness of the four species. Through a process of hypothesis testing, the students work through the three sets of four homologous chromosomes and most come to recognize that species %1 and %4 are markedly more similar to each other than to the others, and the same is true for species %2 and %3. Thus, most students begin their phylogram as shown in Figure 3C. However, before the students simply further branch the two sides into symmetrical final branches, a new challenge is given. Students are asked to make a hypothesis regarding which divergence occurred more recently. In other words, students were asked to return to the sets of homologues and make qualitative judgments regarding which pair shows more similarity in their chromosome heat maps: %1 with %4 or %2 with %3. Such patterns of similarity can provide one line of evidence regarding the relative relatedness of the species in terms of evolutionary time (Nachman and Crowell, 2000; Murphy et al., 2005).

    Importantly, each student group will attack this problem with a slightly different approach and this diversity of methodology is encouraged—there is no “right way” to solve the problem and no “answer key” that will verify the correct answer. This reflects how science really works: We speak in “weight of the evidence” and theories that are supported by “multiple lines of reasoning,” not in the absolutes of “correct answers” and foregone conclusions. Additionally, the challenge of deducing relative age of the branch points (Figure 3D) in this exercise provides a nice opportunity to connect with another common way of representing evolutionary relationships: the cladogram. Although cladograms are usually constructed based on shared and derived characteristics, they share with phylograms the fundamental basis of evolution and shared ancestry. Thus, students gain important understanding by learning how to interpret both. Figure 3E shows a cladogram that expresses the conclusion that the divergence between species %2 and %3 occurred earlier than the divergence between species %1 and %4.

    Following the construction of the phylograms, but before we move to the final discussion, we “resurrect” the outlier chromosomes previously set aside because they did not form part of a homologue set shared by all species. It is obvious that the real outlier is the very long chromosome from species %4. We ask students to set this chromosome in front of them and compare to the other outlier chromosomes, especially those from the species that is most related, which they now know is species %1. The realization being sought is that the lone outlier chromosome from species %4, which has no homologue in the other species, has regions of very substantial similarity with two of the other outlier chromosomes from the other species, as shown in Figure 3F. Ayala and Coluzzi (2005) inferred that an ancestor of species %4 possibly suffered a mitotic catastrophe that was repaired erroneously through the fusion of two different chromosomes together. This opens a discussion of chromosomal breakage and repair phenomena such as fusions, translocations, etc.

    Because the activities are now finished and the session is about to proceed to the postlab discussion, this is a perfect opportunity to “break the code” and tell the students that “species %4” in activity three is actually Homo sapiens. Humans indeed have one fewer pair of chromosomes (23) than all other living primates (Zhu et al., 2007). From these analyses, scientists have concluded that the second longest human chromosome is actually the result of a fusion between two smaller chromosomes (%12 and %13 in chimps and great apes), which occurred in a primate ancestor of humans within the last 3 million years (Ijdo et al., 1991). This conclusion is strongly supported by extensive DNA evidence, such as the presence of two telomere-like stretches arranged end-to-end within chromosome %2 and the remnants of an additional centromere (Wienberg et al., 1994; Navarro and Barton, 2003; Zhang et al., 2004). All of these concepts, especially if they have previously been covered in lecture, provide an excellent discussion with the students to connect this exercise to other material covered in introductory biology.

    The Postactivity Discussion

    The discussion at the end of the activity is crucial for “driving home” the main points of this pedagogical method. Several points should be explicitly stressed during this discussion (see Supplemental Material 2). First, the sequences shown in Figure 1, A and B were selected for this exercise essentially at random. There is no reason to think that these genes are somehow exceptional and that selecting other genes would paint a significantly different picture. In fact, if an Internet connection is available, these sequences can actually be used to break the code of which species is which, using the BLAST bioinformatics search tool at the National Library of Medicine's website (http://blast.ncbi.nlm.nih.gov/Blast.cgi). This means that the hypothetical phylograms built in activity one can now be redrawn with the species names shown in Figure 4A.

    Figure 4.

    Figure 4. (A) The phylograms derived from the three exercises with the species identities revealed. (B) A representative cladogram expressing the current scientific consensus regarding the shared ancestry of the five genera examined in this exercise.

    The second activity involves five species, and once again the protein sequences shown in Figure 2 are real, and the identity of these can be revealed through a protein BLAST search. At this point in the discussion, we point out that the SCML1 protein sequences and the GULO pseudogene sequences both led students to conclude that humans and chimpanzees are more related to each other than to macaque and orangutan and vice versa. This reinforces the concept of “multiple lines of evidence.” However, because gorilla was not included, the activity one phylograms cannot help resolve the unanswered question of how gorilla best fits into the evolutionary scheme. For evidence on this question, we move on to activity three.

    For activity three, one cannot easily do a bioinformatics search with the chromosome maps. However, an Internet search with the terms “chromosome map [species name]” will show similar examples of these maps so that students can see that these are indeed real maps from these four species. Further, with the addition of the third phylogram, students can now address the question left unresolved from activity two—where gorillas fit into the evolutionary scheme of the apes. The annotated phylogram shown in Figure 4A argues that gorilla and orangutan share a more recent common ancestor than gorilla does with humans and chimps. Thus, the students can return to the sequence data from activity two and observe that, although there were three incidents of gorilla sequence matching humans and chimps and only two where the gorilla sequenced matched with the orangutan and macaque sequence, the chromosome density maps argue that the gorilla is more closely related to orangutans than to humans or chimps. This demonstrates the need for more and longer sequences for comparisons and how evolutionary relationships are explored through many overlapping methods in order to reach a more solidly founded conclusion.

    At this point in the discussion, it is often powerful to demonstrate how the phylograms constructed by the students compare with phylograms drawn by experts in the evolutionary biology of apes and humans (Zhu et al., 2007). If an Internet connection is present, simple Internet searches for “phylogram [species names]” will produce hits that link to different phylograms. Importantly, many different phylograms will be found, with different groupings based on which species and taxonomic groups are included. This helps to underscore the concept that phylograms are drawn to express relationships between species of interest: they are not meant to be all-inclusive. Figure 4B shows the current scientific consensus regarding the evolutionary history of the five genera involved in this activity.

    ASSESSMENT OF THE ACTIVITY

    As this activity was designed, implemented, and refined, we took efforts to assess the degree to which it accomplishes the original goal of gains in student learning through explicitly engaging the scientific process. Toward that end, we monitored several aspects of the student experience. First, each term we collected student work and assessed how successful they were at completing each activity as expected. This resulted in substantial revisions of the activity worksheets and refinement of the activity itself. These revisions to the exercise improved the students' ability to understand and complete the challenges such that, in the present form, the success rate is >80%, >70%, and >60%, respectively, for the three activities (data not shown). The lower rate of success indicates progressively challenging activities, but we observe that even students who are unable to reach the expected conclusions on their own are able to comprehend the methodologies during the postactivity discussions. We have wondered whether guided inquiry or a problem-based research approach assist the students with these challenges.

    A second form of assessment that we analyzed was the performance on lecture exam questions related to this topic. For this comparison, we arranged a case-control experimental design and two different sections of Bio104 were selected. Both groups had 28 students and the same instructor for the lecture part of the course, in which all course topics are taught. The control group completed a traditional laboratory exercise on evolution, phylogeny, and classification: chapters 20 and 21 of Biology in the Laboratory (Helms et al., 1998), while the experimental group completed the exercise described here. Then, we compared performance on the course exam, which is common among all sections and is relatively unchanged year to year.

    As Figure 5A shows, the two groups' general exam scores indicate that the control group was composed of measurably higher-performing students than the experimental group. However, because this difference is <10% and within the 95% confidence interval for each group, we considered the groups comparable for the purposes of this assessment. We identified three questions on exam one that specifically address the issue of phylogenetics and the deduction of evolutionary relationships (described in Experimental Methods). Importantly, both groups were taught this material by the same instructor, and both groups worked from the same textbook, from which these three questions derived (Biology, 7th ed. (Campbell and Reece, 2005). Figure 5A shows that, despite scoring lower on the exam overall, the experimental section slightly outperformed the control group on all three of these select exam questions. Although these differences are not dramatic, they are consistent, especially when considering that phylogeny was just one concept on an exam covering four weeks' worth of material.

    Figure 5.

    Figure 5. (A) Performance of the control and experimental sections of students on all course exams, the first exam, both with error bars indicating the 95% confidence interval, together with three specific exam questions that explicitly test comprehension of phylogeny and natural selection. (B) Percent change of average student responses to eight questions on a pre- and posttest survey measuring acceptance of the modern theory of evolution by natural selection. Positive values indicate an overall group change toward more acceptance of modern evolutionary theory, while negative values indicate change toward less acceptance. The text of the survey questions and a description of the calculations are found in the Experimental Methods.

    Finally, we performed a third mode of assessment aimed at inferring student perceptions regarding evolution. As part of an ongoing assessment project regarding teaching the process and nature of science, we utilized pre- and postsurveys to scrutinize student perceptions regarding the scientific theory of evolution by natural selection, how those perceptions are affected by learning more about the theory in a formal biology course, and what role, if any, this activity plays in the alteration of those perceptions. For this inquiry, we used the same control and experimental groups described above. At the beginning of the semester, both groups were given a survey instrument previously validated to reveal student perceptions regarding evolution and natural selection. Then, both groups were surveyed again 2 wk after the first examination, which was thus 1 mo after the execution of this experimental laboratory activity. More detail regarding the composition and scoring of the survey instrument is included in the Experimental Methods section. Briefly, all survey responses were scaled 1–5 and calculations were performed to yield a “percent change” value for each question, with a positive value indicating an increase in acceptance of the scientific theory of evolution by natural selection.

    As seen in Figure 5B, a noticeable difference between the two groups was observed. In the control group, depending on the particular question, group responses sometimes reflected slightly increased acceptance of evolution and sometimes indicated slightly decreased acceptance of evolution. The experimental group, however, responded to instruction about evolution in a dramatically more consistent manner. Regardless of the question, the average scores on all questions concerning the acceptance of evolution showed an upward deflection, indicating that, as a whole, the group more consistently came to accept the scientific validity of modern evolutionary theory. This provides support for a breakthrough study (Lombrozo et al., 2008) that found that student perceptions and acceptance of the theory of evolution are directly impacted by their understanding of the nature and process of science and research.

    CONCLUSIONS

    The inquiry-based student activity described herein is a novel approach toward the instruction of the practice of molecular phylogeny and systematics. Such approaches are strongly mandated, both because of recent threats to proper biology education in our country due to poor understanding of evolutionary theory (Miller et al., 2006; Ayala, 2008) and because this approach has been shown to be more effective than traditional approaches to teaching (O'Hara, 1997; Robbins and Roy, 2007; Lombrozo et al., 2008). Although the skills that are required and reinforced by this group exercise are part and parcel of most any introductory biology curriculum, these activities may also be applicable to students in biology courses at the nonmajor and even secondary education levels. No advanced quantitative skills are necessary, nor is a high-level understanding of molecular biology or evolutionary theory. In fact, these exercises are designed to help enlighten these very concepts to students.

    Educators who use educational innovations involving student-centered learning modalities have often encountered student resistance (Giroux, 2001). This has been specifically noted in various inquiry-based methods in science education (Anderson, 2002; Hofstein and Lunetta, 2004) and in efforts to explicitly teach the process and nature of science (McComas et al., 2006). Indeed, in our implementation of these activities, we encountered some initial resistance among our students. This is not surprising, given that introductory science students are often accustomed to being given precise experimental protocols and being told exactly how to proceed in their laboratory courses. Thus, the resistance and confusion we observed was generally limited to the first initiation of the activity as students are instructed to examine the DNA sequences in activity one. During this period, we consider it crucial that the instructor not give in and simply walk them through the activity. One of they key features of our educational approach is that students must actively consider the data, contrive different possible methods of analysis, and decide on the strategy they think is best. That there may be a multitude of approaches used by a given class of students is a strength of inquiry-based learning, helping students learn to think for themselves regarding the interpretation of data (Hanauer et al., 2006).

    By completing these exercises, students will mimic the scientific process engaged by contemporary biologists. First of all, the technique of comparative genomics is at the forefront of evolutionary biology, anthropology, structural and molecular biology, and even medical genetics. The first activity provides students with a familiarity of concepts and techniques that they are likely to read or hear about in reports of scientific discoveries in scientific journals and the popular press. Second, students also execute several distinct comparisons, with completely different sources of data, in an effort to explore a single concept: the descent of humankind from primate ancestors. This underscores the scientific practice of pursuing multiple lines of evidence when approaching unresolved scientific questions. Third, the collaborative, cooperative nature of science is illustrated because students are encouraged to work in small groups but also collaborate with other groups. Fourth and perhaps most important, in these exercises, students are not working toward a preconceived conclusion, using a predetermined series of steps, only to reveal something that they probably already learned about as a “known fact.” Instead, students are encouraged to use their prior scientific knowledge, design their own approaches, draw their own unique conclusions, and identify the data that support those conclusions. Such pedagogical approaches have been shown in a variety of contexts to facilitate significant gains not just in content learning but in the understanding and internalization of broad concepts.

    In addition, by withholding the identities of the species in question, students who may have been resistant to the concept of human evolution from primate ancestors are encouraged to let their guard down and work freely on the project at hand. While this aspect of the exercise is by no means required, it is our hypothesis that this could help break through the psychological resistance that some students have to the biological understanding of human origins. We are bolstered in that belief by our survey results, which reveal that, on average, students who explore the concept of phylogeny in this manner are more likely to make gains in their acceptance of modern evolutionary theory than those who complete a more traditional laboratory exercise. We hope that this laboratory exercise will inspire further such approaches and that the arsenal of process-oriented inquiry-based tools for teaching evolutionary theory will continue to grow. In so doing, we can help reverse some of the disturbing trends regarding public acceptance of evolutionary theory, as well as help to educate more budding young scientists about the true nature, process, and practice of science.

    ACKNOWLEDGMENTS

    For this work, N.H.L. was supported by the CCRAA-HSI program of the U.S. Department of Education (grant P031C080210) and A.C. was supported by the FIPSE program of the U.S. Department of Education (grant P116B060183).

    The authors thank Daniel Cocris and Ron Pilette for their crucial help in launching, assessing, and refining these activities.

    REFERENCES

  • Alberts and Labov, 2004 Alberts B., Labov J. B. (2004). From the National Academies: teaching the science of evolution. Cell Biol. Educ. 3, 75-80. LinkGoogle Scholar
  • Alles, 2001 Alles D. L. (2001). Using evolution as the framework for teaching biology. Am Biol. Teach. 63, 20-23. Google Scholar
  • Anderson, 2002 Anderson R. D. (2002). Reforming science teaching: what research says about inquiry. J. Sci. Teach. Educ. 13, 1-12. Google Scholar
  • Ayala, 2008 Ayala F. J. (2008). Science, evolution, and creationism. Proc. Natl. Acad. Sci. USA. 105, 3. MedlineGoogle Scholar
  • Ayala and Coluzzi, 2005 Ayala F.J., Coluzzi M. (2005). Chromosome speciation: humans, Drosophila, and mosquitoes. Proc. Natl. Acad. Sci. USA. 102, 6535-6542. MedlineGoogle Scholar
  • Baum et al., 2005 Baum D. A., Smith S. D., Donovan S.S.S. (2005). EVOLUTION: The tree-thinking challenge. Science 310, 979-980. MedlineGoogle Scholar
  • Campbell and Reece, 2005 Campbell N.A., Reece J.B. (2005). Biology, 7th ed. San Francisco: Pearson Education. Google Scholar
  • Clough, 1994 Clough M.P. (1994). Diminish students' resistance to biological evolution. Am. Biol. Teach. 56, 409-415. Google Scholar
  • Dagher and BouJaoude, 1997 Dagher Z.R., BouJaoude S. (1997). Scientific views and religious beliefs of college students: the case of biological evolution. J. Res. Sci. Teach. 34, 429-445. Google Scholar
  • Evans, 2001 Evans E. M. (2001). Cognitive and contextual factors in the emergence of diverse belief systems: creation versus evolution. Cogn. Psychol. 42, 217-266. MedlineGoogle Scholar
  • Eyre-Walker and Keightley, 1999 Eyre-Walker A., Keightley P. D. (1999). High genomic deleterious mutation rates in hominids. Nature 397, 344-347. MedlineGoogle Scholar
  • Giroux, 2001 Giroux H.A. (2001). Theory and Resistance in Education: Towards a Pedagogy for the Opposition, Santa Barbara, CA: Greenwood Publishing Group. Google Scholar
  • Gosser, 2003 Gosser D. K. (2003). Dynamics of peer-assisted active learning. Abstracts of Papers of the American Chemical Society 226, U258-U258. Google Scholar
  • Hanauer et al., 2006 Hanauer D. I., Jacobs-Sera D., Pedulla M. L., Cresawn S. G., Hendrix R. W., Hatfull G. F. (2006). Inquiry learning: teaching scientific inquiry. Science 314, 1880. MedlineGoogle Scholar
  • Helms et al., 1998 Helms D. R., Helms C. W., Kosinski R. J., Cumings J. R. (1998). Biology in the Laboratory, New York: WH Freeman. Google Scholar
  • Hofstein and Lunetta, 2004 Hofstein A., Lunetta V. N. (2004). The laboratory in science education: foundations for the twenty-first century. Sci. Educ. 88, 28-54. Google Scholar
  • Ijdo et al., 1991 Ijdo J. W., Baldini A., Ward D. C., Reeders S. T., Wells R. A. (1991). Origin of human chromosome 2, an ancestral telomere-telomere fusion. Proc. Natl. Acad. Sci. USA. 88, 9051-9055. MedlineGoogle Scholar
  • Labov and Kline Pope, 2008 Labov J. B., Kline Pope B. (2008). Understanding our audiences: the design and evolution of science, evolution, and creationism. CBE Life Sci. Educ. 7, 20-24. LinkGoogle Scholar
  • Lederman, 1992 Lederman N. G. (1992). Students' and teachers' conceptions of the nature of science: a review of the research. J. Res. Sci. Teach. 29, 331-359. Google Scholar
  • Lederman, 1999 Lederman N. G. (1999). Teachers'understanding of the nature of science and classroom practice: factors that facilitate or impede the relationship. J. Res. Sci. Teach. 36, 916-929. Google Scholar
  • Lombrozo et al., 2008 Lombrozo T., Thanukos A., Weisberg M. (2008). The importance of understanding the nature of science for accepting evolution. Evol. Educ. Outreach. 1, 290-298. Google Scholar
  • Matthews, 1994 Matthews M. R. (1994). Science Teaching: The Role of History and Philosophy of Science, New York: Routledge. Google Scholar
  • McComas et al., 2006 McComas W. F., Clough M. P., Almazroa H. (2006). The role and character of the nature of science in science education. Sci. Educ. 7, 511-532. Google Scholar
  • Meadows et al., 2000 Meadows L., Doster E., Jackson D. F. (2000). Managing the conflict between evolution and religion. Am. Biol. Teach. 62, 102-107. Google Scholar
  • Miller et al., 2006 Miller J. D., Scott E. C., Okamoto S. (2006). Public acceptance of evolution. Science 313, 765-766. MedlineGoogle Scholar
  • Murphy, 2005 Murphy W. J. , et al. (2005). Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Am. Assoc. Adv. Sci. 309, 613-617. Google Scholar
  • Nachman and Crowell, 2000 Nachman M. W., Crowell S. L. (2000). Estimate of the mutation rate per nucleotide in humans. Genetics 156, 297-304. MedlineGoogle Scholar
  • Navarro and Barton, 2003 Navarro A., Barton N. H. (2003). Chromosomal speciation and molecular divergence-accelerated evolution in rearranged chromosomes. Science 300, 321-324. MedlineGoogle Scholar
  • Nishikimi and Yagi, 1991 Nishikimi M., Yagi K. (1991). Molecular basis for the deficiency in humans of gulonolactone oxidase, a key enzyme for ascorbic acid biosynthesis. Am. J. Clin. Nutr. 54, 1203-1208. Google Scholar
  • O'Hara, 1997 O'Hara R. J. (1997). Population thinking and tree thinking in systematics. Zoologica Scripta 26, 323-329. Google Scholar
  • Ohta and Nishikimi, 1999 Ohta Y., Nishikimi M. (1999). Random nucleotide substitutions in primate nonfunctional gene for Image-gulono-lactone oxidase, the missing enzyme in Image-ascorbic acid biosynthesis. Biochim. Biophys. Acta. 1472, 408-411. MedlineGoogle Scholar
  • Perry et al., 2008 Perry J., Meir E., Herron J. C., Maruca S., Stal D. (2008). Evaluating two approaches to helping college students understand evolutionary trees through diagramming tasks. CBE Life Sci. Educ. 7, 193-201. LinkGoogle Scholar
  • Robbins and Roy, 2007 Robbins J. R., Roy P. (2007). The natural selection: identifying and correcting non-science student preconceptions through an inquiry-based, critical approach to evolution. Am. Biol. Teach. 69, 460-466. Google Scholar
  • Rudolph and Stewart, 1998 Rudolph J. L., Stewart J. (1998). Evolution and the nature of science: on the historical discord and its implications for education. J. Res. Sci. Teach. 35, 1069-1089. Google Scholar
  • Schwartz and Lederman, 2002 Schwartz R. S., Lederman N. G. (2002). “ It's the nature of the beast”: the influence of knowledge and intentions on learning and teaching nature of science. J. Res. Sci. Teach. 39, 205-236. Google Scholar
  • Scott and Branch, 2009 Scott E. C., Branch G. (2009). Don't call it “Darwinism.” Evol. Educ. Outreach. 2, 90-94. Google Scholar
  • Shetlar, 2005 Shetlar R. (2005). The effect of active learning strategies in undergraduate biology education. Integr. Comp. Biol. 45, 1193-1193. Google Scholar
  • Smith, 1994 Smith M. U. (1994). Counterpoint: belief, understanding, and the teaching of evolution. J. Res. Sci. Teach. 31, 591-597. Google Scholar
  • Soloway et al., 1999 Soloway E., Grant W., Tinger R., Roschelle J., Mills M., Resnick M., Berg R., Eisenberg M. (1999). Log on education: science in the palms of their hands. Commun. ACM. 42, 21-26. Google Scholar
  • Staver, 1998 Staver J. R. (1998). Constructivism: sound theory for explicating the practice of science and science teaching. J. Res. Sci. Teach. 35, 501-520. Google Scholar
  • van de Vosse, 1998 van de Vosse E. , et al. (1998). Characterization ofSCML1, a new gene in Xp22, with homology to developmental polycomb genes. Genomics 49, 96-102. MedlineGoogle Scholar
  • Wienberg et al., 1994 Wienberg J., Jauch A., Lüdecke H. J., Senger G., Horsthemke B., Claussen U., Cremer T., Arnold N., Lengauer C. (1994). The origin of human chromosome 2 analyzed by comparative chromosome mapping with a DNA microlibrary. Chromosome Res 2, 405-410. MedlineGoogle Scholar
  • Wise and Okey, 1983 Wise K. C., Okey J. R. (1983). A meta-analysis of the effects of various science teaching strategies on achievement. J. Res. Sci. Teach. 20, 419-435. Google Scholar
  • Wu and Su, 2008 Wu H., Su B. (2008). Adaptive evolution of SCML 1 in primates, a gene involved in male reproduction. BMC Evol. Biol. 8, 192. MedlineGoogle Scholar
  • Yunis and Prakash, 1982 Yunis J. J., Prakash O. (1982). The origin of man: a chromosomal pictorial legacy. Science 215, 1525-1530. MedlineGoogle Scholar
  • Zhang et al., 2004 Zhang J., Wang X., Podlaha O. (2004). Testing the Chromosomal Speciation Hypothesis for Humans and Chimpanzees, vol. 14 Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 845-851. Google Scholar
  • Zhu et al., 2007 Zhu J., Sanborn J. Z., Diekhans M., Lowe C. B., Pringle T. H., Haussler D. (2007). Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput. Biol. 3, e247. MedlineGoogle Scholar