are rough notes taken down during the workshop itself by Anya Hinkle with
contributions by Russ Chapman. These notes are intended for archival purposes;
please excuse the rough edges -- we would appreciate getting feedback
from anyone about errors or omissions in this document. They have been
circulated to all participants for comment, but please don't quote people
DEEP GREEN and
DEEP GENE Workshop
17 FEB 2001
Westerbeke Ranch Conference Center, Sonoma, California
See also the meeting summary
1) Brent Mishler made opening remarks followed by introductions of all
2) Brent Mishler:
a) commented on the schedule of events and agenda for the day
b) reported on Friday press briefing at AAAS in San Francisco (more than
100 reporters present) and symposium (standing room only)
c) commented on the history of Deep Green and original grant in 1994 to
coordinate work among labs in phylogenetics. Deep Green has been mentioned
favorably by NSF staff including the Director Rita Colwell as an exemplary
collaboration, and even featured in NSF budget requests to Congress to
highlight the coordination of research among collaborators from different
fields/institutions. Three related, new initiatives have come from Deep
Green so far, leading to lots of coordination funds that can be used in
part to develop additional grant proposals for lab research funds.
1) Deep Gene - bringing together phylogenetics and genomics - a
Bay Area Biosystematists meeting held at Standford in May 2000 led
to an NSF RCN proposal that was funded; need to decide just what will
be done with the funds
2) Deep Time - a second NSF RCN headed by Doug Soltis to integrate the
fossil record into molecular phylogenetics. - (the PDF file of both proposals
were emailed to participants)
3) Biocomplexity - An NSF incubation grant for $100K, to begin collaborations
on genome evolution at the chromosome level; Pam Soltis PI
d)Future goals: It would be fine to have additional "spin-off"
proposals coming from this current activity with the idea of using the
ideas generated in funded meetings (like today's) to stimulate proposals
to fund actual bench work
e) Future goals: We need and want to incorporate more people in this activity,
not just the "core participants" listed in the proposal.
3) Roundtable on Current Research Activities in Participants' Laboratories
and Their Directions for the Future:
a) Rick McCourt: His research
focuses on Charophycean algae in cooperation with Chuck Delwiche and with
paleontologists in France. He is interested in comparative genomics of
Zygnematales using chloroplast and mitochondrial genomes. Major groups
of interest to him are Charophytes, a low diversity group but which have
a good fossil record, and conjugating green algae (Zygnematales) with
about 5000 species. He is interested in the evolution of algae and their
relationship to the land plants. Early efforts focused on phylogenetics
and rooting of land plant phylogeny, and now he is getting more into comparative
genomics, and the use of genes present in land plants, such as MADS box
genes and others, to see what they are doing and following them up through
b) Charles Delwiche: Rick McCourt
described their collaborative work on systematics and taxonomy of basal
streptophytes. In addition to this, the Delwiche lab also works on the
evolutionary origin of chloroplasts, and for this project they are currently
performing an EST study of photosynthetic dinoflagellates. One specific
problem concerning streptophyte phylogeny Delwiche is interested is the
relationship of Mesostigma to streptophytes, and in particular its relationship
to Chaetosphaeridium. Chloroplast genes put Mesostigma at base of the
streptophyte clade but if you look at rRNA Mesostigma pairs with Chaetopshaeridium.
In most particulars the chloroplast phylogeny is consistent with morphological
analyses, but the rRNA data show something quite different. Close analysis
reveals that there are two conflicting signals in the ribosomal data.
While the ribosomal data do include some signal that is consistent with
the chloroplast data, there is a second, conflicting signal that links
Chaetosphaeridium with Mesostigma. This may be the result of convergent
evolution of the ribosomal sequences, perhaps because of independent loss
or modification of one of the ribosomal proteins. Delwiche is looking
at the recently determined crystallographic structure of a bacterial ribosome
to test this hypothesis, and suspects that Chaetosphaeridium and Mesostigma
may have independently lost the ribosomal protein s8.
c) Chris Somerville: His interests have been in chemical diversity in
plants in for many years (this program is more or less coming to an end).
He comments on some of the results on lipid biochemistry obtained over
the years such as how fatty acid diversity arose. He found the enzymes
that modify fatty acids, by changing as few as 4 amino acids they were
able to change major features (i.e. double bond or hydroxyl). He sought
an understanding of how one chemical center, through small geometric changes,
can generate many different lipids. Another result relates to how plant
cell walls are made using Arabidopsis beta galactyltransferases with some
similarity to cellulase synthetase. They make mutations in most of the
genes, characterize the phenotype, and try to learn how they've evolved
to make a wide variety of polymers. They think that a large family of
enzymes has evolved using similar chemistry to polymerize sugars. Maybe
a thousand genes are involved in making cell walls but only three are
currently known; thus they are working on key enzymes via reverse genetics
to identify key enzymes and explain how they work. Other work in the lab
focuses on embryogenesis and looking at mutants with altered embryogenesis
using the genome sequence of Arabidopsis. Today they can get from enzyme
to gene (in "good" cases) in six weeks (six postdoc weeks as
opposed to up to 6 postdoc years a few years ago). For Arabidopsis there
is a rough idea of gene identification for about half the genome by sequence
similarity but we need to understand what the other half of the genes
(currently with unknown function) actually do. They have fairly significant
funding to find out what the gene functions are. There are some 200,000
secondary metabolites in the angiosperms yet there are not enough genes
to explain all of the chemical diversity that exists. Rapid evolution
of function must require some kinds of rules for understanding how different
classes of metabolites evolve.
d) Eric Roalson: (Liz Zimmer's
lab) The Zimmer lab is interested in molecular phylogenetics and evolution
and is currently working in the Gesneriaceae, Asteraceae and Onagraceae
(the latter with funding from a new Mellon Grant). We are also working
in collaboration with Judith Skog on fern phylogenetics. Eric Roalson
himself is working on the integration of developmental genetics with phylogeny,
and studying spur development in flowers in the Gesneriaceae (African
e) Dave Erickson: (Liz Zimmer's
lab) Dave is looking at outcrossing and epistatically interacting genes
(the number of genes involved and their relative effects). Using QTL mapping
and biometrics, he expects an outcrosser to have the advantageous genes
linked in contrast to an inbreeder, where the advantageous genes may be
distributed throughout the genome. He is estimating the number of genes
and how mating structure affects gene order on chromosomes.
f) Michael Zanis: (Soltis' lab)
The lab is continuing to work on angiosperm phylogeny looking at basal
angiosperms (e.g. Amborella and water lilies). They report continued strong
bootstrap support for Amborella as sister to all other angiosperms, but
cannot consistently reject all alternative hypotheses with the 11-gene
data set they have been using. They have been adding full length 26S rDNA
and matK sequences to the angiosperm dataset. They are also involved in
the Floral Genome Project with several other investigators. They are interested
in floral development (MADS box genes in basal angiosperm lineages and
B class genes in Nuphar and Illicium). Also they are looking at population
genetics and evolution of single copy and low copy genes in rare and common
species. He reports on two grants they have going currently. One supports
Biocomplexity work on the role of genome doubling in diversification of
plants and genome evolution following genome duplication. Empirical work
is focused on chromosomal reorganization in recent polyploids. The (other)
Deep Time grant integrates fossil and extant plant data sets.
g) Shauna Somerville: Research
in Shauna Somerville's lab focuses on questions in plant-pathogen interactions
such as "Why are some plants resistant?" and conversely "How
do susceptible plants contribute to disease development?" Most of
the recent work in the Somerville lab is directed towards understanding
the host components that contribute to susceptibility, using a mutant
approach. In addition to the projects on host susceptibility, the Somerville
lab is also studying host responses to foreign or nonhost pathogens using
Arabidopsis thaliana as a host and the barley powdery mildew, as the nonhost
pathogen. The final project is the Somerville lab relates to the use of
DNA microarrays to study global patterns of gene expression in Arabidopsis.
This technology, when coupled to gene expression databases, can be used
to develop "expression signatures" characteristic of plant responses
to attack by various pathogens for example.
Web page: http://carnegiedpb.stanford.edu/shauna/shauna.html
h) Steve Tanksely: His work focuses
on plant variation. His short term evolution project is how plants developed
large fruits, e.g. in Solanaceae (edible tomatoes from very small ancestor
plant). His research asks questions about how many genes are involved
in the process and what to they do? He used a cross between species and
then used QTL mapping to locate the genes for fruit size and shape in
tomato and found 25 loci that seem to account for the variation in tomato.
They have isolated a gene involved in a negative regulatory function.
He is also interested in what kinds of natural mutations occur (e.g. many
small changes in the regulatory region). One example is a change in stigma
insertion to accommodate selfing which is a single locus effect. Another
is the gene for fruit size is also a regulator of cell division to which
mutation reduces amount of gene product (a negative regulator of cell
division). It also shows a very distant similarity to a RAS protein, a
cancer - related gene in humans. What drives morphological evolution?
Eggplant has been studied and a similar gene involved in fruit enlargement
coincides with the tomato. His long term evolutionary question is how
does genome structure evolve over long periods of time (i.e., compare
different families separated in time)? Within the genomes of the two groups,
he would like to use QTL mapping to locate the genes for fruit size and
shape in tomato and eggplant. He needs to find highly conserved single
copy genes to compare among plants. The goal is to understand arrangement
and synteny among genomes.
i) Daphne Preuss: Her lab is
interested in pollination pathways involving proteins located on the surface
of pollen. In order to characterize the surface proteins they use mutants.
Two groups of pollen coat proteins have been purified and sequenced: glycine-rich
oleosins and extracellular lipases. One question is how do the proteins
vary from species to species? Does the diversity of these proteins result
in the ability to mate with stigmas of an appropriate genotype? They would
like to extend their work beyond Arabidopsis. Another project is the characterization
of centromeres, a region that is difficult to sequence. Five centromeres
have been sequenced in Arabidopsis - we now have more information on plant
centromeres than for human and other animal centromeres! One question
is which sequences within the centromere are most important to centromere
functionality? These should be the most conservative regions in the centromere
sequences. Some of the repetitive sequence regions may be involved in
condensation of the DNA. There seems to be signature sequences in these
genes for the species and for the ecotypes. Sarah Hall is working on genes
from different ecotypes and looking at polymorphisms. Conservative sites
may be protein binding sites. An example is a 180 bp repeat, similar to
the human alphasatellite178 bp repeat(180 is the length needed to wrap
a nucleosome). Since each organism has a signature sequence, they are
interested in finding out if the signature sequence plays a role in function.
j) Paul Wolf: His interests are
in fern phylogeny and more recently extending to relationships of vascular
plants (in conjunction with Kathleen Pryer). He is currently interested
in resolving deep land plant branches using genome sequence and structural
data. He is looking at how genomes evolve and how rare and/or complex
rearrangements can be used as phylogenetic markers. The initial focus
is with chloroplast genomes. Questions to be addressed include the resolution
of ambiguity and controversy regarding which extant group is the most
basal lineage of land plants, which groups are sister to the land plants,
and the positions of critical taxa with a long fossil record such as the
Equisetophyta. His current goal is the Biocomplexity proposal
to isolate and sequence about twenty chloroplast genomes. He is working
on developing techniques for analysis and visualization that can be used
to look at the genome on all scales from large scale inversions to small
indels and single base substitutions. These can be used both for visualization
and characterization of evolutionary changes. Dick Olmstead has detected
many phylogenetically-informative INDELS in plastid sequences, that were
useful at different levels. Ray Cranfill has also found length differences
that characterize the moniliforms (ferns and some of their "allies").
Finally, he is interested in comparing blue-green "algal" genome
sequences to chloroplast genomes to examine major rearrangements and trends
in gene movement across genomes since the original endosymbiosis.
k) Yin-Long Qiu: His research
follows two lines of inquiry. He began by sequencing a single gene (rbcL)
to look at the phylogeny of basal angiosperms with extensive taxon sampling
but without robust resolution. He then went on to look at the genomic
structure of organellar genomes. He focused on three introns in the mitochondrial
genes cox2 and nad1, and found that the gain of these introns as evidence
for the basal position of liverworts vis-a-vis hornworts in land plants.
Characterization of more mitochondria introns in his lab and other labs
supports the basal placement of liverworts. Currently, they are sequencing
eight genes across 150 land plants as well as the mitochondrial genomes
of a hornwort and a moss, to resolve several contentious issues in land
plants phylogeny. They have also sequenced five genes from mitochondrial,
chloroplast, and nuclear genomes and identified Amborella, Nymphaeales,
Illiciales-Trimeniaceae-Austrobaileya (ANITA) as the earliest extant angiosperm
l) Michael Sanderson: He and
Marty Wojciechowski are currently working on a difficult genus of angiosperm,
Astragalus. His interest is in using genomics and phylogenetics to understand
relationships in crown groups with recent divergence times. This requires
loci and introns from the nuclear genome since such events would be too
recent for the chloroplast genome. He is looking for nuclear spacers,
introns and third position regions for variability that can be used as
characters for a phylogeny. Because of the small amount of sequence divergence
(2-3%) it will require extensive sequencing of many genes and introns.
m) Yangrae Cho (postdoc in Virginia
Walbot's lab): The Maize Gene Discovery Project has been funded to this
lab for 2 years to support 1) 50,000 EST sequencing, 2)Transposon Tagging
and Mutant Archiving, 3) cDNA microarray fabrication. Currently, over
76,000 ESTs have been sequenced and deposited to GenBank and EST clones
have been distributed to diverse institutes, including individual researchers
upon requests. Transposon tagging, mutant archiving and microarray fabrications
are ongoing efforts. Three different issue specific microarrays were fabricated
at Arizona University and they have been distributed to maize community.
In the near future, 5 additional tissue specific microarrays and unigene
(over 20,000 probes) microarrays will be fabricated. All three categories
of work will be continued for coming three years. In addition to this
initial effort, we are exploring diverse applications of genomic tools
to evaluate genome annotation and to investigate exon splicing. Oligo
microarray method is one of many approaches. Our interest in RCN is in
two major aspects; evolutionary mechanisms of genome diversity and biochemical
n) Claude DePamphilis: His interests
are in parasitic plants, evolutionary genomics, and the use of mitochondrial
sequences in evolution and phylogenetics. He has completed a 2-gene mitochondrial
phylogeny (note that parasites have very rapid rates of gene evolution
for plastid and nuclear genes, and often very reduced plastid genomes)
of over 150 seed plants and angiosperms. Mitochondrial Cox-1 and atpA
together recover a phylogeny very similar to the recent plastid and nuclear
phylogenies, including recovery of the 40 APG orders. In addition, there
was clear resolution for many parasitic groups that were previously unplaceable.
He has been using the RASA approach to try to improve phylogenetic analysis.
In mitochondrial phylogeny studies it is important to remember that RNA-editing
is important; mitochondrial genes seem to be subject to retroprocessing
which has interesting implications. The other area in which they work
is the evolutionary origin of flowers and the floral developmental program.
Several labs (eg., Solti, Ma, Theissen, Albert, Frohlich, Tanksley) were
interested in similar questions and recently proposed a joint plant genome
project. This will primarily involve dense EST sequencing and high throughput
expression analysis of genes expressed during early flower development
in diverse angiosperms, and phylogenetic analysis. The EST approach will
generate many nuclear genes for plant phylogenetic and evolutionary studies.
We have linked this project with another recent proposal led by Brent
Mishler to systematically identify homologs of genes involved in reproductive
processes in ferns and bryophytes.
o) Kathleen Pryer: Kathleen
has had a long-term interest in the systematics and phylogenetics of ferns,
horsetails, and other basal tracheophytes (e.g., Osmunda, Equisetum, Psilotum,
Lycopodium). In a recent publication
that appeared in Nature, Pryer and her colleagues assembled and analyzed
five combined data sets -- from morphology and from four genes -- showing
that horsetails together with ferns form a major group of vascular plants,
that they are the closest living relatives to seed plants, and that they
have had a long evolutionary history separate from seed plants. This refutes
a general idea
that many botanists have, which is that ferns and horsetails are intermediate
transitional stages in plant evolution that eventually led to seed plants.
This deep split in vascular plant evolution has only been proposed once
before by Paul Kenrick and Peter Crane, on the evidence of a single anatomical
character. Efforts to promote developmental and genomic research on model
systems in the horsetail-fern clade (for example, Ceratopteris) will likely
lead to an improved understanding of vascular plant development and evolution.
Pryer is beginning to look at
mitochondrial and other nuclear genes to further resolve higher-level
relationships among non-seed tracheophytes. She is also collaborating
with paleontologists to integrate morphological data from fossil ferns
into phylogenies based on morphological, developmental, and molecular
data. Her work on aquatic heterosporous ferns is focused on better understanding
the evolution of heterosporic phenomena in vascular plants. The heterosporous
genus Pilularia has an exceptionally low chromosome number for ferns and
an astonishingly fast life cycle, indicating that it might also be an
excellent taxon to target for future model organism/genome sequencing
studies. In addition, these heterosporous ferns have indurate, protective
sporocarps that may be useful in physiological studies directed at elucidating
the mechanisms of dessication tolerance in land plant evolution studies.
p) Toby Kellogg: The big question
in which they are interested in is morphological diversification - What
changes in the genes are responsible for such diversity of form? Model
systems have genome maps and/or sequences, mutants, stocks, forward and
reverse genetics, transformation, multiple ways to assess gene expression
(antibodies, in situ, reporter constructs). Such tools are powerful for
model systems, and are still available as long as you can do crossing.
Once you move outside the sterility barrier, you have lost most of your
tools (i.e. mutants, stocks, forward/reverse genetics, transformation).
The grass family provides additional tools for understanding morphological
diversification as well as providing some models (rice has recently been
sequenced) because there is good alpha taxonomy, a good phylogeny, genome
maps, and information on cytology and physiology. Can we correlate molecular
evolution in expression of particular genes with changes in morphology?
To correlate gene expression with morphological change we need to have
a better characterization of the phenotype (developmental morphology and
histology). This includes the identification of candidate genes based
on the following criteria:
1) genes that are developmentally important - are they also evolutionarily
a) knotted1 (Tony Verboom)
b) leafy-Andrew Doust
c) B&C class genes
2) genes with mutant phenotypes which naturally occur in other species
(tassel seed2 - Simon Malcomber)
3) genes whose expression pattern is known to vary among the taxa of interest
(such as photosynthetic genes -Sinha & Kellogg 1996)
4) QTL studies on non-models with interesting phenotypes (S. italic X
S. viridis - Deros & Gale and Doust & Kellogg).
Future challenges involve developing more efficient methods for screening
for gene expression. She addresses a need for rapid primer design (aided
by genome sequences) and universal transformation systems.
q) John Doebley: His research
has two foci: 1) The first concerns the evolution of plant form in maize
and its wild relative teosinte. Here, the Doebley Lab is seeking to identify,
clone and characterize the genes that were involved in the morphological
evolution of maize. They are also seeking to do the same from genes involved
in the morphological evolution of different natural species of teosinte.
2) The second focus is a large-scale population genetics project (populational
genomics) for maize and its relatives that involves labs at two other
universities. They are attempting to define the population structure of
maize and teosinte, estimate gene flow among subpopulations, and determine
intraspecific "phylogenetic" relationships. Toward this goal,
they have currently assayed 200 microsatellite loci across the genome,
and they are trying to increase that number to 500. This large number
of loci will provide the power needed to reconstruct independently the
histories for different segments of the genome (i.e. individual chromosomes).
His collaborators are Major Goodman at North Carolina State and Steve
Kresovich at Cornell
r) Michael Gribskov is from
the San Diego Supercomputer center at UCSD. He is targeting functional
genomics of plants, mostly Arabidopsis. He is currently studying two classes
of enzymes, protein kinases and protein phosphatases. He is trying to
get insertional knockouts from the Wisconsin facility of every one. So
far, only three have a phenotype suggesting high functional redundancy.
He seeks to generate databases, archive data, etc. to build a framework
for information structure. Two major lines of questioning are 1)which
groups of kinases have been elaborated among lineages and which ones common
among plant species and can be traced through time using a phylogeny?
2) (with Mary Lou Guerno) what genes are involved in metal uptake (another
few hundred genes) for example, genes involved in flavonoid biosynthetiss?
He hopes to curate some 700 genes. He would like to address many common
technology needs for performing operations for storing and displaying
trees, and for doing analysis up and down trees. He is also involved with
peripheral work with microarray data, EST assembly of possible splicing
variants (mostly in animals, but could be also in plants), and how one
metabolic pathway changes into another through protein evolution.
s) Neelima Sinha: Her lab is
interested in leaf morphogenesis. Current work is using molecular and
developmental genetics to understand leaf structure and diversity in leaf
shape and degree of complexity . She commented on the NSF Workshop on
Evolution Of Development (EvoDevo) and the Tree of Life held at Washington,
DC. This workshop included representatives from plants, animals, and others.
The workshop proposed that NSF should fund the generation of yacs, bacs,
and EST tools for the next 100 genomes. This would be the takeoff point
for further work in the evolution of development and in resolving ambiguities
at critical nodes in the tree of life. She stressed that when the call
comes out for proposals there should be some idea of the 40 to 60 organisms
the plant group wants to focus on next and encouraged the group to begin
t) Russ Chapman: Research in
his laboratory over the years has focused on the Trentepohliales (subaerial
green algae in the Ulvophyceae). The unusual cluster of ultrastructural
features of these algae makes them unique. He uses RNA sequence data and
other molecular data to understand relationships among the algal lineages,
and the land plant - green algal relationships. The ultrastructure and
biochemistry of Trentepohliales united the group with 4 of the 5 major
green algal lineages (sensu Stewart and Mattox), a strange situation indeed!
The Trentepohliales are in the lineage that did NOT give rise to land
plants (i.e., they are in the Chlorophyta lineage not the Streptophyta
lineage), but the Trentepohliales have a phragmoplast-mediated cell division.
Some of the Charophycean algae closest to land plants (the Coleochaetales,
Charales, and Zygnematales) have a phragmoplast-type cell division similar
to that of the land plants. The presence of a phragmoplast-mediated cell
division in both the Chlorophyta and the Streptophyta lineages indicates
that the complicated fundamental cellular process of phragmoplast-mediated
cytokinesis may have evolved in parallel. Homology or non-homology of
the phragmoplast-mediated cytokinesis in the Trentepohliales vis-a-vis
the charophycean green algae may be demonstrated by comparative analysis
of genes associated with the cytolokinetic process.
Lab web site:
u) Bob Kuzoff: "I am completing
a Katherine Esau postdoctoral fellowship at the University of California
at Davis, in the lab of Charles Gasser, and will be starting my own lab
this fall at the University of Georgia. My graduate work employed phylogenetic
and classical microscopy approaches to explore floral diversification,
especially architectural changes associated with the evolution of ovary
position. As a postdoc I've endeavored to learn and employ molecular-genetic
and bioinformatic techniques to extend my understanding of reproductive
diversification in flowering plants. Presently, I am exploring the molecular-genetic
basis of developmental transformations among ovules associated with shifts
between anatropy and orthotropy, on the one hand, and bitegmy and unitegmy,
on the other. If we take the common ancestor of angiosperms to be bitegmic
and anatropous, then recent phylogenetic findings suggest that there have
been at least 14 transitions from inverted to upright ovules and at least
eight transitions from bitegmy to unitegmy across angiosperm phylogeny.
Through cDNA library screening and EST database searches, I have obtained
numerous orthologs of genes regulating these aspects of ovule development
in Arabidopsis. I am comparing expression patterns for these orthologs
in diverse angiosperms and plan to transform them back into Arabidopsis
to see if they complement corresponding mutants in this species. My lab
at the University of Georgia will continue working in this vein as well
as obtaining and characterizing orthologs
of additional genes relevant to other aspects of ovule and gynoecial development."
v) Mel Oliver: His lab has been interested in understanding the underlying
mechanisms of desiccation tolerance in plants. Much of his work has centered
on the effects of desiccation and rehydration on gene expression in Tortula
ruralis (a moss) and Sporobolus stapfianus (a grass). They are currently
trying to pinpoint the genes that are central to all mechanisms of desiccation
tolerance and those that are unique to individual systems. By doing this
they hope, among other things, to track the evolution of this trait among
all plants. His group has collaborated with an Australian group working
with Sporobolus stapfianus. In his studies he is employing the tools of
comparative genomics including the use of cDNA microarrays for expression
profiling They are also in the functionality of those genes and in collaboration
with David Cove Ralph Quatrano and others is trying to develop a homologous
recombination system with Tortula. They have just begun their microarray
analysis and have developed a small EST library. Their work includes biochemistry,
phylogenetics, and genomics and accumulates data on functionality of proteins
involved in the reassembly and repair of membranes. They have also, in
conjunction with Andrew Wood and Doug Gage, written an NSF proposal dealing
with comparative proteomics of the chloroplast, specifically a comparison
of Tortula and Arabidopsis chloroplast protein compliments.
w) Dennis Wall (summarizing the
Mishler Lab as a whole): The Mishler
lab group is united under the common interest of phylogenetic systematics
and comparative methods. Projects in the lab currently include phylogeny
and biogeography of tropical mosses, California ferns, and medicinal plants
of Polynesia. We have a long-standing interest in the phylogeny of the
green plants in general and mosses in particular, and gather data at both
the molecular and morphological levels. We are also interested in the
theory of how to analyze these data in combined, large-scale fashion,
and how to interpret the resulting trees evolutionarily (e.g., the relationship
between evolution and development of leaves and peristomes, and the evolution
of protein genes including codon usage bias). Several members of the lab
work under an NSF PEET grant on the tropical moss family Calymperaceae
and divide their time between the molecular lab and the field. New lab
interests include incorporating genomics data in plant phylogeny.
4) Scientific Issues:
Introduction: Brent Mishler commented
on the diversity of the group of plant biologists here assembled and the
goals of Deep Gene (what benefits the group activities should provide
for the phylogeneticists and the developmentalist/functionalists). We
hope that some members of this RCN will meet with members from the Deep
Time RCN at the Botanical Society of America meetings in New Mexico in
August 2001. He noted that the methodologies using genomics to build good
phylogenies are applicable to many types of problems from resolving deep
branches to looking at recent diversification events to understanding
the evolution of function and form. He reviewed the utility of good phylogenies
for those interested in functions and development. He first illustrated
the idea that by doing sister group comparisons it is possible to reduce
variance and narrow down predictions relating to the trait. This is done
by comparing closest relatives that show a change in function (i.e. one
taxon has the phenotype and one does not). This approach utilizes phylogenetics
to set the stage for asking questions about the basis for the presence
or absence of the function. In addition to sister group comparisons, ancestral-descendant
comparisons would allow you to track the evolution of a trait from an
ancestral state to its present complexity and find out what the genes
were doing in the less complex systems. This approach would be more informative
than trying to understand the basic elements of a highly derived complex
system by studying complex examples of it. In addition to using the comparative
methods approach to do comparative genomics, genomics can help to build
better phylogenies. When we understand the genomics better we may be able
to develop a better understanding of the evolutionary process.
Discussion plan: start with general
ideas and move on to more specific ones.
COMMENT (Steve Tanksely): It
has been said that phylogenies are more reticulate and less bifurcating
in general than expected (in a recent microbial genomics review), so how
does this effect phylogeny reconstruction since it assumes bifurcation?
COMMENT (Yin-Long Qiu): Most
of us working on molecular phylogenies have assumed that the phylogenies
are mostly bifurcating, but the distinction between prokaryote and eukaryote
systems is significant. And for bacteria the reticulation is more of a
problem but for eukaryotes there is little concern about reticulation
for big questions in the Streptophyta (perhaps more concern at the shallower
COMMENT (Brent Mishler): In a
sense the phylogeny is a self-correcting system in that reticulation might
lead to a "bush" but it wouldn't give you misleading result.
In such a case where there is no strong signal the result would be a lack
of resolution. Also, even for bacteria there are pretty good trees, which
couldn't be developed if there were too much reticulation, implying that
vertical transmission is giving an appreciably strong signal.
COMMENT (Chuck Delwiche): The
precise measure of horizontal gene transfer in prokaryotes is unclear.
Rosie Redfield argues against too much horizontal transfer but Doolittle
says there is a lot (it is the dominant factor). Even if horizontal transfer
is very common you can still construct an organismal phylogeny. Horizontal
gene transfer is a complication but it does not preclude phylogeny reconstruction.
COMMENT (Steve Tanksley): If
horizontal transfer is common in a lineage to the point that every gene
has a different true evolutionary history you can still make a phylogeny
if you have enough genes available.
COMMENT (Yin-Long Qiu): For the
plants so far the horizontal transfer doesn't seem to be a problem. We
are getting similar stories from different genes that are certainly vertically
COMMENT (Brent Mishler): Thus,
it would be good to have a bigger suite of genes and nuclear markers to
COMMENT (Daphne Preuss): Similarly,
the taxon selection available is an important factor. The group should
come up with a list of "critical taxa." We should try to avoid
a one-question-at-a-time approach and get the most data for the money.
COMMENT (Brent Mishler): Web
site development is one of the goals. The Deep Green project did generate
a key taxa list but we need a smaller set now for focus on taxa for genomic
COMMENT (Mel Oliver): We need
a basis for key taxon selection.
COMMENT (Claude DePamphilis):
Other features could help select key taxa for the core list of taxa.
COMMENT (Steve Tanksley): When
NSF first came out with the genomic sequencing programs, Craig Venter
was interested and submitted a major proposal that was turned down in
part because of question about the taxon selection for the project and
help from this group for a well-justified list of 50 plant taxa.
GENERAL DISCUSSION: of EST vs.
genomic sequencing; cost vs. data; prices are going down a lot; ESTs are
quick and less expensive but genomic approaches provide more information
which ultimately will be needed; need to consider size of genome, coverage.
COMMENT (Brent Mishler): Perhaps
it is time to discuss the NSF workshops on a large scale funding for the
Tree of Life - a post-genomics project (meetings at Austin, Davis and
Yale). Terry Yates has mentioned a possible $100 million/year competition
with several types of groups including a single national center like the
ecological center at UCSB plus center-oriented grants (for museums etc.).
Another component would be group oriented like Deep Green and Deep Gene,
and clearly we should attempt to secure one of those grants if they occur.
The final component will be to individual researchers. The biocomplexity
program proposals are due in March. We could submit one for a select group
of (10?) taxa to do chloroplast genomes and one for mitochondrial genomes
for the same taxa. There should be no problem with two proposals if we
avoid redundancy or inefficient use of the funding. They want to fund
about 11 of these and we could ask for two or three. Of course, they must
not be too dependent on each other and not too redundant. The first year
this program was microbial genetics. This year is very focused in terms
of what they wanted to fund via the biocomplexity program.
COMMENT (Mike Sanderson): Another
approach is to choose 20 most difficult plant phylogenetic questions.
COMMENT (Yin-Long Qiu): We really
want to know what happened in genomic evolution and thus the mitochondrial
genome evolution is particularly appropriate and potentially useful. Some
mitochondrial genomes are pretty stable and others (like Chlamydomonas)
are very different.
COMMENT (Brent Mishler): If you
are interested in the process of diversification and radiation, then recent
groups (as opposed to deep lineages) would give you a better chance to
explain the processes.
COMMENT (Daphne Preuss): Arabidopsis
relatives would be very fine targets with CHPs. There are about close
COMMENT (Mel Oliver): Are there
any desiccation tolerant relatives?
COMMENT (Bob Kuzoff): It would
be good to have things worked out for the close relatives and then move
out to other plants not so closely related.
COMMENT (Steven Tanksley): Phylogenetics
and function are two very different trajectories that use different genes
for different questions. For this you need a very good nuclear gene database.
It would be nice to have some closely related plants. Nuclear based datasets
would allow a great deal of other work on nuclear genes.
COMMENT (Michael Zanis): Taxon
sampling should include not only a bunch that span the tree but perhaps
a few that are closely related to allow comparisons.
COMMENT (Toby Kellogg): How much
information can you get from ESTs to answer some of the questions we have
been discussing (a comparable role for a set of genes)?
REPLY (Steve Tanksley): There
are some good questions that can be attacked via ESTs (examples in fruit
COMMENT (Neelima Sinha): We should
think big because the questions that we want to answer over the next 10
years will require ambitious projects and a larger number of taxa--we
should choose 50-60.
COMMENT (Paul Wolf): I agree
with Michael Sanderson's suggestion of focusing on some key questions.
We first need to ask, what are the questions and then where do we sample
and what techniques do we employ?
COMMENT (Steve Tanksley): The
phylogenetic-based taxon sampling is important, it allows us to follow
a gene across lineages.
COMMENT (Brent Mishler): These
are not mutually exclusive goals. It is clear that specific questions
would require different taxon sampling. We already have a Deep Green list
of 100-200 key taxa and could choose 20 key taxa from those. These taxa
would not be appropriate for all questions. This is kind of a community
service, a lesson for plant genomics. Pick 20-30 select genomes and let
people see what they would be doing with them. These are two different
COMMENT (Chuck Delwiche): I agree
these approaches are not mutually exclusive. A stratified sampling technique
might be helpful, as well as 20 crucial questions we'd like to address.
There might a group of about 60 taxa that would be an excellent starting
point even for those questions that require other taxa as well. It is
not a sequencing service to provide information on taxa just because they
are key taxa. For each specific question, would find significant overlap,
and simply provide the most useful resources for near and long time results.
GENERAL DISCUSSION: We don't
even know all the interesting questions are yet. There are interesting
questions we can ask right know. Deep Green did a lot of good things,
but guiding the community to focus on selected taxa was a failure despite
a lot of effort devoted to generating the lists. We need a list of organisms
to help provide a phylogenetic framework. Since the costs are coming down
and the capacity has been developed for the major sequencing projects,
it may not be too important to worry about the selection of the taxa since
we may be able to add taxa pretty easily. The development of analytical
methods to handle the data generated will become very important. The computational
problems are in some cases very complex. We don't have all the analytical
techniques we need to generate the new and better phylogeny even if all
the data were given to us. We will need prototype analysis methods and
5) Business meeting focused on specific activities for the RCN grant this
1) Brent Mishler: Discussion
of the RCN grant operational details:
a) 3 workshops per year (2 in association with a professional meeting
and one as a "retreat"):
i) this meeting
ii) Albuquerque, NM - 2nd week of August
Bot. Soc. Amer.
Deep Time group
Doug Soltis has organized an appropriate symposium
workshop on genomics techniques available
workshop on the "Exemplar Taxa" selection
iii) September Washington, D.C. Plant Genome project PIs will meet in
a hotel in Ballston (satellite meeting? at Arley or some similar place)
Liz Zimmer will host. Possible workshop topic: Tools for Phylogenetic
iv) Phycology Society of America workshop in Estes Park, CO low cost informational
meeting (perhaps a lunch)
b) exchange of graduate students (6 per year at 3 months each)open to
the students of the collaborators
c) summer interns for undergrads 12 per year open to the students of the
d) K-12 outreach for teacher 1 working meeting per year (rotate around
because we can't provide transportation for a large number of participants)
e) web support (grad student)
f) Steering Committee of 6 plus the PI (3 phylogeneticists and 3 genomists,
initially from the original collaborators that wrote the proposal, to
be rotated next year). Suggested slate: Steve Tanksley, Chris Sommerville,
Daphe Preuss, Kathy Pryer, Toby Kellogg, Yin-Long Qiu unanimously approved
g) graduate student representative: Jeff Lewandowski
h) membership/collaborators: should be expanded
i) there is a need to list major groups of taxa on which various
investigators are working (especially important for graduate students
who are trying to choose their dissertation problem so they don't get
scooped etc.) Criteria for choosing taxa are on the Deep Green web page
but need to be revised.
COMMENT (Toby Kellogg): The discussion
has focused on developing better phylogenies through organellar genome
studies but it should be noted that the need for nuclear genes and genomes
studies is key for developmental biologists. Also, antibodies or proteomic
techniques that are important for developmental studies are of interest
and importance to the developmental biologists. Having EST sets available
would help. The in situ hybridization approach is not efficient (too slow)
unless you already know the gene is one that is interesting.
COMMENT (Chris Sommerville):
It is important to develop a large set of ETS for taxa in which were are
interested so we can develop oligos needed to look for genes of interest
in any other species.
COMMENT (Brent Mishler): Early
on we need a set of ETS and need to get a grant to develop such a set,
but remember PIs need to submit proposal - this group doesn't submit proposals.
COMMENT (Chris Sommerville):
For the Arabidopsis group they had workshops and got NSF to issue RFPs
that reflected the recommendations of the community. This way, somebody
will submit the proposals and the work will get done.
COMMENT (Brent Mishler): Agreed,
we need to help guide NSF proactively, but we also need to be applying
for grants as they come up.
COMMENT (Paul Wolf): Are groups
in other countries who are doing this kind of thing? We do want to reduce
overlap and duplication. There followed a general discussion of what is
going on where. Members of this group should share information that they
may have about who is doing what etc.
Concluding remarks by Brent Mishler:
We have had a productive one day meeting and need to continue to share
information and keep thinking about what we can and should be doing.