CIPRES outreachCIPRES outreach

Focus group leader: Brent D. MishlerFocus group leader: Brent D. Mishler

Group members:Group members:M. Donoghue, D. Maddison, D. Swofford, M. Donoghue, D. Maddison, D. Swofford,

T. Warnow, W. WheelerT. Warnow, W. Wheeler

CIPRES outreach activities have focused on CIPRES outreach activities have focused on educating the public about the tree of life and educating the public about the tree of life and phylogenetic analysis. We have developed phylogenetic analysis. We have developed several education modules introducing several education modules introducing concepts such as phylogenetic trees, current concepts such as phylogenetic trees, current knowledge of the tree of life, and the knowledge of the tree of life, and the computational challenges surrounding its computational challenges surrounding its reconstruction. These materials are being reconstruction. These materials are being presented nationally in workshops targeted at presented nationally in workshops targeted at high school science educators, and are being high school science educators, and are being made available on the web for free download.made available on the web for free download.

CIPRES OutreachCIPRES Outreach

The Jepson Herbarium is presenting a series The Jepson Herbarium is presenting a series of workshops for the educated public on The of workshops for the educated public on The Tree of Life. One-day workshops in this special Tree of Life. One-day workshops in this special series cover topics related to current techniques series cover topics related to current techniques and recent developments in our understanding and recent developments in our understanding of the evolutionary tree of life. The plan is to of the evolutionary tree of life. The plan is to develop a solid template for the workshops at develop a solid template for the workshops at Berkeley (tested mostly in the Bay Area), then Berkeley (tested mostly in the Bay Area), then to export these templates to our collaborating to export these templates to our collaborating institutions back east and help their public institutions back east and help their public programs people present similar workshops programs people present similar workshops there. The events so far have been fully there. The events so far have been fully subscribed and were praised by the participants.subscribed and were praised by the participants.

• Modern Techniques for Reconstructing the Tree of LifeModern Techniques for Reconstructing the Tree of Life

December 11, 2004 December 11, 2004

• Some Like it Hot: Diversity and Ecology in the Archaea (the Some Like it Hot: Diversity and Ecology in the Archaea (the

Third Domain of Life)Third Domain of Life) February 5, 2005 February 5, 2005

• What Happened to “Plants”?What Happened to “Plants”? February 26, 2005 February 26, 2005

• Ferns and Flowering Plants: What We Thought vs. What Ferns and Flowering Plants: What We Thought vs. What

We Know We Know April 23, 2005 April 23, 2005

• Species ConceptsSpecies Concepts February 25, 2006 February 25, 2006

• Tree Thinking for EducatorsTree Thinking for Educators March 11, 2006 March 11, 2006

• Hominid EvolutionHominid Evolution March 25, 2006 March 25, 2006

• Molecular Phylogenetic TechniquesMolecular Phylogenetic Techniques April 8, 2006April 8, 2006

Jepson Workshops presented:Jepson Workshops presented:

Educational Website Educational Website developmentdevelopment

• The CladisticulesThe Cladisticules - Created originally by Tom Stidham at - Created originally by Tom Stidham at UCB, this exercise introduces students to the steps in a basic UCB, this exercise introduces students to the steps in a basic cladistic analysis, and such concepts as homology and cladistic analysis, and such concepts as homology and homoplasy.homoplasy.

• Getting to the Roots of Plant EvolutionGetting to the Roots of Plant Evolution - Developed in - Developed in conjunction with Staci Markos of the Jepson Herbarium, conjunction with Staci Markos of the Jepson Herbarium, and the Green Tree of Life grant, this education module and the Green Tree of Life grant, this education module covers the major events in land plant evolution, genomic covers the major events in land plant evolution, genomic and morphological characters, and cladistic analysis.and morphological characters, and cladistic analysis.

• Building the Tree of LifeBuilding the Tree of Life - This web education module - This web education module builds on the basic concepts presented in the exercises builds on the basic concepts presented in the exercises above, and introduces the use of molecular data and above, and introduces the use of molecular data and computer-based analysis.computer-based analysis.

Phylogenetic analysis of the cladisticulesData Matrix

(Solution)

1 2 3 4 5 6 7

head fused to thorax yes (0) no (1)

feet two toes (0) three toes (1)

numebr of legs four (0) six (1)

antennae absent (0) present (1)

horns absent (0) present (1)

thorax white (0) hour glass (1)

abdomen white (0) black (1)

Joe (OG) 0 0 0 0 0 0 0

April 1 1 0 0 1 0 1

Mike 1 1 1 1 0 0 0

Tanya 1 1 1 1 0 1 1

Bobby 1 0 0 0 0 0 0

Jason 1 1 1 0 0 0 0

Jerry 1 1 1 1 0 1 0

Jane 1 1 0 0 1 0 1

Getting to the Roots of Plant Getting to the Roots of Plant Evolution: Evolution:

Genomics and the Reconstruction of Genomics and the Reconstruction of

the Tree of Lifethe Tree of Life

Sponsored by the National Science Foundation, the Deep Gene Sponsored by the National Science Foundation, the Deep Gene Research Coordination Group, CIPRES, and the Jepson Research Coordination Group, CIPRES, and the Jepson

Herbarium, UC Berkeley.Herbarium, UC Berkeley.

Phylogenetic Analysis of the Green PlantsData Matrix-Solution

1.inv. repeatabsent (0)present (1)

2.inv. gene position no (0) yes (1)

3.cuticle absent (0) present (1)

4. stomata absent (0) present (1)

5. xylem & phloem absent (0) present (1)

6. megaphyll absent (0) present (1)

7. sporophyte domin. no (0) yes (1)

8.seed absent (0) present (1)

9.flower absent (0) present (1)

Green algae 0 0 0 0 0 0 0 0 0

Liverworts 1 0 1 0 0 0 0 0 0

Mosses 1 0 1 1 0 0 0 0 0

Lycophytes 1 0 1 1 1 0 1 0 0

Ferns 1 1 1 1 1 1 1 0 0

Gymnosperms

1 1 1 1 1 1 1 1 0

Angiosperms

1 1 1 1 1 1 1 1 1

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.

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.

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”.

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.

New educational module under development by a New educational module under development by a group of graduate students at UC Berkeley, group of graduate students at UC Berkeley, supported by CIPRES:supported by CIPRES:

Cactus phylogeny exercise:Cactus phylogeny exercise:

spinesspines

areoleareoleCereus Cereus spsp..

Inferior and Inferior and recessedrecessedovaryovary

areolesareoles

Ferocactus sp.Ferocactus sp.

Phylogenetics of Early-Diverging Phylogenetics of Early-Diverging Cactus LineagesCactus Lineages by Ruth Kirkpatrick, by Ruth Kirkpatrick, Abby Moore, Bianca Knoll, Vicente Garcia, Abby Moore, Bianca Knoll, Vicente Garcia, Andy Murdock, Michael Park, and Anna Andy Murdock, Michael Park, and Anna LarsenLarsen

II. Now perform a cladistic analysis of the already filled in DNA sequence data matrix: Here is the entire length of the molecular sequence data generated from the original research of Edwards et al. (2004) and “pruned” of species not used in this lab. The original data matrix in its entirety is stored at TreeBASE (http://www.treebase.org/treebase/).

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1) connecting with the familiar through legible labels, common 1) connecting with the familiar through legible labels, common names, and pictures.names, and pictures.2) simplification, with detail-on-demand - not all the data all the 2) simplification, with detail-on-demand - not all the data all the time, it's too much, but those who need it can retrieve it.time, it's too much, but those who need it can retrieve it.3) the ability to work at different scales of specificity, not just with 3) the ability to work at different scales of specificity, not just with the leaf nodes. So to be able to label and interact with larger the leaf nodes. So to be able to label and interact with larger groupings, such as "Birds" or "Green Plants" or "Lilies."groupings, such as "Birds" or "Green Plants" or "Lilies."4) avoid perpetuating notions that trees display progress by using 4) avoid perpetuating notions that trees display progress by using radial layouts and/or interactivity that changes the order of things. radial layouts and/or interactivity that changes the order of things. 5) support learning the conventions biologists use for branch 5) support learning the conventions biologists use for branch lengths by actively labeling what convention is being used, and by lengths by actively labeling what convention is being used, and by showing the relationships between the different conventions for the showing the relationships between the different conventions for the same set of organisms same set of organisms

Summary of conclusions I:Summary of conclusions I:

For outreach, teachers want...For outreach, teachers want...1) simple trees they can use to illustrate a biological 1) simple trees they can use to illustrate a biological concept, that are...concept, that are...2) ...labeled with common names, scientific names, and 2) ...labeled with common names, scientific names, and illustrations or photos (familiar)illustrations or photos (familiar)3) to show alternative trees for the same group of 3) to show alternative trees for the same group of organisms, in order to teach about the nature of science organisms, in order to teach about the nature of science (how scientists do their work)(how scientists do their work)4) all of this wrapped up into a proven curriculum that has 4) all of this wrapped up into a proven curriculum that has been developed in collaboration with professional been developed in collaboration with professional educators and meets their state standards.educators and meets their state standards.

Summary of conclusions II:Summary of conclusions II:

LINKS TO AToLLINKS TO AToL

•There is no funding for general AToL outreach, so There is no funding for general AToL outreach, so

we have linked to the CIPRES outreach pages from we have linked to the CIPRES outreach pages from

the AToL website.the AToL website.

•Many AToL grants have outreach components, Many AToL grants have outreach components,

and we will continue to use the AToL / CIPRES and we will continue to use the AToL / CIPRES

outreach pages to connect and leverage these outreach pages to connect and leverage these

efforts.efforts.