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arrFiles=new Array();arrFiles[0]=new Array("TMPjov2hcnfc3.htm","Tree Thinking Group: Search","","","within All text Title Keywords Descriptions using All words Any words Exact phrase © Tree Thinking Group 2004. All rights reserved. University of Pittsburgh, Pittsburgh, PA 15260.");arrFiles[1]=new Array("classroom.html","Tree Thinking Group: Resources - Classroom Ready","","","Classroom Ready All In the Family http://www.pbs.org/wgbh/evolution/change/family/index.html This is a Macromedia Flash based interactive tutorial on how evolutionary relationships are determined. It emphasizes the differences between looking at superficial morphological characteristics and shared ancestry. It does include some nice images which can be used to address homology and analogy. This is part of the collection of educational resources developed to support the PBS Evolution series. Quote from source: Test your skills at judging who \'s who on the tree of life while you learn about the tools and methods of cladistics. Cladistics a practical primer on CD-ROM Skelton, P. W., A. Smith, et al. (2002). Cladistics a practical primer on CD-ROM.Cambridge, The Open University; Cambridge University Press. This CD-ROM and book contain an interactive introduction to the logic and practical aspects of doing cladistic analyses. It works on both MAC and PC platforms. See R. P. Guralnick \'s review in Palaeontologia Electronica for additional information. Quote from source: Cladistics and phylogenetic reconstruction are subjects which biology students find quite difficult to grasp when taught from conventional textbooks. This CD provides students with a complete self-study introductory course in phylogenetic reconstruction using cladistic analysis. Classification: Arbitrary, or Not? http://www.indiana.edu/~ensiweb/lessons/cl.intro.html This lesson plan by Martin Nickels is part of the Evolution and the Nature of Science Institutes (ENSI) materials. It includes a full set of materials in PDF format. Quote from source: Students working in teams classify furniture, share their categories and rationales, then note how their different schemes vary, perfectly logical and useful, but completely arbitrary. They then see how living organisms are classified, and note how these groupings are natural, nearly always reflecting the same ancestral relationships in nested hierarchies, regardless of the deeper criteria. Such patterns are revealed with a look at several phylogenetic trees of primates. Finally, teachers are encouraged to give their students lab experience collecting data from a variety of primate characteristics (skulls, chromosomes, and hemoglobin), to see for themselves the congruency of those data sets. Classroom Cladogram of Vertebrate/Human Evolution http://www.indiana.edu/~ensiweb/lessons/c.bigcla.html This lesson plan by Larry Flammer is part of the Evolution and the Nature of Science Institutes (ENSI) materials. It includes a full set of materials in PDF format. Quote from source: Students prepare the components for building a Colossal Classroom Cladogram of vertebrate evolution, then put it together, showing the gradual, mosaic accumulation of the traits which we, as humans, possess. A major purpose of this is to dramatize the evidence that we (and in fact all living things) didn \'t suddenly pop into existence, but clearly evolved as an accumulation of traits over vast periods of time. A follow-up discussion helps focus on these concepts. Deep Time http://www.pbs.org/wgbh/evolution/change/deeptime/index.html This is a Macromedia Flash based interactive collection of information to help students learn about deep time. An animated timeline allows the user to look at changes (geological, transformations, and extinctions) in different geological eras. This is part of the collection of educational resources developed to support the PBS Evolution series. Quote from source: Explore 4 billion years of life on Earth, and discover major transformations, geological changes, and extinction episodes. Evolution Collection from the Woodrow Wilson Institute http://www.accessexcellence.org/AE/AEPC/WWC/1995/ This Access Excellence site is an archive of the materials collected during the 1995 Woodrow Wilson Institute on Teaching Evolution. It contains labs and other teaching materials including the following which involve phylogeny. From Restriction Maps to Cladograms by Aleta Sullivan and JoAnne Dombrowski. Constructing a Phylogenetic Tree Using DNA Sequence Data by Mark Gabler. Using Amino Acid Sequences to Show Evolutionary Relationships by Gwynn Pealer and Steve Ferris. Molecular Biology and Primate Phylogenetics by John Banister-Marx. Quote from source: We offer the collection to our fellow teachers to use as they like. You \'ll find some items here that are modifications of exercises that are familiar to many and others that have been developed anew by the participants. No one will find a use for everything we \'ve produced, but even if you only use one or two exercises and in so doing deepen your students \' appreciation for evolution and thus for all of biology, we \'ll be enormously pleased. -- From the Preface Introduction to Phylogeny: How to Interpret Cladograms http://biology.fullerton.edu/biol402/phylolab_new.html This online tutorial and quiz was developed by Professor Eernisse as part of his Molecular Systematics course at California State University – Fullerton. Quote from source: Welcome to the online Cladogram Exercise 1 Web site. This online assignment will help you get more comfortable with cladograms. They are not as confusing as you probably thought they were. After completing the following steps, you will be on your way. Molecular Sequence & Primate Evolution: Amino Acid Difference in Beta Hemoglobin in Primates http://www.indiana.edu/~ensiweb/lessons/mol.prim.html This lesson plan by Craig Nelson and Martin Nickels is part of the Evolution and the Nature of Science Institutes (ENSI) materials. It includes a full set of materials in PDF format. Quote from source: Students compare differences in amino acids in the beta hemoglobin from representative primates, complete a matrix of those differences, and from these data, construct and interpret cladograms as they reflect relationships and timing of divergence. Names & classifying living things http://www.backyardnature.net/names.htm This is a very interesting resource written by Jim Conrad as part of the Backyard Nature site. It has a collection of information about the practical and biological importance of naming and grouping conventions for living organisms. The text is rich with approachable examples and is written in an engaging narrative format. Some of the sections include: Lumpers and splitters; On the beauty of scientific names; and, How many kinds of plants and animals are there? Quote from source: Names can be thought of as handles our minds can use to get a grasp on nature \'s mind boggling diversity, and classification enables us to see for ourselves the general course that evolution takes in nature. Here is an example of how having a good background in names and classification gave me a buzz the other day: ... Understanding Evolution: An Evolution Web Site for Teachers http://evolution.berkeley.edu/ This is a vast and comprehensive resource for teachers. It is divided into sections on Learning Evolution and Teaching Evolution. The content is organized to reflect different learning goals, misconceptions, and the relationship between understanding the nature of science relates to learning evolution. For tree thinking discussions be sure to check out The History of Life: Looking at the Patterns , Scott Dawson \'s essay Lessons in the Diversity and Evolution of Eukaryotes , and the collection of History of Life lesson plans . Quote from source: This site is a collaborative project of the University of California Museum of Paleontology and the National Center for Science Education. Support was provided by the National Science Foundation and the Howard Hughes Medical Institute. University of California Museum of Paleontology http://www.ucmp.berkeley.edu/ The UCMP has a well deserved and long standing reputation as an online source of high quality education materials relating to the history of life on Earth. Several specific resources from this extensive collection are highlighted elsewhere in this bibliography including Understanding Evolution , and Explorations Through Time . Quote from source: The mission of the University of California Museum of Paleontology is to investigate and promote the understanding of the history of life and the diversity of the Earth \'s biota through research and education. What did T. Rex taste like: An introduction to how life is related http://www.ucmp.berkeley.edu/education/explorations/tours/Trex/guide/index.html This University of California Museum of Paleontology (UCMP) teaching resource covers a lot of important topics in the development, interpretation and use of cladograms. It is presented in a highly structured web interface that has the feel of programmed instruction. Be sure to look at the teacher resources including assessment tools for looking at students \' understanding of cladograms. Quote from source: What Did T. rex Taste Like? is an introduction to cladistics, the most commonly used method of classification today. Cladistics organizes living things by common ancestry and evolutionary relationships, enabling us to better understand life \'s present diversity and evolutionary history.This module presents a simplified version of the process used to generate cladistic analyses and demonstrates its predictive power. Explorations Through Time is a series of interactive, web-based educational modules that address topics such as fossils, the history of life, biological evolution, the science of paleontology and the scientific process. Back to the Top © Tree Thinking Group 2004. All rights reserved. University of Pittsburgh, Pittsburgh, PA 15260.");arrFiles[2]=new Array("evolprop_05.html","Tree Thinking Group: Evolution Proposal","","","Symposium Proposal The missing piece of the evolution-education puzzle: Teaching phylogenetics at introductory undergraduate and precollege levels David A. Baum, Dept. of Botany, University of Wisconsin, Madison WI and Samuel S. Donovan, Dept. of Instruction and Learning, School of Education, University of Pittsburgh, PA Rationale. Evolution is first and foremost about descent from common ancestry and, thus, it is virtually impossible to think clearly about evolution without utilizing “tree-thinking.” In contrast to the great attention that has been focuses in recent years on the teaching of natural selection, virtually no attention has been paid to the teaching of phylogenetics. In order to take advantage of evolution as an organizing framework for understanding the unity and diversity of life and to be able to think clearly about the relationships between taxonomic groups, biology students must adopt a descent with modification perspective. Additionally, across biological disciplines from ecology to genomics, there is a growing emphasis on understanding the role of phylogenetic relationships in the interpretation of comparative data. The premise of this symposium is that evolution, and hence biology as a whole, cannot be taught properly without explicitly addressing the interpretation of phylogenies. Further, to effectively teach tree-thinking we need to know more about the common misconceptions that students have and the curricular tools that are available to help students develop a robust scientific understanding of descent with modification. Given the relative youth of phylogenetic systematics, and the paucity of research into students understanding of phylogenies, it is imperative that academic scientists take a leading role in educating undergraduates and especially future and present K-12 teachers. Our specific aims for this symposium are: 1) To clarify and refine the claim that tree-thinking should play a central role in the teaching of evolutionary biology at the college and precollege levels 2) To present educational research on the problems students face in understanding phylogenies 3)	To present some novel curricular materials that can be useful 4) To highlight the leadership role that academic scientists should be playing in training future K-12 teachers in introductory biology classes at college and current K-12 teachers through the development of conceptual arguments, curricular materials and outreach activities. Proposed speakers (25 minutes each) David A. Baum (Professor, Dept. of Botany, Univ. of Wisconsin) “The challenge of teaching tree-thinking: major misconceptions and their remedies” David Baum has been teaching introductory college courses with a major phylogenetic component for eight years and has taught four workshops for high school biology teachers on integrating phylogenies into the high school biology classroom. Recently he has been conducting research on student misconceptions in phylogenetics and has developed new curricular materials. Samuel S. Donovan (Asst. Professor, Dept. of Instruction & Learning, Univ. Pittsburgh) “Reading topologies: A study of students \' understanding of relationships displayed in trees” Sam Donovan is a science educator and chair of the Society for the Study of Evolution education committee. This presentation will describe the results of research into how students interpret branching diagrams and the importance of this skill for other aspects of evolutionary reasoning. Susan Offner (Biology Teacher, Lexington High School, MA) “The advantages of using phylogenetic trees in biology teaching” Sue Offner, an experienced biology teacher, has been integrating phylogenies into her curriculum since 1998. She has also written articles on the tree of life for American Biology Teacher and has mentored high school students doing phylogenetic science fair projects, several of whom have gone on to gain statewide recognition for their work. Michael J. Donoghue (Professor, Dept. Ecology and Evolution, Yale University) “Using phylogenies as a framework for ecology and biogeography” Michael Donoghue has long been an advocate of using phylogenies to teach evolution. He has implemented this vision in undergraduate courses at Harvard and Yale. Additionally, as director of the Peabody Museum, he has been involved in outreach activities to K-12 schools in the Newhaven area. Kirsten Fisher (Graduate student, Dept. Integrative Biology, Univ. of California, Berkeley) “Lessons from the tree of life: the use of language in teaching phylogenetics” Kirsten Fisher will present insights emerging from her work through the Deep Gene Initiative to educate K-12 teachers in phylogenetics and through her connections to the UC Museum of Paleontology, which has developed the “Journey into Phylogenetic Systematics” tutorial. Jon C. Herron (Lecturer, Dept. of Biology, Univ. of Washington) Simulation-based tutorials for teaching tree thinking. Jon Herron has been teaching evolution at the University of Washington for eleven years and is coauthor of Evolutionary Analysis, a leading undergraduate text on evolution. He will present simulation software and tutorials he has developed for helping students learn phylogenetic reasoning. Manda Clair Jost (Post-doc, Section of Integrative Biology, Univ. of Texas) “Using trees to teach biodiversity” Manda Clair Jost has a long-standing interest in teaching and has taught a workshop for high school teachers on the Tree of Life. With her post-doc advisor, David Hillis, she has thought about effective teaching of biodiversity at the college and precollege levels. Back to the Top © Tree Thinking Group 2004. All rights reserved. University of Pittsburgh, Pittsburgh, PA 15260.");arrFiles[3]=new Array("getting.html","Tree Thinking Group: Resources - Getting Started","","","Getting Started Classification: A beginner \'s guide to some of the systems of biological classification in use today Jones, S. & A. Gray (1983). Classification: A beginner \'s guide to some of the systems of biological classification in use today. London: British Museum (Natural History). Unfortunately, this useful introductory volume is out of print. However you can sometimes find it used from online retailers. Quote from source: This booklet is based on Classification - a permanent exhibition at the Natural History Museum. It has been written by Dr. Susan Jones and Mrs. Anne Gray of the Department of Public Services, in collaboration with their colleagues throughout the Museum. The classification & evolution of caminalcules http://www.bioone.org/ Gendron, R. P. (2000). The classification & evolution of caminalcules. The American Biology Teacher 62(8):570-576 This article provides a nice introduction to the Caminicules as a resource for teaching evolution. The collection of 77 imaginary organisms was invented by Joseph Camin and this article describes several exercises using them that engage students in realistic evolutionary inquiry. Quote from source: For the purpose of teaching evolution to college and high school students, the Caminalcules offer several important advantages (McComas & Alters 1994). First, because Caminalcules are artificial organisms, students have no preconceived ideas about how they should be classified or how they are related. This means that students have to concentrate on principles rather than prior knowledge when constructing a phylogenetic tree or classification. Second, unlike everyday objects such as fasteners, the Caminalcules have a ‘‘real’’ evolutionary history, complete with a detailed fossil record. Climbing the Tree of Life: Taxonomy and Phylogeny http://www.bscs.org/page.asp?id=Curriculum_Development%7CHigh_School_9-12%7Ctaxonomy_Development_Bio This CD-ROM based resource was developed by the Biological Sciences Curriculum Study (BSCS) and contains a variety of exercises that engage students in exploring the relationships between species. Quote from source: Climbing the Tree of Life: Taxonomy and Phylogeny for High School biology takes advantage of student \' interest in biodiversity and concern about its decline to introduce concepts of taxonomy and phylogeny, the nature and methods of science, and the personal and social relevance of science. Features include interactive, inquiry-oriented activities with videos, animations, simulations, and printable documents; off-computer research; individual and collaborative learning; and a teacher \'s implementation guide. The comparative method, hypothesis testing and phylogenetic analysis http://www.bioone.org/ Singer, F., J. B. Hagen, et al. (2001). The comparative method, hypothesis testing and phylogenetic analysis. The American Biology Teacher 63(7): 518-523. This introductory article explores the relationships between comparative approaches in biology and assumptions about evolutionary relationships. It contains several classroom activities. Quote from Source: Textbook discussions of scientific methodology often focus almost exclusively upon controlled experiments, but biologists also use many non-experimental techniques for testing hypotheses. Particularly important are the comparative methods developed for phylogenetic analysis by biologists who study systematics. Today, these comparative methods can be applied at multiple levels of organization from behavior and ecology, to more traditional levels of gross anatomy and development, and downward to information carrying macromolecules (DNA, RNA and proteins). Nothing in biology makes sense except in the light of evolution http://www.pbs.org/wgbh/evolution/library/10/2/text_pop/l_102_01.html Dobzhansky, T. (1973). Nothing in biology makes sense except in the light of evolution. The American BiologyTeacher 35(March): 125-129. This oft cited American Biology Teacher article is still an important resource for biology educators. Quote from source: Seen in the light of evolution, biology is, perhaps, intellectually the most satisfying and inspiring science. Without that light it becomes a pile of sundry facts some of them interesting or curious but making no meaningful picture as a whole. Order and diversity in the living world: Teaching taxonomy and systematics in schools Crisci, J. V., J. D. McInerney, et al. (1993). Order and diversity in the living world: Teaching taxonomy and systematics in schools. Reston, VA, National Association of Biology Teachers. Quote from source: Recommended grade level: 1-8+. Order and Diversity in the Living World is a small book that presents a rationale for classroom study of biological diversity and the relationships between different organisms. It also offers a brief review of the current state of diversity and rate of species extinction, identifies standards that should encourage changes in the way systematics is taught in the classroom, and gives directions for 10 sample activities that involve students in doing systematics in the classroom rather than simply reading about the nature of this subdiscipline. -- Quoted from http://www.nap.edu/readingroom/books/rtmss/2.62.html Phylogeny Wing of University of California Berkeley, Museum of Paleontology http://www.ucmp.berkeley.edu/exhibit/phylogeny.html This rich collection of resources from the University of California - Berkeley, Museum of Paleontology (UCMP) is a great place for students to orient to the importance of phylogeny for understanding the unity and diversity of life on earth. The major exibits include a Phylogeny of Life section that can be accessed by taxon or geological period, and an introduction to cladistics called, Journey Into Phylogenetic Systematics. Quote from source: The Phylogeny Wing is the largest of our museum \'s on-line exhibit halls, with more than 235 individual exhibits, many with multiple pages. The wing provides a survey of biodiversity, focusing on major lineages of organisms. Many of these lineages have gone extinct or currently exist at a much lower diversity than in the past, so there may be large exhibits on groups of organisms that are unfamiliar to you. They are featured because they play an important role in the history of life on earth. What, if anything, is a zebra? Gould, S. J. (1983). What, if anything, is a zebra? Hen \'s teeth and horse \'s toes: Further refections in natural history. New York, W. W. Norton & Co. In this short essay Gould uses cladistics to examine the appropriateness of the classificatory category zebra. There is a nice study guide developed by Craig Nelson with suggestions for how to engage students as they read this essay. ENSI reading guide Quote from source: The potential dilemma for zebras is simply stated: they exist as three species, all with black-and-white stripes to be sure, but differing notably in both numbers of stripes and their patterns. ... Do these three species a single evolutionary unit? Do they share a common ancestor that gave rise to them alone and to no other species of horse? Or are some zebras more closely related by descent to true horses or to asses than they are to other zebras? If this second possibility is an actuality, ... there is, in an important evolutionary sense, no such thing as a zebra. Back to the Top © Tree Thinking Group 2004. All rights reserved. University of Pittsburgh, Pittsburgh, PA 15260.");arrFiles[4]=new Array("index.html","Tree Thinking Group Home","","","About the tree thinking group The Tree Thinking Group is a loose association of people , including researchers, teachers and students, who are interested in teaching and learning evolutionary biology effectively. There are, of course, many groups that are interested in improving evolution education and you can find out about some of them on our resource pages . What makes this effort stand out somewhat is our focus on tree thinking — that is, the use of a phylogenetic perspective for making sense of biology. We are just getting started but you can browse some of the products that are currently available and under development. This site is currently being coordinated by Sam Donovan at the University of Pittsburgh and you should feel free to contact him if you have questions, comments, suggestions, or you would like to get updates on the project. A Brief Introduction to Tree Thinking Site Developments November 10 - Public debut of Tree Thinking Group site, ver. 1.0. August 25 - Seach function moved to a seperate page. Added new links, and made links more uniform in appearence. July 15/17 - Overhaul of pages upgrade to ver. 0.5, along with typo fixes and other minor corrections. New search function added and functional. Please feel free to use it. Send comments or bug reports to: webmanager June 1 - Links section had a major revamp. Almost in complete working order. May 27, 2004 - Preliminary launch, ver. 0.1. Everything barring the Links section should be working. Still gathering linka and working the bugs out. These bugs are nothing like cicadas , and should be fixed soon. Back to the Top © Tree Thinking Group 2004. All rights reserved. University of Pittsburgh, Pittsburgh, PA 15260.");arrFiles[5]=new Array("intro.html","Tree Thinking Group Introduction","","","A Brief Introduction to Tree Thinking Seen in the light of evolution, biology is, perhaps, intellectually the most satisfying and inspiring science. Without that light it becomes a pile of sundry facts some of them interesting or curious but making no meaningful picture as a whole. Dobzhansky, T. (1973). Nothing in biology makes sense except in the light of evolution. The American Biology Teacher 35(March): 125-129. Much in evolution makes more sense in the light of phylogeny. Hillis, D. M. and J. J. Bull (1991). Of genes and genomes. Science 254: 528. Evolutionary biologists think about biological phenomena in terms of how those observations fit within the branching structure of genealogical relationships between species. They recognize the roles of descent from common ancestry and evolutionary modification in establishing patterns of similarity and difference among groups of organisms. In short, they see biology through the perspective of phylogeny. The adoption of a tree thinking perspective is not compatible with some informal ways of thinking about biological groups and the relationships among them. The figures below represent three very different sets of assumptions about the nature of species. In the first panel species are represented as fixed and separate types. To a first approximation, this is what we experience in our everyday interactions with organisms. The second panel shows species as different steps along an evolutionary (developmental) trajectory. Given our human-centric experience it is easy to see why we would place our species at the top of this ladder. The third panel emphasizes both the historical relationships among species and their non-linear, or branching, divergence. Tree thinking involves being able to incorporate these historical and non-linear features into one \'s biological sense making. Back to the Top © Tree Thinking Group 2004. All rights reserved. University of Pittsburgh, Pittsburgh, PA 15260.");arrFiles[6]=new Array("other.html","Tree Thinking Group: Resources - Other","","","Other Resources Constructing phylogenies Bilardello, N. and L. Valdes (1998). Constructing phylogenies. The American Biology Teacher 60(5): 369-373. This How-To-Do-It article addresses the mathematical properties of trees and other types of graphs. It discusses the elements of trees, minimum weight spanning trees, an rooted cubic trees. A molecular dataset and 6 classroom exercises are included. Quote from source: A graph is a mathematical structure that is often used to show relations between elements of a set. These elements are depicted by points or vertices and can be labeled with symbols. If two elements are related, they are connected with a line called an edge. Evolution and the nature of science: On the historical discord and its implications for education http://www3.interscience.wiley.com/cgi-bin/jhome/31817 Rudolph, J. L., & Stewart, J. (1998). Evolution and the nature of science: On the historical discord and its implications for education. Journal of Research in Science Teaching, 35(10), 1069-1089. Quote from source: Research in the teaching and learning of evolutionary biology has revealed persistent difficulties in student understanding of fundamental Darwinian concepts. These difficulties may be traced, in part, to science instruction that is based on philosophical conceptions of science that are no longer viewed as adequately characterizing the diverse nature of scientific practice, especially in evolutionary biology. This mismatch between evolution as practiced and the nature of science as perceived by researchers and educators has a long history extending back to the publication of Darwin \'s theory of natural selection. An examination of how this theory was received by the scientific community of the time may provide insight into some of the difficulties that students have today in learning these important biological concepts... ForensicEA: Phylogenetics simulation software for evolutionary analysis http://faculty.washington.edu/herronjc/SoftwareFolder/ForensicEA.html This is a great simulation tool for helping students get started with the idea of independence of populations and divergence. Jon Herron at the University of Washington wrote this software to complement his textbook Evolutionary Analysis. The site has nice teaching resources and introductory materials as well as the software. Runs on Mac and PC. Quote from source: ForensicEA lets the user explore the logic of phylogeny reconstruction. The program creates populations of virus particles. The populations evolve by genetic drift. The user can sample and compare nucleotide sequences from the populations. Various simulations let the user collect and analyze data on: genetic drift within a single population; divergence of populations by drift; and variation among populations on a known phylogeny. In search of deep time: Beyond the fossil record to a new history of life Gee, H. (1999). In search of deep time: Beyond the fossil record to a new history of life. New York: Free Press. Gee, an editor at the journal Nature, describes the conceptual difficulty involved when reasoning about deep time and uses this as a base from which he examines the historical development of cladistics. It really helped me think about the ways we draw inferences from trees. The origin of species by means of natural selection, or, The preservation of favoured races in the struggle for life http://www.bbc.co.uk/education/darwin/origin/ Darwin, C. (1985). The origin of species by means of natural selection, or, The preservation of favoured races in the struggle for life. Harmondsworth ; New York, Penguin. A classic, and very readable. The description of descent with modification accompanying the only figure in the book (a line drawing of branching and extinction) is interesting. You can read Darwin \'s description of the diagram in the the probable effects... section of Chapter 4 - Natural Selection . A reproduction of the tree diagram is available here . The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during former years may represent the long succession of extinct species. At each period of growth all the growing twigs have tried to branch out on all sides, and to overtop and kill the surrounding twigs and branches, in the same manner as species and groups of species have at all times overmastered other species in the great battle for life. the limbs, divided into great branches, and these into lesser and lesser branches, were themselves once, when the tree was young, budding twigs, and this connection of the former and present buds by ramifying branches may well represent the classification of all extinct and living species in groups subordinate to groups. Phylogenetics 1.0 http://bioquest.org/bedrock/terre_haute_03_04/phylogenetics_1.0.ppt This PowerPoint file by Tony Weisstein provides a nice overview of several important issues in phylogenetic analysis. It addresses the differences between evolutionary trees and phylograms, rooted and unrooted trees, and several tree building techniques. Phylogenetics, the science of who \'s related to who http://www.ucmp.berkeley.edu/IB181/VPL/Phylo/PhyloTitle.html As part of the Virtual Paleobotanical Laboratory at the Univeristy of California - Berkeley Museum of Paleontology this lab was designed by Nan Arens and others for an undergraduate course. It contains a significant introduction to phenetics and cladistics that uses a fair amount of technical vocabulary. The lab activity is built around specific plant specimens but the procedure could be modified to take advantage of local resources. Quote from source: In this week \'s lab you will learn how to reconstruct evolutionary relationships. Biologists have experimented with a variety of methods for interpreting who is related to whom, however, many of these methods did not well reflect the process that we believe underlies evolutionary relationships. After reading about the evolution of the methods, you will try your skills on some living plants in the Mesozoic Garden opposite the T. rex, in the Atrium of VLSB. PhylTree http://aleph0.clarku.edu/~djoyce/java/Phyltree/cover.html This web based Java program written by David Joyce at Clark University is used to demonstrate and complement brief discussions of phylogeny, mutation, distance and reconstruction algorithms . Quote from source: These few pages describe the problem of reconstructing phylogenetic trees with the help of a Java applet. I wrote the applet to discover more about the java language and the API interface. Scientific knowledge of the past is possible: Confronting myths about evolution and scientific methods http://www.bioone.org/ Cooper, R. A. (2002). Scientific knowledge of the past is possible: Confronting myths about evolution and scientific methods. American Biology Teacher 64(6): 427-32. This essay discusses the nature of evolutionary biology as a historical science and how narrow definitions of science can appear to be in conflict with evolutionary inquiry. It also provides a historical overview of some of the methods used by scientists to investigate the past. Quote from source: This article presents the argument that, contrary to creationists claims and public perception, a variety of methods are used in science and among those methods are some that enable scientists to understand the past. TreeEdit http://evolve.zps.ox.ac.uk/software.html?id=treeedit This Mac application written by Andrew Rambaut and Mike Charleston from the University of Oxford allows you to reroot trees, rotate branches, and rearrange trees that are in the NEXUS format. Quote from source: TreeEdit is an application for organizing, viewing and manipulating sets of phylogenetic trees. It is intended as a tool for preparing sets of trees for use in phylogenetics packages such as PAUP. Back to the Top © Tree Thinking Group 2004. All rights reserved. University of Pittsburgh, Pittsburgh, PA 15260.");arrFiles[7]=new Array("papers.html","Tree Thinking Group: Posters","","","Papers Establishing a context for student inquiry in the historical sciences Paper to be presented the National Association for Research in Science Teaching MeetingDallas, TX. April 4-7, 2005 Abstract: Much of the current science curriculum reform is driven by the goal of engaging students in realistic aspects of science practice. The emphasis on understanding what scientists do requires careful consideration of the nature of science from a disciplinary perspective. Unfortunately, there has been little attention paid to the unique features of inquiry in the historical sciences. Without explicit attention to the nature of historical scientific inquiry students will not have the conceptual tools to engage in disciplinary reasoning in evolutionary biology, geology, cosmology and paleontology. This paper reports on an analysis of philosophical, historical, disciplinary and educational literature and presents a framework for addressing the goals, methods, and epistemological basis of historical scientific inquiry in science curricula. The framework makes the distinction between modeling and historical reconstruction as two interdependent goals of historical inquiry. It also addresses the narrative structure of claims about historical events and the standards for argumentation when the focus is on the casual basis for pasts events. The framework for characterizing historical scientific inquiry is then used to articulate a set of design principles which can inform the development of curricula that give students opportunities to engage in realistic inquiry in the historical sciences. An introduction to inquiry in evolutionary biology Donovan, S. (2001). An introduction to inquiry in evolutionary biology. Working Paper for The National Center for Improving Student Learning and Achievement in Mathematics and Science (NCISLA). Wisconsin Center for Education Research. Madison, WI. Contact the author for the paper. Abstract: The goal of this short paper is to provide some introduction to the scientific practices of evolutionary biologists. You will find that this is not a collection of things we know about evolution, but instead an analysis of how evolutionary biologists come to know what they know. This distinction, between what is known and how knowledge is developed, has been an important one for the MUSE project. Traditionally, curricula grow from a desire to share an established body of knowledge with students. Although we too believe that learning some of the “facts” is important to understanding a discipline, we feel that it is equally important that students develop some familiarity with the practices that contributed to the development of that knowledge. Using the nature of evolutionary inquiry as a guide for curriculum development Donovan, S. (2001). Using the nature of evolutionary inquiry as a guide for curriculum development. Presented at The International History and Philosophy of Science and Science Teaching (IHPST) Annual Meeting, Denver, CO November 7-11, 2001. Contact the author for the paper. This paper is an attempt to provide an alternative framework for considering the organization of instruction in evolutionary biology. Instead of focusing on enumerating the “essential facts” known from past inquiries this framework is built to reflect the practices of evolutionary biologists. Instead of characterizing understanding as familiarity with particular products of evolution research this framework emphasizes the ways that we come to know things in evolutionary biology. Specifically, this framework is informed by three broad characteristics of evolutionary inquiry: the nature of questions; the nature of explanations; and, the nature of arguments. The first, the nature of questions, involves understanding something about what drives research. The second, the nature of explanations, reflects the ways that real world phenomena are linked to theoretical causal systems (models). And the third, the nature of arguments, focuses on the criteria by which explanations are evaluated. Eye on Education: Using Bioinformatics in the Undergraduate Classroom Musante, Susan. (2004). Eye on Education: Using Bioinformatics in the Undergraduate Classroom. BioScience 54(7). 625. Full text PDF from Ingenta Select HTML version from AIBS This article describes the BEDROCK Bioinformatics Education Project and some of the faculty projects it supports. Back to the Top © Tree Thinking Group 2004. All rights reserved. University of Pittsburgh, Pittsburgh, PA 15260.");arrFiles[8]=new Array("personnel.html","Tree Thinking Group: People","","","People David Baum Department of Botany University of Wisconsin EMAIL: dbaum@wisc.edu Steven Brewer Biology Department University of Massachusetts Amherst EMAIL: sbrewer@bio.umass.edu Michael Donoghue Ecology and Evolutionary Biology Peabody Museum of Natural History Yale University EMAIL: michael.donoghue@yale.edu Samuel Donovan Department of Instruction and Learning Learning Research and Development Center University of Pittsburgh EMAIL: sdonovan@pitt.edu Maura C. Flannery Professor of Biology College of Professional Studies St. John \'s University EMAIL: flannerm@stjohns.edu Brian T. Foley HIV Genetic Sequences, Immunology,Drug Resistance, Protein 3D Structures, andPrimate Vaccine Trials Databases http://www.hiv.lanl.gov EMAIL: btf@lanl.gov Alan Giese Department of Biology Arizona State University EMAIL: Alan.Giese@asu.edu David Hornack Biological Sciences University of Pittsburgh EMAIL: dhornack@pitt.edu John R. Jungck Biology Department Beloit College EMAIL: jungck@beloit.edu Stacey Kiser Science Department Lane Community College EMAIL: kisers@lanecc.edu Maggie Koopman Department of Botany University of Wisconsin EMAIL: mmkoopman@wisc.edu Jeffrey S. McKinnon Dept. of Biological Sciences University of Wisconsin-Whitewater EMAIL: mckinnoj@uww.edu Ethel Stanley BioQUEST Curriculum Consortium Beloit College EMAIL: stanleye@beloit.edu Brian White Biology Department University of Massachusetts - Boston EMAIL: brian.white@umb.edu Anton Weisstein	Beloit College EMAIL: Laura Wilcox University of Pittsburgh EMAIL: lwilcox@mtlsd.net Back to the Top © Tree Thinking Group 2004. All rights reserved. University of Pittsburgh, Pittsburgh, PA 15260.");arrFiles[9]=new Array("posters.html","Tree Thinking Group: Posters","","","Posters Assessing tree thinking and its role in understanding evolution Poster presented at the Four Year College Section of the National Association of Biology Teachers Meeting Chicago, IL. November 10-13, 2004 Authors: Sam Donovan web poster [64 kb GIF] full poster [732 KB PDF] Abstract: Understanding evolution involves knowing something about both the mechanisms involved in evolutionary change and the history of life on earth. Most introductory biology curricula emphasize models of evolutionary change but do little to explicitly address historical reconstruction. The phylogenetics instruction there is generally emphasizes tree building or the genealogical relationships among particular groups of organisms (e.g., the primate phylogeny). Familiarity with the broad consequences of descent with modification can provide an important framework for organizing biological knowledge. The assessments described here address a variety of tree-thinking understandings and skills including reading and comparing tree topologies, using the information in trees to understand biological patterns, and relating evolutionary concepts to tree diagrams. The goal of developing these assessments was to articulate a range of learning outcomes related to the use of tree diagrams in evolutionary biology, provide feedback for faculty and students about their understanding, and to guide curriculum development that adopts a more sophisticated and systematic approach to teaching about this important aspect of understanding the reasoning involved in doing evolutionary biology. Tree figures in texts: A framework for unpacking their educational potential Poster presented at the Society for the Study of Evolution Meeting Ft. Collins, CO. June 26-30, 2004 Authors: Sam Donovan, Laura Wilcox web poster [119 KB GIF] full poster [3.1 MB PDF] Abstract: Tree figures play at least two important roles in introductory biology texts. They describe relationships between groups of organisms, often in the form of phylogenetic trees. Additionally, they provide a context for displaying various evolutionary patterns and concepts within a descent with modification framework. In both of these roles the message carried in tree figures depends on understanding a variety of mathematical, graphical and disciplinary conventions for reading trees. Interpreting tree figures is further complicated by the use of different tree types and the inclusion of extra-topological information. This poster presents a framework for characterizing tree figures in a way that highlights the biological information embedded in these representations. A preliminary analysis of figures from several introductory texts is used to demonstrate the information richness and conceptual complexity of the tree representations. Educational implications related to the importance of, and strategies for, helping students developtree reading skills are also discussed. Not losing the forest for the trees: Learning to compare trees and assess support for phylogenetic hypotheses Poster presented at the Study of Evolution Meeting Ft. Collins, CO. June 26-30, 2004 Authors: Sam Donovan, David Hornack web poster [54 kb GIF] full poster [4.9 MB PDF] Abstract: Too often, particularly in the context of evolution education, trees are treated as true phylogenies rather than hypotheses. Concomitant with this overemphasis on reifying a single tree, the emergence of molecular data is sometimes treated as a panacea for resolving phylogenetic disputes. An alternative approach to evolution education involves engaging students with some of the complexity involved in using multiple data sources to build trees and infer phylogenies. This poster presents a set of teaching resources built around the 17 data sets included in the Whippo-1 collection on the position of Cetacea in the Artiodactyla phylogeny (Gatesy, et al. 1999). The activities can be used to address general issues of tree reading, comparisons of trees to identify areas of congruence and conflict, details of using different types of molecular data, and as a launching point for more extended investigations of phylogenetic questions. BEDROCK \'s problem spaces: Educational resources for evolutionary bioinformatics. Poster presented at the Society for the Study of Evolution Meeting Ft. Collins, CO. June 26-30, 2004 Authors: Sam Donovan, John Jungck, Tony Weisstein, Ethel Stanley, Rama Viswanathan, Tia Johnson, John Greenler, Stacey Kiser, Amanda Everse, Kihachiro Umezaki, David Hornack web poster [94 KB GIF] full poster [4.9 MB PDF] Abstract: This poster introduces a collection of on-line educational resources that are part of the NSF funded BEDROCK Bioinformatics Education Project. We use the idea of a problem space to describe a way of organizing diverse kinds of resources to support collaboration and student inquiry. While individual problem spaces are built around diverse areas such as viral epidemiology, species conservation, protein structure analysis, and invasive species phylogeography they all share several features. Each problem space is designed to engage students and faculty in collaborative research like problem solving. This involves, in part, identifying open research questions, rich data sets and access to a variety of research quality tools. The problem spaces also share an emphasis on the importance of adopting an evolutionary perspective when working with the comparative analysis of molecular data. Additional information can be found online at http://bioquest.org/bedrock/problem_spaces/ . Bioinformatics problem solving: An introduction to bioinformatics education Poster presented at Moving K-12 Teachers into 21st Century Science with 21st Century Technology: Building the Educational Grid for Preservice Training Meeting Arlington, VA. May 31, 2001 Authors: Sam Donovan, Ethel Stanley, Kathleen Greene Poster available online Abstract: Computational molecular biology is redefining what it means to do biological research. The analysis of molecular sequence and structure data has opened new doors into both basic research (e.g., mechanisms for evolutionary change, gene identification) and into applications of biotechnology to solve real-world problems (e.g., in agriculture, conservation, health and medicine). This poster is an introduction to some of the molecular biology of hemoglobin and how analysis of this important protein can be used to study phenomena across biochemistry, physiology, population genetics and evolution. Evolution as a Basis for Bioinformatics Education Poster presented at the New Paradigms in Teaching Introductory and Cell Biology Continuing the Dialogue on Genomics: A Revolution in Progress, Symposium at the American Society for Cell Biology Meeting San Francisco, CA. December 9-13, 2000 Authors: John R. Jungck, John Greenler, and Sam Donovan Available online Abstract: With the extraordinary number of opportunities available to scientists with expertise in bioinformatics, numerous institutions are developing curricula for both undergraduate and graduate students. These curricula tend to foreground mathematics and computer science in bioinformatics education and thus many students major in these two disciplines with a minimal exposure to biology. Unfortunately, these programs have to date ignored any deep education in evolutionary biology. BioQUEST has a long history of trying to help undergraduates learn long term strategies of research by working on open-ended problems with powerful professional tools with a consistent learner-centered pedagogical philosophy: problem posing, problem solving, and persuading peers. In this case, we (http://www.bioquest.org/bioinformatics) have combined the use of a powerful bioinformatics package, Biology Workbench, (http://workbench.sdsc.edu) developed at the supercomputer centers at the University of Illinois and the University of California San Diego, with typologies of evolutionary problem solving that we have developed to differentiate between spatial, temporal, and genealogical hypotheses or between evolutionary, genetic, and developmental biological levels of analysis. Back to the Top © Tree Thinking Group 2004. All rights reserved. University of Pittsburgh, Pittsburgh, PA 15260.");arrFiles[10]=new Array("products.html","Tree Thinking Group: Posters","","","Posters Assessing tree thinking and its role in understanding evolution Poster presented at the Four Year College Section of the National Association of Biology Teachers Meeting Chicago, IL. November 10-13, 2004 Authors: Sam Donovan web poster [64 kb GIF] full poster [732 KB PDF] Abstract: Understanding evolution involves knowing something about both the mechanisms involved in evolutionary change and the history of life on earth. Most introductory biology curricula emphasize models of evolutionary change but do little to explicitly address historical reconstruction. The phylogenetics instruction there is generally emphasizes tree building or the genealogical relationships among particular groups of organisms (e.g., the primate phylogeny). Familiarity with the broad consequences of descent with modification can provide an important framework for organizing biological knowledge. The assessments described here address a variety of tree-thinking understandings and skills including reading and comparing tree topologies, using the information in trees to understand biological patterns, and relating evolutionary concepts to tree diagrams. The goal of developing these assessments was to articulate a range of learning outcomes related to the use of tree diagrams in evolutionary biology, provide feedback for faculty and students about their understanding, and to guide curriculum development that adopts a more sophisticated and systematic approach to teaching about this important aspect of understanding the reasoning involved in doing evolutionary biology. Tree figures in texts: A framework for unpacking their educational potential Poster presented at the Society for the Study of Evolution Meeting Ft. Collins, CO. June 26-30, 2004 Authors: Sam Donovan, Laura Wilcox web poster [119 KB GIF] full poster [3.1 MB PDF] Abstract: Tree figures play at least two important roles in introductory biology texts. They describe relationships between groups of organisms, often in the form of phylogenetic trees. Additionally, they provide a context for displaying various evolutionary patterns and concepts within a descent with modification framework. In both of these roles the message carried in tree figures depends on understanding a variety of mathematical, graphical and disciplinary conventions for reading trees. Interpreting tree figures is further complicated by the use of different tree types and the inclusion of extra-topological information. This poster presents a framework for characterizing tree figures in a way that highlights the biological information embedded in these representations. A preliminary analysis of figures from several introductory texts is used to demonstrate the information richness and conceptual complexity of the tree representations. Educational implications related to the importance of, and strategies for, helping students developtree reading skills are also discussed. Not losing the forest for the trees: Learning to compare trees and assess support for phylogenetic hypotheses Poster presented at the Study of Evolution Meeting Ft. Collins, CO. June 26-30, 2004 Authors: Sam Donovan, David Hornack web poster [54 kb GIF] full poster [4.9 MB PDF] Abstract: Too often, particularly in the context of evolution education, trees are treated as true phylogenies rather than hypotheses. Concomitant with this overemphasis on reifying a single tree, the emergence of molecular data is sometimes treated as a panacea for resolving phylogenetic disputes. An alternative approach to evolution education involves engaging students with some of the complexity involved in using multiple data sources to build trees and infer phylogenies. This poster presents a set of teaching resources built around the 17 data sets included in the Whippo-1 collection on the position of Cetacea in the Artiodactyla phylogeny (Gatesy, et al. 1999). The activities can be used to address general issues of tree reading, comparisons of trees to identify areas of congruence and conflict, details of using different types of molecular data, and as a launching point for more extended investigations of phylogenetic questions. BEDROCK \'s problem spaces: Educational resources for evolutionary bioinformatics. Poster presented at the Society for the Study of Evolution Meeting Ft. Collins, CO. June 26-30, 2004 Authors: Sam Donovan, John Jungck, Tony Weisstein, Ethel Stanley, Rama Viswanathan, Tia Johnson, John Greenler, Stacey Kiser, Amanda Everse, Kihachiro Umezaki, David Hornack web poster [94 KB GIF] full poster [4.9 MB PDF] Abstract: This poster introduces a collection of on-line educational resources that are part of the NSF funded BEDROCK Bioinformatics Education Project. We use the idea of a problem space to describe a way of organizing diverse kinds of resources to support collaboration and student inquiry. While individual problem spaces are built around diverse areas such as viral epidemiology, species conservation, protein structure analysis, and invasive species phylogeography they all share several features. Each problem space is designed to engage students and faculty in collaborative research like problem solving. This involves, in part, identifying open research questions, rich data sets and access to a variety of research quality tools. The problem spaces also share an emphasis on the importance of adopting an evolutionary perspective when working with the comparative analysis of molecular data. Additional information can be found online at http://bioquest.org/bedrock/problem_spaces/ . Bioinformatics problem solving: An introduction to bioinformatics education Poster presented at Moving K-12 Teachers into 21st Century Science with 21st Century Technology: Building the Educational Grid for Preservice Training Meeting Arlington, VA. May 31, 2001 Authors: Sam Donovan, Ethel Stanley, Kathleen Greene Poster available online Abstract: Computational molecular biology is redefining what it means to do biological research. The analysis of molecular sequence and structure data has opened new doors into both basic research (e.g., mechanisms for evolutionary change, gene identification) and into applications of biotechnology to solve real-world problems (e.g., in agriculture, conservation, health and medicine). This poster is an introduction to some of the molecular biology of hemoglobin and how analysis of this important protein can be used to study phenomena across biochemistry, physiology, population genetics and evolution. Evolution as a Basis for Bioinformatics Education Poster presented at the New Paradigms in Teaching Introductory and Cell Biology Continuing the Dialogue on Genomics: A Revolution in Progress, Symposium at the American Society for Cell Biology Meeting San Francisco, CA. December 9-13, 2000 Authors: John R. Jungck, John Greenler, and Sam Donovan Available online Abstract: With the extraordinary number of opportunities available to scientists with expertise in bioinformatics, numerous institutions are developing curricula for both undergraduate and graduate students. These curricula tend to foreground mathematics and computer science in bioinformatics education and thus many students major in these two disciplines with a minimal exposure to biology. Unfortunately, these programs have to date ignored any deep education in evolutionary biology. BioQUEST has a long history of trying to help undergraduates learn long term strategies of research by working on open-ended problems with powerful professional tools with a consistent learner-centered pedagogical philosophy: problem posing, problem solving, and persuading peers. In this case, we (http://www.bioquest.org/bioinformatics) have combined the use of a powerful bioinformatics package, Biology Workbench, (http://workbench.sdsc.edu) developed at the supercomputer centers at the University of Illinois and the University of California San Diego, with typologies of evolutionary problem solving that we have developed to differentiate between spatial, temporal, and genealogical hypotheses or between evolutionary, genetic, and developmental biological levels of analysis. Back to the Top © Tree Thinking Group 2004. All rights reserved. University of Pittsburgh, Pittsburgh, PA 15260.");arrFiles[11]=new Array("projects.html","Tree Thinking Group: Resources - Projects","","","Projects American Institute of Biological Sciences http://www.aibs.org/ AIBS is becoming an important resource for science educators. Of particular interest to those of us teaching about evolution include: ActionBioscience.org which has a peer reviewed collection of evolution articles for educators and the general public. Evolution: Understanding Life on Earth which was the title of the 2002 Annual Meeting and the presentations are available (free of charge) to watch online from the virtual library. Evolutionary Science and Society: Educating a New Generation which was a two-day special symposium that was cosponsored by BSCS and the NABT. Quote from source: The American Institute of Biological Sciences was established as a national umbrella organization for the biological sciences in 1947 by 11 scientific societies as part of the National Academy of Sciences. An independent non-profit organization since 1954, it has grown to represent more than 80 professional societies and organizations with a combined membership exceeding 240,000 scientists and educators. BEDROCK Bioinformatics Education Project http://bioquest.org/bedrock/ This project site contains lots of resources for getting started with the analysis of molecular sequence and structure data to teach biological principles. The project emphasizes engaging students in research like problem solving and the use of an evolutionary perspective for making sense of comparative bioinformatics techniques. The problem spaces have collections of data and curricular materials around issues like HIV evolution, chimpanzee conservation, and the phylogenetic position of whales. Quote from source: BEDROCK (Bioinformatics Education Dissemination: Reaching Out, Connecting, and Knitting-together) is an NSF-funded project aimed at integrating bioinformatics throughout the undergraduate biology curriculum, using an inquiry-based approach in which students explore and analyze actual data in a way that recreates the experience of conducting research. Biological Sciences Curriculum Study http://www.bscs.org/ Credited with putting evolution back into biology textbooks in the 1960, BSCS continues to support excellence in science education through their curriculum development and teacher professional development activities. Quote from source: The Biological Sciences Curriculum Study (BSCS) is a nonprofit corporation that develops and supports the implementation of innovative science education curriculum for students in kindergarten through college. BSCS has developed integrated science programs for elementary and middle schools, and biology programs for high school and college students. In addition, BSCS provides professional development for the improvement of science education and conducts research and evaluation that demonstrates the effectiveness of reform-based science programs. BSCS is a leader in the field of science education because of our support for the teaching of evolution, our comprehensive approach to improved science teaching and learning, and our development and implementation of the BSCS 5E instructional model. The BioQUEST Curriculum Consortium http://bioquest.org The BioQUEST resources and community are an important resource for biology educators. Since 1986, BioQUEST has coordinated projects that engage students in problem posing, problem solving and peer persuasion. Quote from source: The BioQUEST Curriculum Consortium actively supports educators interested in the reform of undergraduate biology and engages in the collaborative development of curricula. We offer the following resources: The BioQUEST Library, BQ Notes, The BioQUEST Website, publications by project staff and participants, workshops and presentations for institutions and organizations, and support of an extended BioQUEST community. We encourage the use of simulations, databases, and tools to construct learning environments where students are able to engage in activities like those of practicing scientists. Evolution and the Nature of Science Institutes http://www.indiana.edu/~ensiweb/home.html Widely recognized as an important source of high quality evolution teaching units, ENSI continues to expand and serve teachers. Several specific resources from this extensive collection are highlighted elsewhere in this bibliography including Classification: Arbitrary or not? and, Molecular Sequences & Primate Evolution . Quote from source: The main objective of ENSI is to improve the teaching of evolution in High School Biology courses by encouraging teachers to teach evolutionary thinking in the context of a more complete understanding of modern scientific thinking. Modeling for Understanding in Science Education http://www.wcer.wisc.edu/ncisla/muse/ This curriculum development and educational research project from the National Center for Mathematics and Science at the University of Wisconsin – Madison has a detailed set of materials for teaching natural selection . Quote from source: Modeling for Understanding in Science Education (MUSE) is a collaborative project of university researchers, high school teachers, and students. The educational units found here are based on several years of research at a local high school. Each of these units contains extensive information and materials for use in middle school and/or high school classrooms. National Center for Science Education http://www.ncseweb.org/ The NCSE plays an important role supporting teachers who face resistance to teaching evolution and defending evolution education in public schools. Quote from source: The National Center for Science Education (NCSE) defends the teaching of evolution in public schools. We are a nationally-recognized clearinghouse for information and advice to keep evolution in the science classroom and scientific creationism out. National Conference on the Teaching of Evolution http://www.ucmp.berkeley.edu/ncte/ Quote from source: The purpose of the National Conference on the Teaching of Evolution (NCTE) was to bring together a broad representation of scientific, educational, and other interested professional organizations to improve the quality and accessibility of materials that support the teaching of evolution. The focus of the meeting was to develop an action plan to ensure that evolutionary principles are taught in pre-college, college, and teacher preparation classrooms as well as in the informal science environment. The proceedings from the meeting will be published by the Geological Society of America. The Tree of Life Project http://phylogeny.arizona.edu/tree/phylogeny.html This web site is a great place to reinforce the relationships between taxa and how they can be used to organize biological knowledge. Some of the well documented groups have images, references and links to other resources. It is also interesting because as an active research site it contains nice discussions of current phylogenetic controversies. See for example the discussion of bat phylogenetic relationships . Quote from source: A multi-authored, distributed Internet project containing information about phylogeny and biodiversity. The Tree of Life is a project containing information about the diversity of organisms on Earth, their history, and characteristics. The information is linked together in the form of the evolutionary tree that connects all organisms to each other. Back to the Top © Tree Thinking Group 2004. All rights reserved. University of Pittsburgh, Pittsburgh, PA 15260.");arrFiles[12]=new Array("resources.html","Tree Thinking Group: Resources - Getting Started","","","Getting Started The classification & evolution of caminalcules http://www.bioone.org/ Gendron, R. P. (2000). The classification & evolution of caminalcules. The American Biology Teacher 62(8):570-576 This article provides a nice introduction to the Caminicules as a resource for teaching evolution. The collection of 77 imaginary organisms was invented by Joseph Camin and this article describes several exercises using them that engage students in realistic evolutionary inquiry. Quote from source: For the purpose of teaching evolution to college and high school students, the Caminalcules offer several important advantages (McComas & Alters 1994). First, because Caminalcules are artificial organisms, students have no preconceived ideas about how they should be classified or how they are related. This means that students have to concentrate on principles rather than prior knowledge when constructing a phylogenetic tree or classification. Second, unlike everyday objects such as fasteners, the Caminalcules have a ‘‘real’’ evolutionary history, complete with a detailed fossil record. The comparative method, hypothesis testing and phylogenetic analysis http://www.bioone.org/ Singer, F., J. B. Hagen, et al. (2001). The comparative method, hypothesis testing and phylogenetic analysis. The American Biology Teacher 63(7): 518-523. This introductory article explores the relationships between comparative approaches in biology and assumptions about evolutionary relationships. It contains several classroom activities. Quote from Source: Textbook discussions of scientific methodology often focus almost exclusively upon controlled experiments, but biologists also use many non-experimental techniques for testing hypotheses. Particularly important are the comparative methods developed for phylogenetic analysis by biologists who study systematics. Today, these comparative methods can be applied at multiple levels of organization from behavior and ecology, to more traditional levels of gross anatomy and development, and downward to information carrying macromolecules (DNA, RNA and proteins). Nothing in biology makes sense except in the light of evolution http://www.pbs.org/wgbh/evolution/library/10/2/text_pop/l_102_01.html Dobzhansky, T. (1973). Nothing in biology makes sense except in the light of evolution. The American BiologyTeacher 35(March): 125-129. This oft cited American Biology Teacher article is still an important resource for biology educators. Quote from source: Seen in the light of evolution, biology is, perhaps, intellectually the most satisfying and inspiring science. Without that light it becomes a pile of sundry facts some of them interesting or curious but making no meaningful picture as a whole. Order and diversity in the living world: Teaching taxonomy and systematics in schools Crisci, J. V., J. D. McInerney, et al. (1993). Order and diversity in the living world: Teaching taxonomy and systematics in schools. Reston, VA, National Association of Biology Teachers. Quote from source: Recommended grade level: 1-8+. Order and Diversity in the Living World is a small book that presents a rationale for classroom study of biological diversity and the relationships between different organisms. It also offers a brief review of the current state of diversity and rate of species extinction, identifies standards that should encourage changes in the way systematics is taught in the classroom, and gives directions for 10 sample activities that involve students in doing systematics in the classroom rather than simply reading about the nature of this subdiscipline. -- Quoted from http://www.nap.edu/readingroom/books/rtmss/2.62.html PhyCom:: A Phylogenetic Community http://www.yphy.org/phycom/ Quote from source: Phylogeny Wing of University of California Berkeley, Museum of Paleontology http://www.ucmp.berkeley.edu/exhibit/phylogeny.html This rich collection of resources from the University of California - Berkeley, Museum of Paleontology (UCMP) is a great place for students to orient to the importance of phylogeny for understanding the unity and diversity of life on earth. The major exibits include a Phylogeny of Life section that can be accessed by taxon or geological period, and an introduction to cladistics called, Journey Into Phylogenetic Systematics. Quote from source: The Phylogeny Wing is the largest of our museum \'s on-line exhibit halls, with more than 235 individual exhibits, many with multiple pages. The wing provides a survey of biodiversity, focusing on major lineages of organisms. Many of these lineages have gone extinct or currently exist at a much lower diversity than in the past, so there may be large exhibits on groups of organisms that are unfamiliar to you. They are featured because they play an important role in the history of life on earth. Tree of Life Project http://tolweb.org/tree/phylogeny.html Quote from source: What, if anything, is a zebra? Gould, S. J. (1983). What, if anything, is a zebra? Hen \'s teeth and horse \'s toes: Further refections in natural history. New York, W. W. Norton & Co. In this short essay Gould uses cladistics to examine the appropriateness of the classificatory category zebra. There is a nice study guide developed by Craig Nelson with suggestions for how to engage students as they read this essay. ENSI reading guide Quote from source: The potential dilemma for zebras is simply stated: they exist as three species, all with black-and-white stripes to be sure, but differing notably in both numbers of stripes and their patterns. ... Do these three species a single evolutionary unit? Do they share a common ancestor that gave rise to them alone and to no other species of horse? Or are some zebras more closely related by descent to true horses or to asses than they are to other zebras? If this second possibility is an actuality, ... there is, in an important evolutionary sense, no such thing as a zebra. Back to the Top © Tree Thinking Group 2004. All rights reserved. University of Pittsburgh, Pittsburgh, PA 15260.");arrFiles[13]=new Array("science.html","Tree Thinking Group: Resources - Science/Philosophy","","","Science/Philosohpy Homage to Clio, or, toward an historical philosophy for evolutionary biology http://rjohara.net/cv/1988SZ.html O \'Hara, R. J. (1988). Homage to Clio, or, toward an historical philosophy for evolutionary biology. Systematic Zoology 37(2): 142-155. In this article Robert O \'Hara brings the philosophy of history to bear on discussions of the theory and practice of systematics and evolutionary biology. Part of his analysis draws sharp distinctions between the idea of a chronicle and narrative history. He also explores the difference between non-evolutionary questions about the states of characters and evolutionary questions about changes in characters. Both html and PDF versions of the article are available on-line. Quote from source: The ability to analyze evolutionary “why” questions in this way comes from what I call “tree thinking” (after Mayr’s “population thinking”). Tree thinking is absolutely necessary for answering almost all evolutionary “why” questions. A pre-evolutionary perspective on diversity results in what may be called “group thinking,” and state questions arise out of group thinking; it is tree thinking that allows one to convert a question of state into an evolutionary question of change. Phylogeny Programs http://evolution.genetics.washington.edu/phylip/software.html This huge annotated and cross referenced list of phylogenetics tools is maintained by Joseph Felsenstein at the University of Washington. Some of the listed software is free and available on the web while others are commercial tools that require licensing. You might want to consider the free programs PHYLIP - for building trees, and Phylodendron - for drawing trees. Quote from source: Here are some 194 of the phylogeny packages, and 18 free servers, that I know about. It is an attempt to be completely comprehensive. I have not made any attempt to exclude programs that do not meet some standard of quality or importance. Updates to these pages are made about twice a year. Population thinking and tree thinking in systematics http://rjohara.net/cv/1997Scripta.html O \'Hara, R. J. (1997). Population thinking and tree thinking in systematics. Zoologica Scripta 26: 323-329. A substantive introduction to the shift in perspective associated with tree thinking. Quote from source: Two new modes of thinking have spread through systematics in the twentieth century. Both have deep historical roots, but they have been widely accepted only during this century. Population thinking overtook the field in the early part of the century, culminating in the full development of population systematics in the 1930s and 1940s, and the subsequent growth of the entire field of population biology. Population thinking rejects the idea that each species has a natural type (as the earlier essentialist view had assumed), and instead sees every species as a varying population of interbreeding individuals. Tree thinking has spread through the field since the 1960s with the development of phylogenetic systematics. Tree thinking recognizes that species are not independent replicates within a class (as earlier group thinkers had tended to see them), but are instead interconnected parts of an evolutionary tree. It lays emphasis on the explanation of evolutionary events in the context of a tree, rather than on the states exhibited by collections of species, and it sees evolutionary history as a story of divergence rather than a story of development. Just as population thinking gave rise to the new field of population biology, so tree thinking is giving rise to the new field of phylogenetic biology. Tree basics, tree inference, and tree thinking http://www.abo.fi/fak/mnf/biol/nni/lec_nadler3.htm This on-line lecture by Steven Nadler at the University of California, Davis provides a basic introduction to phylogeny and the inferences made during tree building. It was presented as part of a course held at the Huso Biological Station, Abo Akademi University in Aland, Finland, in 2001. Quote from source: By the 1970 \'s, tremendous progress had been made in both the theory and practice of phylogenetics. Tree-thinking -- using phylogenetic trees as investigative tools -- is now a common research theme in all fields of biology. Open any issue of a biological journal (where research results are reported) and you are sure to find phylogenetic trees being used to understand biological processes. Therefore, it is essential for you to have an understanding of the basic elements of phylogenetic trees -- such as how they are constructed and interpreted. This handout will cover 2 topics: I. Tree terminology - providing basic information for understanding and interpreting phylogenetic trees. II. Tree inference - 1 example of how trees are constructed and used to study character evolution. Back to the Top © Tree Thinking Group 2004. All rights reserved. University of Pittsburgh, Pittsburgh, PA 15260.");arrFiles[14]=new Array("search.html","Tree Thinking Group: Search","","","within All text Title Keywords Descriptions using All words Any words Exact phrase © Tree Thinking Group 2004. All rights reserved. University of Pittsburgh, Pittsburgh, PA 15260.");arrFiles[15]=new Array("talks.html","Tree Thinking Group: Talks","","","Talks Reading topologies: A study of students \' understanding of relationships displayed in trees Scheduled for presentation as part of the symposium, The missing piece of the evolution-education puzzle: Teaching phylogenetics at introductory undergraduate and pre-college levels at the Evolution Meetings Fairbanks, AK. June 10-14, 2005 Symposium Chairs: David Baum, Sam Donovan HTML proposal Proposal PDF This presentation will describe the results of research into how students interpret branching diagrams and the importance of this skill for other aspects of evolutionary reasoning. Teaching the tree of life: What is tree thinking and why is it important for understanding evolutionary biology? Presented as part of the Tree of life panel in the symposium, Evolutionary science and society: Educating a new generation at the National Association of Biology Teachers Meeting Chicago, IL. November 10-13, 2004 Panel Chair: Christopher Haufler slides – coming soon Symposium Information from AIBS Tree thinking involves adopting a phylogenetic perspective when reasoning about patterns in biological phenomena. This presentation will provide an overview of the importance of tree thinking for making sense of the unity and diversity of life and identify areas where students have difficulties working with trees. Back to the Top © Tree Thinking Group 2004. All rights reserved. University of Pittsburgh, Pittsburgh, PA 15260.");arrFiles[16]=new Array("teaching.html","Tree Thinking Group: Teaching Resources","","","Teaching Resources Tree thinking assessments will be available soon. If you would like to be notified when they are available please contact Sam Donovan The WHIPPO Problem Space The WHIPPO Problem Space is a collection of resources for teaching and learning about phylogenetics and bioinformatics. The materials are built around a series of molecular sequence datasets that can be used to look at the evolutionary relationships between whales and hippopotami – hence WHIPPO. It is part of the BEDROCK Bioinformatics Education Project. Back to the Top © Tree Thinking Group 2004. All rights reserved. University of Pittsburgh, Pittsburgh, PA 15260.");