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CIPRES outreach

CIPRES outreach. Focus group leader: Brent D. Mishler Group members: M. Donoghue, D. Maddison, D. Swofford, T. Warnow, W. Wheeler.

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CIPRES outreach

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  1. CIPRES outreach Focus group leader: Brent D. Mishler Group members: M. Donoghue, D. Maddison, D. Swofford, T. Warnow, W. Wheeler

  2. CIPRES outreach activities have focused on educating the public about the tree of life and phylogenetic analysis. We have developed several education modules that are served on the web for free download. We have taught workshops targeted at high school science educators, and other members of the educated public. And finally we developed a traveling museum exhibit and supported a movie! CIPRES Outreach

  3. CIPRES outreach has developed several education modules introducing concepts such as phylogenetic trees, current knowledge of the tree of life, and the computational challenges surrounding its reconstruction. These materials were presented nationally in workshops targeted at high school science educators, and are being made available on the web for free download. CIPRES Education Modules

  4. Educational Website development • The Cladisticules - Created originally by Tom Stidham at UCB, this exercise introduces students to the steps in a basic cladistic analysis, and such concepts as homology and homoplasy. • Getting to the Roots of Plant Evolution - Developed in conjunction with Staci Markos of the Jepson Herbarium, and the Green Tree of Life grant, this education module covers the major events in land plant evolution, genomic and morphological characters, and cladistic analysis. • Building the Tree of Life - This web education module builds on the basic concepts presented in the exercises above, and introduces the use of molecular data and computer-based analysis.

  5. Getting to the Roots of Plant Evolution: Genomics and the Reconstruction of the Tree of Life Sponsored by the National Science Foundation, the Deep Gene Research Coordination Group, CIPRES, and the Jepson Herbarium, UC Berkeley.

  6. Introduction to the Lycophyta (Club mosses and scale trees) 7. Lycopodium, a lycophyte with microphylls The most significant feature of lycophytes is the microphyll, a kind of leaf that has arisen and evolved independently from the leaves of other vascular plants (megaphylls). The microphyll has only a single unbranched strand of vascular tissue (xylem and phloem), whereas megaphylls have multiple veins, usually branching one or more times within the leaf. According to one widely accepted theory (diagrammed below), microphylls evolved as outgrowths, called enations, of the main axis of the plant. Megaphylls evolved by fusion of branch systems. Microphylls cover the sporophyte, the dominant life phase in Lycophytes. The lycophytes are a small and inconspicuous group of plants today, but in the Carboniferous some lycophytes were forest-forming trees more than 35 meters tall. Lycophytes are the oldest extant group of vascular plants, and they dominated major habitats for 40 million years. The club mosses (Lycopodiales) are usually evergreen, and have been used as Christmas decorations, though their flammable spores and increasing rarity has made this illegal in some states. Other lycophytes, such as Selaginella, may form extensive carpets in the understory of wet tropical forests. 8. Evolution of microphylls (showing enations) and megaphylls.

  7. Phylogenetic Analysis of the Green Plants Data Matrix-Solution

  8. This web education module was created through the support of the Cyberinfrastructure for Phylogenetic Research project (CIPREs), an open collaboration funded by the National Science Foundation.

  9. In the previous exercise, you experienced building a cladogram from a data table. Now imagine that you wanted to construct a cladogram showing the evolutionary relationships of every organism that is alive today. Clearly, such a project is way too complex to complete by hand.

  10. As you learned before, all of life is related through evolution, and all of these evolutionary relationships can be represented by a branching (tree-shaped) diagram known as a cladogram. The cladogram for all living things is sometimes referred to as the “tree of life”.

  11. There are not many features of a bacterium, orchid, or frog that are appropriate for comparison. In this case, and in most real attempts at building a data table for the tree of life, the features that are compared exist at the molecular level, usually in the sequence of nucleotides that compose the DNA for a particular gene.

  12. The Jepson Herbarium is presenting a series of workshops for the educated public on The Tree of Life. One-day workshops in this special series cover topics related to current techniques and recent developments in our understanding of the evolutionary tree of life. The events have been fully subscribed and were praised by the participants.

  13. Jepson Workshops presented • Modern Techniques for Reconstructing the Tree of LifeDecember 11, 2004 • Some Like it Hot: Diversity and Ecology in the Archaea (the Third Domain of Life) February 5, 2005 • What Happened to “Plants”? February 26, 2005 • Ferns and Flowering Plants: What We Thought vs. What We Know April 23, 2005 • Species Concepts February 25, 2006 • Tree Thinking for Educators March 11, 2006 • Hominid Evolution March 25, 2006 • Molecular Phylogenetic TechniquesApril 8, 2006

  14. Jepson Workshops presented (cont.) • Microbial Diversity: The Final Frontier January 20, 2007 • Evolution and Genomics: The New Modern Synthesis January 27, 2007 • Assembling (and using) the Fungal Tree of Life February 3, 2007 • "Arm-chair" Tree-Building: Phylogenetic Analysis Using Bioinformatic Resources February 10, 2007 • Vertebrate Phylogenetics March 10, 2007 • Phylogenetics and Populations January 19, 2008 • Diversification and Radiations February 9, 2008 • Beneath the Crown: A Paleobotanical Perspective on the Green Tree of Life June 14, 2008

  15. Jepson Workshops presented (cont.) • Insect Diversity and Coevolution October 18, 2008 • Beneath the Crown: A Paleobotanical Perspective on the Green Tree of Life June 14, 2008 • Insect Diversity and Coevolution October 18, 2008 • California Biogeography and Phylogenetics March 7, 2009 • The Origin and Evolution of Dinosaurs April 25, 2009 . . ?

  16. Tree of Life Institutes at the American Museum of Natural History Institutes for high school teachers and students were developed under the supervision of co-PI Ward Wheeler. The American Museum of Natural History held its first CIPRES Tree of Life Institute on July 10-14, 2006. The second CIPRES Tree of Life Institute was held on July 9-17, 2007. The third and final CIPRES Tree of Life Institute was held at the American Museum of Natural History in late July, 2008. The Institutes introduced teachers and students from New York City to the use of cladistics and modern computational techniques for the analysis of morphological and molecular data to investigate the Tree of Life. AMNH scientists, instructors and graduate students showed participants the research conducted at the Museum, fossil and modern morphological data, the rapidly expanding molecular data sets, and the tools used to analyze this information.

  17. Tree of Life Institutes at the American Museum of Natural History (cont.) Scientists presented their work and lead tours of their facilities. The participants collected and analyzed their own morphological data using two computer programs: Mesquite and POY. The Institutes also include use of the new Sackler Educational Laboratory in the Spitzer Hall of Human Origins to give participants hands-on experience in gel electrophoresis and use of the great ape teaching collections for measurement of morphological characteristics of this group. Through these Institutes, participants developed an understanding of the data, the tools, and the techniques used in the study of phylogenetics. The students took that with them as they continue their science training here at the Museum and the teachers have developed plans to integrate these concepts into their high school curriculum.

  18. Some key elements of an exhibit: What is phylogeny -- phylogenetic relationship? The size of the Tree of Life -- how big is the problem? How do we make inferences about relationships? How certain are we about phylogenetic hypotheses? How does the tree relate to time and space? What can we learn from the Tree of Life? Why is this important? Some key practical issues: Intended audience Size/cost Modularity/replicability Interactives/games Personalities/thrill of discovery

  19. http://www.peabody.yale.edu/exhibits/treeoflife/index.html

  20. The exhibition includes the following major elements: Several films, including (a) an introductory animation of a growing tree; (b) a 12-minute movie on the meaning of phylogeny and the associated computational issues; and (c) a 4-minute movie on the importance of the Tree of Life for science and society; A section on inferring character evolution, featuring computer animations showing the morphing of body forms along the branches of an arachnid phylogeny (accompanied by a living scorpion and a living whip scorpion); A segment on convergent evolution, featuring living carnivorous plants and living succulent plants (including Pereskia cacti with leaves); An installation on extreme divergence, featuring a dinosaur skull and a hummingbird, and a panel on the water lotus and water lilies;

  21. Major elements (cont.): A set of exhibits on new Tree of Life discoveries, featuring (a) two living elephant shrews and an installment on elephants and other Afrotheria; and (b) the story of the relationships of Rafflesia (the world's largest flower) to tiny-flowered euphorbs; Two panels on the computational complexity of inferring phylogenetic relationships across the entire Tree of Life; A section on the practical uses of phylogenetic trees, featuring (a) a panel on making predictions based on phylogeny, including snake venoms and the "poison" in poison ivy; and (b) a section on diseases (HIV, rabies, etc.) and agriculture. A touch-screen game that invites children to help a house cat find it's way from the base of the Tree of Life up to the felid branch; to succeed, player answer questions that test their ability to properly "read" a phylogenetic tree.

  22. and a movie! Discovering the Great Tree of Life

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