Transcript Impediments to phylogenetic understanding of the green plants

CIPRES outreach:
The second year
Focus 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.
Teaching teachers about the tree of
life and how to discover it
Selected workshops and presentations aimed at high school
science teachers have included:
• A round-table discussion on the tree of life and computational
challenges, presented at the Botanical Society of America
Educational Forum in Snowbird, Utah on July 31, 2004.
• A hands-on workshop on teaching phylogenetics, the tree of
life, and basic computer-based phylogenetic analysis, presented
August 1, 2004 at the Botanical Society of America annual
conference in Snowbird, Utah.
• A hands-on workshop on teaching phylogenetics and the tree of
life, presented at the California Science Teacher Association
annual meeting, October 15, 2004 in San Jose, California (this
was attended by more than 150 enthusiastic people).
Activities (cont.)
• A talk on the use of language in teaching phylogenetics
was presented in a symposium on phylogenetics education
at the 2005 Evolution meetings in Fairbanks, Alaska.
• a hands-on workshop on teaching phylogenetics, the tree
of life, and basic computer-based phylogenetic analysis,
was presented at the Botanical Society of America annual
conference in Austin, Texas in July 2005.
• A summer program for high-school students and teachers
is being developed, initially at the American Museum of
Natural History, to focus on problems at the intersection
of biology and information technology.
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 and planned
• 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.
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Phyloge ne tic analys is of the cladis ticule s
Data M atrix
(Solution)
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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
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0
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Mike
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Tanya
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Bobby
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Jason
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Jerry
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Jane
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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.
Introduction to the Lycophyta
(Club mosses and scale trees)
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.
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.
8. Evolution of microphylls (showing enations) and megaphylls.
Phylogenetic Analysis of the Green Plants
Data Matrix-Solution
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inv.
repeat
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present
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inv.
gene
position
no (0)
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cuticle
absent
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present
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stomata
absent (0)
present
(1)
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xylem &
phloem
absent (0)
present
(1)
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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
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Liverworts
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Mosses
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Lycophytes
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Ferns
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Gymnosperms
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Angiosperms
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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
group of graduate students at UC Berkeley,
supported by CIPRES:
Cactus phylogeny exercise:
spines
Ferocactus sp.
Cereus sp.
areole
areoles
Cladistics 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
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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.
New York TImes
From http://ucjeps.berkeley.edu/TreeofLife/hyperbolic.php
Preliminary taxonomy of visualization approaches to
nested data structures.
matrix
indented text
whole tree depth first (like this list)
whole tree breadth first (many dichotomous keys)
path-plus-breadth lineage browser (BIOT, GenBank, old parts of tol website)
space-filling
linear: set-based display (Prometheus)
2-D: "tree"-map
"trees" - branching diagrams
navigated left-to-right
static - (Paup and many published trees)
interactive presentation
of fixed views (current tol website)
of dynamic views (taxonTree)
navigated bottom to top
static - (MacClade)
dynamic
hyperbolic (PEG)
center-to-outside layout
circle (UCMP Evolution website)
spiral
sphere (WALRUS)
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.
Conclusion and Future Work
Involve Teachers!
Test recommended features for learning
outcomes
Continue user-centered design and
development