Systematics: A Course of Lectures

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What Species Mean. Felines of the World. Bird Species. The Art of Naming. Phylogenetic Trees Made Easy. Shrews, Chromosomes and Speciation. The Evolutionary Biology of Species. Computational Phylogenetics. Phylogenies in Ecology. Other titles from Wiley.

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Tropical Rain Forests. Geological History of Britain and Ireland. Essentials of Tortoise Medicine and Surgery. Second, using real datasets that challenge students to apply scientific concepts and analysis is key to learning scientific thinking Wise and Okey, ; Soloway et al. These active-learning methods are often met with student confusion and resistance, especially if they have not learned this way before Gosser, ; Shetlar, 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, ; Hanauer et al.

Several new educational resources have emerged that specifically give attention to the methods and practice of the modern field of systematics Clough, ; Alles, ; Perry et al. 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. 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, ; Lombrozo et al. 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.

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All three activities were conducted in one 2. 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.

The three phylogeny-related exam questions referred to in the Assessment of the Activity section were as follows:. If two modern organisms are distantly related in an evolutionary sense, then one should expect that…. In evolutionary terms, the more closely related two different organisms are, the…. 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.

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. 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.

Phylogenetic trees - Evolution - Khan Academy

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. 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:. I agree with the scientific evidence that dates the earth to more than 4 billion years of age. Although some scientists claim otherwise, the earth is not more than 10, years old. I agree with the theory that, over the course of time, the positions of the great land masses continents have undergone many dramatic changes. 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.

I believe that, over many generations, natural selection has contributed to the gradual evolution of animals and plants into their present forms. 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. I feel that a large body of evidence supports the Darwinian theory of evolution by natural selection. I support the theory that the biological species, Homo sapiens Human beings evolved from an earlier species of primates.

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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. Because human beings are mammals, I believe that they have a shared ancestry with all other mammals. I believe that human beings descended to their present form through natural processes, including natural selection.

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. 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.

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.

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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. The complete student handout for this exercise is provided as Supplemental Material 1, while the complete instructor guide is provided as Supplemental Material 2.

In the first activity, students are given four short DNA sequences Ohta and Nishikimi, , shown in Figure 1 A, with a brief description. 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. 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. Examine the four gene sequences below and mark any differences among the sequences that you can find. Discuss the following questions with your lab partner: Do you notice any specific pattern?

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E&EB - Lecture 15 - Phylogeny and Systematics | Open Yale Courses

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. 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, ; Meadows et al.

The DNA sequences are derived from a pseudogene, which opens up an interesting discussion in itself Nishikimi and Yagi, ; Eyre-Walker and Keightley, As students begin to examine the DNA sequences, they have little trouble identifying the differences between the species, highlighted in Figure 1 B. 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.

Books A Course of Lectures Systematics

Eventually, students focus on the differences marked with asterisk in Figure 1 B, and nearly all student pairs draw a phylogram similar to that shown in Figure 1 C. 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 1 C is indeed the most parsimonious relationship based on these DNA sequences data not shown.