CIPRES outreach
Focus group leader: Brent D. Mishler
Group members:
M. Donoghue, D. Maddison, D. Swofford,
T. Warnow, W. Wheeler
CIPRES Outreach
CIPRES outreach activities have focused on
educating the public about the tree of life and
phylogenetic analysis. We have 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
are being presented nationally in workshops
targeted at high school science educators, and
are being made available on the web for free
download.
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 plan is to develop a
solid template for the workshops at Berkeley
(tested mostly in the Bay Area), then to export
these templates to our collaborating institutions
back east and help their public programs people
present similar workshops there. The events so
far have been fully subscribed and were praised
by the participants.
Jepson Workshops presented:
• Modern Techniques for Reconstructing the Tree of Life
December 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 Techniques April 8, 2006
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.
Phylogenetic Analysis of the Cladisticules Data Matrix
1
head fused to thorax
yes (0)
no (1)
2
feet
two toes (0)
three toes (1)
3
number of legs
four (0)
six (1)
4
antennae
absent (0)
present (1)
5
horns
absent (0)
present (1)
6
thorax
white (0)
hour glass (1)
7
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 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.
Phylogenetic Analysis of the Green Plants
Data Matrix-Solution
1.
inv. repeat
absent (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.
sporophy
te 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
Gymnosperm
s
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 developed by a group of graduate
students at UC Berkeley, supported by CIPRES:
Published at: http://www.phylo.org/sub_sections/outreach/outreach_module.html
Cactus phylogeny exercise:
spines
Ferocactus sp.
Cereus sp.
areole
areoles
Phylogenetics of Early-Diverging
Cactus Lineages by Ruth Kirkpatrick,
Abby Moore, Bianca Knoll, Vicente Garcia,
Andy Murdock, Michael Park, and Anna
Larsen
Inferior and
recessed
ovary
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
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/).
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
Summary of Conclusions I:
1) Connecting with the familiar through legible labels, common names
and pictures.
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.
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 groupings,
such as "Birds" or "Green Plants" or "Lilies.“
4) Avoid perpetuating notions that trees display progress by using
radial layouts and/or interactivity that changes the order of things.
5) Support learning the conventions biologists use for branch lengths
by actively labeling what convention is being used, and by showing
the relationships between the different conventions for the same
set of organisms
Summary of Conclusions II:
For outreach, teachers want...
1) Simple trees they can use to illustrate a biological concept, that
are...
2) Labeled with common names, scientific names, and illustrations
or photos (familiar)
3) To show alternative trees for the same group of organisms, in
order to teach about the nature of science (how scientists do
their work)
4) All of this wrapped up into a proven curriculum that has been
developed in collaboration with professional educators and
meets their state standards.
LINKS TO AToL
• There is no funding for general AToL outreach,
so we have linked to the CIPRES outreach
pages from the AToL website.
• Many AToL grants have outreach components,
and we will continue to use the AToL / CIPRES
outreach pages to connect and leverage these
efforts.