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Introductory Activities TEACHER’S GUIDE Introduction Dean Madden Introductory NCBE, University of Reading activities Version 1.0 CaseCase Studies introduction Introductory activities The activities in this section explain the basic principles behind the construction of phylogenetic trees, DNA structure and sequence alignment. Students are also intoduced to the Geneious software. Before carrying out the activities in the DNA to Darwin Case studies, students will need to understand: • the basic principles behind the construction of an evolutionary tree or phylogeny; • the basic structure of DNA and proteins; • the reasons for and the principle of alignment; • use of some features of the Geneious computer software (basic version). The activities in this introduction are designed to achieve this. Some of them will reinforce what students may already know; others involve new concepts. The material includes extension activities for more able students. Evolutionary trees In 1837, 12 years before the publication of On the Origin of Species, Charles Darwin famously drew an evolutionary tree in one of his notebooks. The Origin also included a diagram of an evolutionary tree — the only illustration in the book. Two years before, Darwin had written to his friend Thomas Henry Huxley, saying: ‘The time will come, I believe, though I shall not live to see it, when we shall have fairly true genealogical trees of each great kingdom of Nature.’ Today, scientists are trying to produce the ‘Tree of Life’ Darwin foresaw, using protein, DNA and RNA sequence data. Evolutionary trees are covered on pages 2–7 of the Student’s guide and in the PowerPoint and Keynote slide presentations. Page 3 of the Student’s guide is the instructions for making the tree from biscuits. DNA and protein structure Although this is well-covered in all relevant textbooks, a DNA model and animated (QuickTime) slideshow of DNA structure are provided. Sequence alignment This is shown using an animated QuickTime( ) slideshow. Copyright © Dean Madden, 2011 2 www.dnadarwin.org introduction 1. Evolutionary trees This activity introduces students to the use of tree diagrams (phylogenies) to show evolutionary relationships. General reading The making of the fittest. DNA and the ultimate forensic record of evolution by Sean B. Carroll (2009) Quercus Books (Paperback) ISBN: 978 1847247247. A popular lay account of some of the molecular evidence for evolution. Reading the story in DNA: A beginner’s guide to molecular evolution by Lindell Bromham (2008) Oxford University Press (Paperback) ISBN: 978 0199290918. An engaging textbook on molecular evolution, which assumes no specialist mathematical knowledge and takes the reader from first principles. A science primer. Just the facts: A basic introduction to the science underlying NCBI resources (2004) National Center for Biotechnology Information. This document from the National Center for Biotechnology Information in the USA, provides a clear introduction to the principles of systematics and molecular phylogenetics. It can be read on-line at: http://www.ncbi.nlm.nih.gov/ About/primer/phylo.html Scientific publications These papers can be accessed free-of-charge, online. Evolution of the domestic cat Johnson, W. E. et al (2006) The late Miocene radiation of modern Felidae: A genetic assessment. Science 311, 73–77. doi: 10.1126/science.1122277 Driscoll, C. A. et al (2007) The Near Eastern origin of cat domestication. Science 317, 519–523. doi: 10.1126/science.1139518 Re-evolution of teeth in the marsupial frog, Gastrotheca guentheri Wiens, J. J. (2011) Re-evolution of lost mandibular teeth in frogs after more than 200 million years, and re-evaluating Dollo’s Law. Evolution (online advance publication). doi: 10.1111/j.1558-5646.2011.01221.x Requirements Each student or working group will need: • cut-outs of the biscuits on page 6 of this document (these could be laminated for re-use) • a sheet of A3 paper • a ruler and pencil or pen • copies of worksheets. Copyright © Dean Madden, 2011 3 www.dnadarwin.org introduction Presentations Teachers may find the PowerPoint or Keynote presentation helpful for introducing this exercise. Educational aims The activity introduces the concept of showing evolutionary relationships in a tree diagram (phylogeny). The ‘biscuit’ activity can be used as a diagnositic tool to evaluate students’ understanding of evolution, before or after teaching the subject. It emphasises how phylogenies based on phenotype alone can be misleading and introduces the concept of generating evolutionary trees based on nucleic acid and protein sequence data. The Extension material on pages 5 and 6 can be used for more able students or as homework. Prequisite knowledge Some knowledge of the basic concepts of evolution, including selection and speciation, would be useful. It is also helpful if students know the basic terms used to describe evolutionary trees e.g., root, branch, node. Classroom organisation There are several ways of using the exercise. One strategy would be to divide the class into small groups of 2–3 students and to ask each group to devise an evolutionary tree using the biscuit cut-outs. Each group then reports back to the entire class, explaining the reasons for their decisions and describing how they think the biscuits have ‘evolved’. To ensure that the discussion is meaningful, it may help to give students a list of words and phrases that they must use in their descriptions. For example: selection, speciation, convergent evolution, adaptation, mutation, common ancestor, branch, node, outgroup etc. A strategy that has proved effective is for the teacher to eavesdrop on the discussion in each group as they are devising their trees, then to choose a relatively articulate group to give their presentation first. This will then ‘set the tone’ for the other groups’ feedback. With large classes, it may prove impractical for all groups to report back, in which case just three or four groups may be asked to describe their trees verbally, then all groups can be asked to produce a written description. The exercise can also be undertaken using a selection of real biscuits, although this activity is more open-ended and hence less predictable. Health and safety regulations will have to be considered if the biscuits are to be eaten afterwards. Copyright © Dean Madden, 2011 4 www.dnadarwin.org introduction Other useful resources Simulating evolution A practical exercise in which students produce a phylogenetic tree using screws, nuts and bolts, paperclips, etc. Devised by John Barker, based on an Open University activity. Downloadable from: www.eurovolvox.org/ protocols.html Building a phylogenetic tree An exercise devised by Wojciech Grajkowski of the Science Festival School, Warsaw, in which students construct data matrices for three groups of organisms, then use them to generate phylogenies. Downloadable from: www.eurovolvox.org/protocols.html Wellcome Trust Tree of Life TheWellcome Trust Tree of Life is a six-minute animated evolutionary history presented by Sir David Attenborough. The video can be downloaded for classroom use, as can the supporting interactive tree, to be viewed using a Web browser (requires Adobe Flash 10+). An audio-free version of the video is also available for dubbing with your own soundtrack. Several additional educational resources and an animated video presentation of evolution are all free to download. www.wellcometreeoflife.org Tree of Life Web Project TheTree of Life Web Project is a collaborative effort of biologists from around the world. On more than 9,000 Web pages, the project provides information about the diversity of organisms on Earth, their evolutionary history (phylogeny), and characteristics. http://tolweb.org/tree/ Interactive Tree of Life (European Molecular Biology Laboratory) This is an advanced online tool for the display and manipulation of phylogenetic trees. It provides most of the features available in other tree viewers, and offers a novel circular tree layout, which makes it easy to visualize trees. Trees can be exported to several graphical formats, both bitmap- and vector-based. Even if you don’t want to generate your own trees, you can explore the pre-computed interactive diagrams on this site. http://itol.embl.de/ National Center for Biotechnology Information (NCBI) The NCBI hosts a major collection of databases of genetic information that is used by research scientists world-wide. The Web site includes some excellent educational materials, including a primer on systematics and molecular phylogenetics. http://www.ncbi.nlm.nih.gov/ Copyright © Dean Madden, 2011 5 www.dnadarwin.org introduction Existing (extant) species Fossil common ancestor Existing (extant) species Fossil common ancestor 6 introduction Tree 1 Tree 2 Tree 3 Copyright © Dean Madden, 2011 7 www.dnadarwin.org introduction Answers to the questions on the worksheets Page 3 There are three possible ways of constructing the evolutionary tree from biscuits. These are shown here and in the slide presentations. Page 5 a. Variations in the rate of evolution may lead to organisms being placed in the wrong place on an evolutionary tree (they may look very different when they are in fact closely-related). b. Any examples of convergent evolution could be suggested here, for example, wings in bats and birds, camera-like eyes in primates and cephalopods, streamlined body shapes in dolphins and sharks. c. For example, the genes controlling skin colour in humans have diverged very rapidly, meaning that humans look different when in fact they are all the same species. d. For evolution to go ‘in reverse’, similar selection pressures would have to apply, but once genetic diversity has been lost, the chances of successive mutations occurring to exactly recreate the original trait are remote. e. If a tree is prepared based on similarity, a re-evolved trait may cause a species to be incorrectly grouped with distantly-related organisms. f. All organisms have DNA or RNA, so there is a direct means for comparing them, which is not necessarily the case with other characteristics.
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