of Prior Support:
Several of us (P. Soltis, D. Soltis, J. Doyle, M. Sanderson) have
been actively involved in the Green Plant Phylogeny Research Coordination
Group (GPPRCG or "Deep Green") since its inception in 1994. Deep
Green was organized to coordinate the reconstruction of the phylogeny
of all green plants, a major branch of the tree of life (over 500,000
sponsored meetings and workshops, and fostered large collaborations
on various groups of green plants (e.g., algae, bryophytes, ferns,
essence, however, the Deep Green initiative was modeled, in part,
on the success achieved by angiosperm systematists in their large
collaborative efforts to reconstruct phylogeny across all major
groups of angiosperms.This
was a grass roots effort that was initiated in 1991-1992 by D. Soltis
and M. Chase; it received no formal funding, but quickly resulted
in a highly successful major collaboration among 42 investigators
who provided a topology for angiosperms based on 500 rbcL sequences
(Chase et al., 1993).
the publication of the first comprehensive phylogenetic tree for
angiosperms (Chase et al., 1993) was a series of 13 companion papers
focused on major subgroups of angiosperms (organized by D. Soltis,
M. Chase, R. Olmstead). Together these 14 papers constituted an
entire issue of the Annals of the Missouri Botanical Garden (volume
80, number 3; 1993) and revealed the enormous advances that could
be achieved via collaboration on a grand scale.
and cooperation among angiosperm systematists have continued. D.
Soltis, P. Soltis, and D. Nickrent organized a collaboration of
17 investigators that resulted in a nuclear-based (18S rDNA) topology
for angiosperms (D. Soltis et al., 1997). Additional large collaborations
involving 16 investigators (organized by D. Soltis, P. Soltis, and
M. Chase) resulted in the compilation of a data set for three genes
(atpB, rbcL, 18S rDNA; nearly 5000 bp per species) for 560 species
analyses of this data set have resulted in a highly resolved and
well-supported topology for angiosperms (P. Soltis et al., 1999a;
D. Soltis et al., 2000). These collaborations have produced some
of the largest phylogenetic analyses ever undertaken on any group
of organism, resulting in a formal reclassification of the angiosperms
by The Angiosperm Phylogeny Group (APG, 1998), an international
group of 29 systematists.
This is the
first time that a major group of organisms has been reclassified
based largely on molecular phylogenetic hypotheses. Significantly,
it was conducted by a large group of investigators, rather than
by a single "expert," as has been the longstanding tradition in
all areas of systematics. In addition, numerous other papers have
subsequently resulted from the collaborations that we informally
initiated nearly a decade ago (e.g., Savolainen et al., 2000a, b;
Chase et al., 2000; D. Soltis et al., 1998; Mort et al., 2000).
have been extended from angiosperms to involve phylogenetic studies
of all land plants (P. Soltis et al., 1999b; Mishler et al., in
prep.). These collaborations have not only resulted in a firm understanding
of angiosperm relationships (APG, 1998; D. Soltis et al., 2000),
but also fundamentally altered the manner in which all systematists
approach the phylogenetic analysis of large data sets.
in many large, problematic groups of organisms (e.g., fungi, bacteria,
insects) requires the compilation and phylogenetic analysis of data
sets (DNA sequences and/or nonmolecular traits) for numerous taxa.
Although the phylogenetic analysis of large data sets involving
hundreds of exemplars often is central to understanding relationships
within many groups, the feasibility of analysis of these data sets
has been debated (reviewed in D. Soltis and Soltis, 1998; Chase
and Albert, 1998).
some maintained that large data sets were intractable and could
not be analyzed phylogenetically (see Graur et al., 1996). Significantly,
as a direct result of the efforts of collaborative research among
plant systematists, recent empirical and simulation studies suggest
that large data sets are much more tractable than thought only a
few years ago (Hillis, 1996; Graybeal, 1998).
is the addition of taxa and characters (a total evidence approach),
as demonstrated by D. Soltis et al. (1998). The large data sets
of angisoperm systematists were also a stimulus for the development
of computational advances, such as "fast" or "quick" search techniques
including the fast bootstrap (Swofford, 1998) and the parsimony
jackknife (Farris et al., 1996), and improved search algorithms
such as the RATCHET (Nixon, 1999).
our involvement with Deep Green and APG we are very familiar with
the benefits of collaborative science and also have considerable
experience in organizing and facilitating such undertakings. As
a result, we feel that our collective expertise will result in the
success of the current undertaking, "Deep Time," an integration
of paleontology and phylogenetics.
or flowering plants, comprising over 250,000 species and approximately
400 families, are, by far, the largest clade of plants and represent
the dominant group of land plants today. Putting things in perspective,
the angiosperms are at least five times as speciose as the vertebrates.
In both morphology
and chemistry, the angiosperms are highly diverse. In size, they
range from plants known as duckweeds (the genus Lemna) that
are roughly a millimeter in length to Eucalyptus trees well
over 100 meters in height. They also encompass enormous floral diversity,
with flowers ranging from less than a millimeter (Lemna, Lepuropetalon)
to a meter (Rafflesia) in diameter, and possessing just a
few floral organs (Chloranthaceae) to hundreds (Monimiaceae).
Owing to this
enormous diversity, the relationships among extant flowering plants
have, until recently, been highly contentious. Because of the apparent
sudden appearance of a diverse array of early angiosperms in the
fossil record, Charles Darwin referred to the origin of the flowering
plants as "an abominable mystery."
studies have shown that Early Cretaceous angiosperms were much less
diverse than was thought in Darwin's time; nonetheless, fossil evidence
indicates that the angiosperms radiated rapidly. Although there
are reports of earlier angiosperm remains, the oldest fossils that
are indisputably angiosperms are from the Early Cretaceous, about
130 million years ago (Sun et al., 1998; reviewed in Dilcher, 2000;
Crane, 1993; Crane et al., 1995; Magallón-Puebla et al., 1999).
Based on fossil
evidence, the angiosperms radiated rapidly after their origin, with
extensive diversity already apparent by 115 million years ago. By
90-100 million years ago, the angiosperms had become the dominant
floristic element on Earth. By 75 million years ago, many clades
corresponding to modern orders and families were already present.
have been realized in both angiosperm phylogenetics and paleobotany
during the past decade. We review the recent accomplishments of
both groups below.These
critical developments set the stage for the Research Coordination
Angiosperm Phylogenetics Until recently, the radiation of the angiosperms
was thought to have occurred so rapidly that many systematists thought
it might not be possible to identify the oldest extant angiosperm
lineages (see Chase and Cox, 1998). Furthermore, the circumscription
of, and relationships among, the major groups of angiosperms were
uncertain, with different modern classifications proposing different
patterns of relationship (e.g., Cronquist, 1981; Takhtajan, 1987,
1999; Thorne, 1992).
In large part
through the contributions of molecular systematics, our understanding
of extant angiosperm relationships and evolution has changed dramatically
in the past decade. Early studies using cladistic analysis of morphological
data (e.g., Donoghue and Doyle, 1989; Doyle and Donoghue, 1986;
Loconte and Stevenson, 1991) challenged long-standing views of angiosperm
relationships and evolution and quickly set the stage for molecular
sequencing efforts have prompted some of the largest phylogenetic
analyses ever conducted, ultimately resulting in a highly resolved
and well-supported topology for many of the angiosperms. Beginning
with individual genes such as rbcL and 18S rDNA, angiosperm systematists
constructed large DNA data sets containing hundreds of species (e.g.,
Chase et al., 1993; Soltis et al., 1997).
analysis of such large data sets was controversial, angiosperm systematists
combined data sets for different genes, revealing that one solution
to the computational problems large data sets pose is the addition
of taxa and genes (D. Soltis et al., 1998; Chase and Cox, 1998).
Other efforts have combined molecular and non-molecular data sets
(Doyle et al., 1994; Nandi et al., 1998; Doyle and Endress, 2000).
data set to date involves 560 angiosperms (and seven outgroup taxa)
sequenced for three genes (~5,000 bp per taxon). The topology provides,
for the first time, strong support (as measured by bootstrap or
jackknife values) for much of the spine of the tree, and for most
major clades (Fig. 1). Other studies have implications for the closest
relatives of the angiosperms (Bowe et al., 2000; Chaw et al., 2000).
1. Overview of angiosperm relationships based on phylogenetic
analyses of a data set of 567 taxa each sequenced for three genes
(from P. Soltis et al., 1999a). The relationships depicted among
basal angiosperms have been modified to reflect the increased
resolution and support realized in the analyses of data sets of
six genes and over 12,000 bp per taxon (Zanis et al., submitted)
and subsequent analyses based on ten genes and ~20,000 bp per
taxon (Zanis et al., in prep.). Similarly, relationships among
core eudicot lineages reflect new insights based on the recent
analysis of a four-gene data set of ~8,000 bp per taxon (Senters
et al., 2000). Numbers above branches are bootstrap values.
We review here
the topology for living angiosperms; this firm understanding of
extant angiosperm relationships is a major stimulus for the proposed
RCN (Fig. 1). Overview of angiosperm relationships based on phylogenetic
analyses of a data set of 567 taxa each sequenced for three genes
(from P. Soltis et al., 1999a).
depicted among basal angiosperms have been modified to reflect the
increased resolution and support realized in the analyses of data
sets of six genes and over 12,000 bp per taxon (Zanis et al., submitted)
and subsequent analyses based on ten genes and ~20,000 bp per taxon
(Zanis et al., in prep.).
relationships among core eudicot lineages reflect new insights based
on the recent analysis of a four-gene data set of ~8,000 bp per
taxon (Senters et al., 2000). Numbers above branches are bootstrap
values. Overview of angiosperm phylogeny--A series of recent studies
using different genes and different molecular approaches all agree
in identifying the same early branches of the angiosperm tree for
living taxa (P. Soltis et al., 1999a; D. Soltis et al., 2000; Qiu
et al., 1999; Parkinson et al., 1999; Mathews and Donoghue, 1999;
Graham and Olmstead, 1999).
The early branches
of the angiosperms are Amborella (a shrub endemic to New
Caledonia), the Nymphaeales (the water lilies), and the shrubs/lianas
Illicium, Schisandra, Trimenia, and Austrobaileya.
In addition to these early branches, there are a number of other
lineages of "basal angiosperms": monocots, Laurales, Magnoliales,
Chloranthaceae, Piperales, and Winterales (APG, 1998). Based on
the three-gene topology, each of these lineages is well supported,
but relationships among them were unclear (but see below).
Many of these
early-diverging angiosperms possess pollen with a single groove,
or aperture (line of weakness). Significantly, contrary to longstanding
classifications, there is no monocot-dicot split in the flowering
plants. In addition, the fact that the first branches of the topology
are well supported and not species rich and are followed by a number
of speciose clades suggests that the initial explosive radiation
of the angiosperms did not coincide directly with the origin of
flowering plants, but likely occurred slightly later (cf. Mathews
and Donoghue, 1999; P. Soltis et al., 2000).Following these basal
angiosperm lineages, the remaining angiosperms, representing the
majority (75%) of flowering plants, form a well-supported clade
referred to as the eudicots.
The early branches
of the eudicots are well supported and include Ranunculales, Proteales,
Trochodendraceae, and Buxaceae. These are followed by the core eudicots,
a clade that includes well-supported major groups such as asterids,
rosids, Caryophyllales, and Saxifragales. Additional resolution
and support of relationships among core eudicots has been achieved
by adding entire 26S rDNA sequences to the exisiting three-gene
matrix (Senters et al., 2000).
among Basal Angiosperms--Recent analyses have clarified those deep-level
relationships among basal angiosperm lineages that remained uncertain
in the three-gene analyses. Via the analyses of data sets of six
genes and over 12,000 bp (Zanis et al., submitted) and subsequent
analyses based on ten genes and ~20,000 bp (Zanis et al., in prep.),
relationships among these lineages are also well supported (Fig.
1), a result critical to this proposal.
analyses indicate relationships among major clades of basal angiosperms
identical to those reported by Qiu et al. (1999), but now all nodes
are strongly supported. Following the grade of Amborella, Nymphaeales,
and Illicium/Schisandra/Trimenia/ Austrobaileya, the clade
of Ceratophyllaceae + monocots is sister to all remaining angiosperms.
The Ceratophyllaceae/monocot clade is, in turn, followed by Chloranthaceae,
which are sister to all remaining angiosperms. Following Chloranthaceae,
Magnoliales and Laurales are strongly supported as sister groups,
as are Winterales/Piperales; together, these four lineages also
form a well-supported clade that is sister to the eudicots (Fig.
Paleobotany During the past 20 years there have been great strides
in developing techniques of investigation for early angiosperm remains,
great increase in the collection and description of fossil material
of early angiosperms, and an intense analysis of these fossil data
with special reference to floral morphological characters in relationship
to time of occurrence (Dilcher, 1979; Crane et al., 1995; Friis
et al., 1999; Magallón-Puebla et al., 1999; Crepet et al., in press).
of information available from fossil leaf, fruit, flower, pollen
grains, or wood allows us to use character-based comparisons with
extant angiosperms across taxonomic lines. These data can be assembled
from megafossils, mesofossils, and microfossils, which all yield
new information about taxonomic diversity and characters of early
amounts of data are becoming available each year. For example, Lower
Cretaceous sediments from Portugal recently yielded 105 different
kinds of flowers with 13 associated pollen types by the study of
mesofossils (Friis et al., 1999). Mesofossils are those small floral
buds, fruits, seeds, flowers, or plant parts recovered by sieving
the sediments. Mesofossils also have been studied from Cretaceous
sediments in New Jersey (e.g., Nixon and Crepet, 1993; Herendeen
et al., 1993, 1994; Crepet and Nixon, 1988a, b; Gandolfo et al.,
1998a, b, c; Crepet et al., in press), and Maryland through Georgia
(e.g., Crane et al., 1993, 1995; Herendeen et al., 1995, 1999; Crane
and Herendeen, 1996; Keller et al., 1996; Sims et al., 1998, 1999)
where numerous new taxa have been described. Reports of early angiosperm
flowers in China, which predate any other known flowers (e.g., Sun
et al., 1998), come from the megafossil record.
One of these
was reported as uppermost Jurassic, 142-145 million years old, but
this age was revised to 120 million years and is the subject of
some debate at this time. This emphasizes the need for us to include
a working group to evaluate the ages reported for the fossil material.
Also, we need to evaluate the fossils to be included in character-based
analyses of fossil angiosperm remains, such as those used by Magallón-Puebla
et al. (1999) to infer the presence of particular groups on the
major branching points of angiosperm phylogeny.
Deep Time Research Coordination Network-Deep Time RCN
above, molecular data have provided a robust phylogeny for extant
angiosperms. Concomitantly, paleobotanists have greatly improved
our understanding of early angiosperm diversity. Integrating fossils
into the tree of living taxa remains essential for understanding
not only the origin of extant angiosperm groups, but also the origins
of their structures (Doyle, 1998a, b). However, such attempts to
integrate fossils and extant taxa in phylogeny reconstruction have
been rare (e.g., Nixon and Crepet, 1998; Keller et al., 1996; Magallón-Puebla
et al., 1996; Eklund, 1999).
systematists and paleobotanists potentially have much in common
and each group has made major strides in the past decade, there
has been surprisingly little communication and integration of data
between the two areas. Systematists are often unaware of the significance
of fossil discoveries and of the characterizations of these fossils;
paleobotanists do not always think phylogenetically and hence lack
full appreciation of the excellent phylogenetic framework presently
available for living angiosperms.
Until the 1970s,
for example, fossil taxa were typically placed in relationship to
living genera. With few exceptions, paleobotanists have been reluctant
to define and name extinct angiosperm families or orders (reviewed
in Dilcher, 2000). The paucity of attempts to integrate fossils
into a phylogenetic framework can also be attributed to a necessary
reliance on morphology. That is, a morphological matrix for living
taxa into which to integrate fossils is a necessity, yet attempts
to formulate such matrices for angiosperms are relatively recent
and still incomplete (Nandi et al., 1998; Doyle and Endress, 2000).
attention to the formidable problems of character analysis has tended
to wane in the understandable enthusiasm for molecular systematics.
Other factors responsible for the lack of interdisciplinary work
include the difficulty in characterizing many fossils, and the analytical
issues that must be considered when integrating fossils into a phylogenetic
is now appropriate to develop a new synthesis of angiosperm paleobotany
and systematics/phylogenetics and a theory for integrating paleontological
and neontological perspectives. The required phylogenetic framework
for angiosperms is now in place (P. Soltis et al., 1999a; D. Soltis
et al. 2000; Qiu et al., 1999; Zanis et al., submitted) to provide
the underpinning for such a project.
considerable progress has been made in developing a morphological
matrix for basal lineages of angiosperms (Doyle and Endress, 2000).
The paleobotanical and plant systematics communities are each well
organized and exhibit a spirit of collaboration and cooperation;
these factors enhance the opportunities for interdisciplinary collaboration.
interactions between reseachers in both areas recently have been
established and strengthened (e.g., the sharing of unpublished morphological
and DNA sequence data by Doyle and Endress, 2000 and P. Soltis et
al., 2000). Hence, our proposed collaboration to integrate early
fossil angiosperms into a phylogenetic framework seems both timely
proposed RCN, we will use our collective expertise on Cretaceous
angiosperms and angiosperm phylogeny to develop a paradigm for the
integration of paleontology and phylogenetics. For several reasons,
we will focus initially on early angiosperm fossils (Cretaceous
in age), rather than all angiosperms.
- The early
diversification of the angiosperms is a critical time period of
are so numerous both in terms of extant groups and fossil taxa
that it would be difficult to begin with an all-encompassing analysis.
this project will focus on the Cretaceous record. This time period
corresponds to the origin and explosive radiation of early angiosperms
and the early branches of the eudicots (see Fig. 1). Importantly,
these are also the branches of the angiosperm topology that are
now best understood (Fig. 1); although the groups of core eudicots
are clear and well supported, their interrelationship is still uncertain
issues that we consider here and the approaches that we develop
will ultimately be applicable to all angiosperms, as well as to
other groups of green plants and other lineages of organisms in
our RCN quickly expanding to include other angiosperm fossils. For
this reason, several of the researchers included in this proposal
(as well as others to be invited) work on fossils of a more recent
age (e.g., Tertiary). In this way we are already anticipating and
preparing for future research that will include all angiosperms.
These and other researchers can contribute to the development of
analytical approaches for integrating fossils and extant taxa and
can immediately apply the approaches and tools developed for early
angiosperms to fossil angiosperms of a more recent age.
mission of Deep Time will be to facilitate, coordinate, and stimulate
new research at the interface of paleobotany, geology, and systematics/phylogenetics.
Our goal is not to co-opt the research of individual investigators,
but to promote new research opportunities. If, for example, a new
early angiosperm fossil is discovered and described and those investigators
wish to explore the possible phylogenetic placement of this fossil,
Deep Time will provide a vehicle for promoting that research by
facilitating contact/research among appropriate investigators.
Time opens new avenues of research, but does not compromise the
ongoing efforts of individuals. In the example provided, the phylogenetic
placement of this new fossil emerges as a separate research endeavor
from its initial description, representing a research opportunity
that paleobotanists perhaps would not normally consider.
It is our hope
that through Deep Time it will become a standard procedure for paleobotanists
to seek phylogenetic placement of fossils. Our considerable experience
with Deep Green has made us aware not only of the benefits of such
large collaborative efforts, but also of potential problems.
with Deep Green is that some working groups are too large to be
effective. We will therefore promote smaller working groups because
in our experience this is the most efficient and effective fashion
to promote research. This does not imply that Deep Time will be
exclusionary; to the contrary, we intend to maximize participation
by paleobotanists, systematists, geologists, and theoreticians via
a number of avenues (see below). For example, a number of investigators
other than those listed as Core Participants are interested in participating
at some level: B. Mishler, M. Donoghue, J. Davis, N. Arens, G. Brenner,
V. Krassilov, and L. Golovneva.
We feel that
by developing modest-sized working groups we will increase the speed
at which we make progress and enhance our chances of success. We
envision five major components to this collaboration:
and correct characterization of fossils to be analyzed;
time estimation of fossils;
of a morphological data matrix for clades of extant angiosperms;
of fossils into the angiosperm tree;
of branch points in the cladogram and studies of molecular evolution.
areas form the basis of five "Focus Groups," each of which is discussed
below, with initial group leaders listed. Participation is not restricted
to a single Focus Group; participants may be involved in one or
more of these groups.
Characterize and prioritize fossils (D. Dilcher, P. Herendeen, S.
remains are abundant and diverse in sediments of Cretaceous age
(e.g., Doyle, 1969; Doyle and Hickey, 1976; Dilcher, 1979; Dilcher
and Crane, 1984; Rodr’guez-de la Rosa and Cevallos-Ferriz, 1994;
Crane et al., 1995; Crane and Herendeen, 1996; Sims et al., 1998,
1999; Friis et al., 1999; Herendeen et al., 1999; Magallón-Puebla
et al., 1999; Dilcher, 2000). However, all fossils are not of equal
utility or value for phylogenetic studies. They range from single
pollen grains that may or may not possess distinctive identifying
features, to plants that are known from flowers, fruits, seeds,
pollen, and other plant parts.
be treated as exemplars, and we will establish criteria by which
fossils will be selected for inclusion in phylogenetic analyses.
Fossils that are reasonably complete and thus can be scored for
sufficient morphological characters (see below) can be included
in cladistic analyses to explore phylogenetic relationships and
evolutionary significance (e.g., Keller et al., 1996; Magallón-Puebla
et al., 1996, 1997; Crepet and Nixon, 1998).
do not have sufficient characters to yield a stable result will
be resolved in different positions on the cladogram and thus cause
the collapse of some clades in the consensus tree.Thus,
fossils that are reasonably complete will be targeted over those
that are more fragmentary.
"reasonably" is not a simple matter, and simply rejecting fragmentary
fossils is not appropriate because an incomplete fossil may possess
a single unique structure that is a synapomorphy for a single extant
group, with the result that the fossil is unequivocally resolved
on the cladogram (e.g., Magallón-Puebla et al., 1996).
are insufficiently complete to withstand cladistic analysis may
be of significance in other ways. For example, fossil triaperturate
pollen grains are referable to the "eudicot" clade, and therefore
the oldest fossil pollen grains of this form represent the minimum
age for the eudicot clade. Thus, fossils that cannot be included
in cladistic analyses can be of significance in analyses of evolutionary
is one significant difference between the fossils that are included
in cladistic analyses and those that are not. Current interpretations
of systematic relationships of fossils that are included in cladistic
analyses need not be correct because they can be reassessed using
the results of the analysis. In contrast, the identity of fossils
that are not included in cladistic analyses (e.g., triaperturate
pollen), but will be used to date divergences, must be correct.
fossils must be evaluated and selected with care. In selecting fossils,
our goal will be to maximize taxonomic diversity by seeking out
representatives of as many angiosperm clades as possible.
representation of clades through time is important for investigations
of rates of molecular evolution (see below). D. Dilcher, P. Herendeen,
and S. Magallón-Puebla will coordinate the discussions of
selection criteria and facilitate the prioritization and the selection
Correct time estimates (P. Herendeen, R. Christopher, R. Lupia)
be included in phylogenetic analyses and treated exactly like the
extant exemplars. Indeed, that has been the approach that Herendeen
and colleagues have taken in evaluating the relationships and implications
for floral evolution in Cretaceous angiosperms (e.g., Keller et
al., 1996; Magallón-Puebla et al., 1996). In fact, the age
of the fossils can be disregarded entirely if one chooses to do
discards the one unique aspect that fossils bring to evolutionary
studies-time. Fossils represent the minimum age of the taxon to
which the fossil can be assigned. When a fossil is included in a
phylogenetic analysis and occupies a stable placement on the cladogram,
it will represent the minimum age for the node where it is attached.
Thus, accurate understanding of the age of fossils is critical to
maximizing their utility.
The ages of
diverse localities from which fossils are collected are often open
to reinterpretation due to the discovery of new evidence or more
accurate dating methods. It is therefore important that age estimates
be as accurate as possible. Fossil sites that are amenable to radiometric
dating are relatively trouble-free and generally do not present
problems in estimation of age.
determination for fossil deposits derived from terrestrial sediments
in geological settings that lack appropriate rock for radiometric
dating can be more difficult. In such cases biostratigraphy using
dispersed pollen, spores, and other microfossils (palynology) must
be used to establish relative ages (e.g., Christopher, 1978, 1979;
Doyle and Robbins, 1977; Doyle, 1992).
between terrestrial palynological assemblages and assemblages from
near-shore marine deposits, which are generally easier to date using
radiometric methods, are used to assign an age to the terrestrial
deposits. To assist in this work we have included as Core Participants
two investigators with expertise in biostratigraphy: R. Christopher
and R. Lupia (both are in Departments of Geology). R. Christopher,
a palynological biostratigrapher who has worked on Cretaceous age
sediments, especially of eastern North America, will work with R.
Lupia, P. Herendeen, and others to determine which fossil sites
have accurate dates and which require additional study for an accurate
assessment of age.
Construction of a morphological matrix (D. Soltis, J. Doyle, W.
We will need
to establish guidelines for the characters used in construction
of a morphological matrix. As noted, the study of morphological
characters and problems of character analysis has received less
attention as more effort has been focused on molecular systematics.
of morphology is required for a synthetic analysis of fossils and
training and expertise in both paleomorphology and neomorphology
will be an important contribution of this RCN. An initial goal is
to develop a working list of morphological characters that could
potentially be used for extant taxa. Several existing data sets
can serve as starting points (Doyle and Endress, 2000; Nandi et
data matrices, it will be very important to take into consideration
the limitations that fossils impose. That is, of the many morphological
characters that can potentially be used for extant angiosperms,
which characters are actually present in fossils? For example, epicuticular
wax characters or features of embryology may be appropriate for
a morphological data set for living taxa, but of limited utility
for integrating fossils because they are not preserved. Many early
angiosperm fossils are fragmentary, in some cases known primarily
from pollen (see Characterize and prioritize fossils, above).
fossils are incomplete and lack some suites of characters (e.g.,
epicuticular wax, molecular data), this is not sufficient justification
to exclude these characters, which may be important in revealing
relationships among extant taxa. The issue of missing data in fossil
and extant taxa is addressed in the next section: Integrating fossils
into the angiosperm tree.
have been selected, they will be divided into their component states;
coding of these characters (e.g., presence vs. absence, multi-state,
continuous) will be another important consideration. Researchers
will also need to determine whether the species in the existing
DNA data sets will be used as terminals and their morphological
characters scored, or whether an entire family will be used as the
terminal and the variation encompassed by that family taken into
consideration. For example, Asimina and Annona are placeholders
for Annonaceae in D. Soltis et al. (2000).
These two genera
could be used as terminals and their morphological features alone
considered, or the variation across the entire Annonaceae could
be taken into account (Rannala et al., 1998; Kron and Judd, 1997;
Doyle and Endress, 2000). Annonaceae are a good example of the problems
that need to be discussed, because in both morphological and molecular
analyses, Asimina and Annona are both deeply nested within the family
and Anaxagorea is sister to the remainder of the family (Doyle and
Le Thomas, 1996). Hence, to accomodate greater phylogenetic diversity
for the family, the latter genus should probably be included as
a terminal if placeholders are used.
of a morphological matrix for living flowering plants will begin
by several groups of researchers working on separate groups of extant
plants. One group of researchers, for example, may take primary
responsibility for Winterales, another group for Magnoliales, monocots,
and so on. Conversely, some working groups may want to focus on
the careful evaluation of a particular character or suite of characters
to clarify homology and coding.
ties and collaborations in place among angiosperm systematists (APG)
will be extremely useful at this point in the process, as will the
existing Deep Green network. At this stage our research endeavor
will approach the interface between research coordination and actual
research (gathering/assembling of morphological characters). The
RCN will promote the coordination of this effort, but will not fund
the actual gathering of data.
assembling a morphological data matrix could be sought elsewhere.
More likely, the process will continue to be conducted by small
groups of investigators with expertise in particular groups, but
with the effort coordinated via RCN funding. The Deep Time RCN will
also play a vital role in coordinating the next research phase,
the compilation of morphological data into a single matrix.
of assembling a global data matrix from the many different sets
of disparate and overlapping characters for individual groups will
be crucial topics of discussion at workshops. Once the data have
been compiled for extant groups, researchers will then need to reevaluate
characters and refine the matrix for inclusion of fossils; some
characters may be considered unsuitable or uninformative, for example,
and therefore would be removed. It will be critical to have the
ability to bring together researchers to discuss and evaluate options
for constructing a global angiosperm matrix.
the Deep Time RCN will facilitate the compilation of a final, comprehensive
morphological data matrix for extant angiosperms.
Integrating fossils into the angiosperm tree (P. Soltis, J. Doyle,
fossils have rarely been integrated in a phylogenetic context for
any group, the Deep Time RCN will have several critical features
of data analysis to consider and discuss, both methodological and
analytical. The concepts and principles that are needed are still
not clear, and a major contribution of this RCN will be to stimulate
their development. Primary issues are missing data and the combinability
of molecular and morphological data sets.
envision three general approaches for placing fossils in the correct
phylogenetic position, and other alternatives may arise.
the taxa in the morphological matrix to conform to the DNA-based
topology already available and conduct a phylogenetic analysis
of the morphological matrix with fossils included. This approach
assumes that the molecular-based tree is correct and that the
inclusion of fossil groups would not change our inference of relationships
among extant groups.
the morphological matrix, with and without fossils, can be analyzed
phylogenetically. This approach does not take advantage of the
wealth of information provided by molecular analyses, but it allows
relationships among extant taxa to vary with the addition of fossils.
- All characters,
morphological and DNA, are used together to construct cladograms;
this can be done, both with and without fossils. Comparison of
the results among these analyses would follow. In some cases,
the differences between the analyses will likely be minimal. In
other cases, there may be substantial differences that will need
to be discussed and explored in more detail. Analyses that include
and omit fossils will allow us to assess the topological impact
of including fossil taxa. Fossils may play a critical role in
determining the final topology (e.g., Donoghue et al., 1989; Doyle,
and methodological issues involved in integrating extant and fossil
taxa will be addressed in a workshop dedicated to these issues in
Year 4 of the funding period.
Calibration of branch points in cladogram/molecular evolution (P.
Soltis, M. Sanderson)
are integrated into a phylogenetic framework, they can be used to
calibrate branch points in the cladogram, given that the improved
estimates of the ages of the fossils will be available (see II,
above). These divergence times will open up new research possibilities,
such as providing estimates of the ages of particular cladogenic
events and analysis of diversification rates (e.g., Sanderson and
Donoghue, 1994; Sanderson, 1997, 1998).
Given a good
phylogenetic framework, this information can also be used to date
nodes for which fossil data are lacking, using molecular clock methods
or related methods that allow for variation in rates of molecular
evolution (Sanderson, 1998). These estimates of divergence times
will also facilitate the study of molecular evolution of the genes
used to generate the cladograms (e.g., rbcL, atpB, 18S rDNA), plus
other genes that are currently under study in the angiosperms.
will link the Deep Time RCN with the proposed RCN uniting plant
phylogenetics and genomics ("Deep Gene," B. Mishler, PI). One of
the goals of Deep Gene is to provide a framework for studying the
evolution of genes and gene famiies across the angiosperms and ultimately
across all green plants. To facilitate successful coordination between
the two RCNs, D. Soltis, P. Soltis, and Y.-L. Qiu are Core Participants
in Deep Gene, in addition to their roles in Deep Time.
We will implement
the following activities to ensure the success of Deep Time: annual
meetings, workshops, student travel awards, student research training
awards, and website development.
An annual meeting
will be held in conjunction with the annual meeting of the Botanical
Society of America (BSA) on the day or days immediately following
the BSA meeting. In this manner, we can keep travel costs down,
given that most participants would attend the BSA meetings.
In Year 5 (2005),
the annual meeting will be held in conjunction with the XVII International
Botanical Congress (IBC) in Vienna.In
Year 1, the annual meeting will be two days in length to allow the
paleobotanists and systematists to "educate" each other on their
most recent accomplishments.
Day 1 will
be a presentation of paleobotanical perspectives and goals, and
Day 2 will be a presentation of systematics/phylogenetics perspectives
and goals. During each subsequent year, the annual meeting will
be held for only one day. During each annual meeting the goals and
objectives for the following year will be established; progress
to date will be discussed.
of postdocs and undergraduate and graduate students will be encouraged
One or two
two-day workshops per year will deal with the specific objectives
proposed (1-4 above).
In Year 1,
we will have workshops that will:
the fossil prioritization list, and
character guidelines (i.e., develop character lists and character
coding for extant taxa and discuss the limitations imposed by
In Year 2,
workshops will be held on:
and correct time estimates for fossils on the priority list, and
of the morphological data matrix with discussion of problems in
combining data matrices for different taxa.
In Year 3,
a single workshop will be held dealing with the integration of fossils
into the morphological matrix for extant taxa. This workshop will
be of broad conceptual interest outside of the Deep Time RCN and
will be organized to draw upon the expertise of biologists and theoreticians
outside of Deep Time.
In Year 4,
the single workshop will focus on
of branch points using fossil dates, and
- new analyses
of molecular evolution.
In Year 5,
a single workshop will be held prior to the IBC in Vienna to coordinate
presentations for the IBC and to plan for the IBC.
A similar series
of planning workshops was sponsored by Deep Green prior to the XVI
IBC in St. Louis in 1999 and was in large part responsible for the
cohesion of the symposia on green plant phylogeny. The angiosperm
workshop, for example, held in May, 1999, at Washington State University,
brought together the participants in the three angiosperm phylogeny
symposia and allowed them to collaborate and modify their presentations
prior to the IBC. We envision similar success with the proposed
workshop in Year 5.
of undergraduates, graduate students, and postdocs is critical for
the growth and development of the integrative research we propose.
We will award up to 10-15 student travel awards of $500 each per
year during the first four years of the funding period to attend
and participate in the annual meeting and/or the specialized workshops.Funds
are requested to provide 20 awards of $1000 each for travel to the
IBC in Year 5.
In that we
are proposing to train a new generation of students with interdisciplinary
skills, we envision two categories of research training opportunities.
Funds are not requested for research per se but to provide research
awards will allow students to visit a laboratory representing
a different discipline from that of the student's advisor for
up to two months. For example, a student in paleobotany could
visit a lab in molecular systematics, phylogenetics, or geology
to become directly exposed to research in those areas related
to his/her own research. Alternatively, a student in molecular
systematics or molecular evolution could visit a lab studying
angiosperm morphology and character analysis. Four such awards
of up to $2000 each will be made in Years 1 and 5, 5 in Year 2,
and 10 in Years 3 and 4.
training awards will allow students to attend one of several courses
available in phylogenetic theory and practice (e.g., Woods Hole;
Bodega Bay). Four such awards of up to $1000 each will be made
in Years 1 and 2, and six will be made in Years 3 and 4.
of a website for the Deep Time RCN is critical to the success of
this network. In addition to providing background information on
the Deep Time initiative and its goals, the website will serve as
a mechanism to connect the Deep Time participants.
A News and
Topics Page will highlight both phylogenetics and fossils in the
scientific and popular news.
Discussion Page will provide a forum for dialogue and exchange of
information among participants. This page will also allow us to
reach potential participants whom we have not yet identified and
to interact with those who have not yet participated in our meetings
and workshops. Through this mechanism we hope to expand the network
as the network develops.
Also on the
Deep Time website will be appropriate phylogenetic trees presently
available for basal angiosperms and early-branching eudicots and
a detailed geologic history of the Cretaceous. Very early in the
development of the website we will also begin to provide phylogeny
updates to the Tree of Life and TreeBASE; links to both will be
We will also
use the website as a repository for published data, such as the
molecular and morphological data sets available for angiosperms.
matrices (DAMs) will also be reported on the website. The Morphological
DAM will provide the character list, character-state coding, and
taxon list (with both species as terminals and a mixture of species
and clades as terminals cf. Doyle and Endress, 2000) that are developed
by the Morphological Matrix Focus Group. The DAM will also indicate
which data are available and where.
a page that would allow one to click on a specific cell and be linked
to a page that shows what data are available for that cell and where.
For example, if one clicked on floral characters for Ericales, a
page listing the relevant publications by Judd and Kron and others
would appear. Also, if appropriate, this page would indicate the
name and contact for any participant who wishes to share unpublished
DAM will provide the names, organs, dates, references, and contacts
of relevant fossils. The fossil priority list will also be posted
here. We propose to develop a "Virtual Fossil Collection" that will
serve as both a research tool and an educational vehicle.
drawings, and images from microscopy of Cretaceous fossils, beginning
with those on the priority list, will be incorporated into the collection.
The rationale for this is that few systematists are keenly aware
of the fossils and their morphologies. We plan to design this collection
with a magnification feature that will allow viewers to zoom in
on a specific structure or region of the image.
of this feature may require consultation with a software developer
such as Inxight, with whom Deep Green has worked to develop the
hyperbolic phylogenetic trees on the Deep Green website. We will
include only those images that have been donated to the collection
and those published images for which we have obtained copyright
permission. Each image will be labelled with the name of the author
and the Deep Time RCN label. Relevant references for each image
will also be provided.
Fossil Collection will also serve as an important educational tool
for students at a variety of levels. To promote this educuational
component, we will have links to the Botanical Image Collection
of the award-winning website of the Botanical Society of America
with its well-developed educational outreach (see below for details).
We will establish
links to the websites of other research networks, including Deep
Green and Deep Gene, to promote connections among these projects,
and to various phylogenetics sites, such as the site of the University
of California--BerkeleyŐs Museum of Natural History, for outreach
Time RCN--Organization and Structure
for co-PIs: We understand that NSF's RCN Working Group anticipates
a single PI for most RCN proposals. This RCN is broadly based and
ambitious, and we strongly feel that the proposed network is enhanced
by shared leadership among a PI and multiple co-PIs. D. Soltis,
P. Soltis, D. Dilcher, and P. Herendeen are all very dedicated to
the success of Deep Time. All four have contributed equally to the
proposal and have already demonstrated an ability to work together
are trying to bridge the gap between two disciplines (paleobotany
and phylogenetics/systematics), the leadership of the RCN requires
a strong presence of both groups. Strong representation from both
systematics and paleobotany will help inspire possible participants
from both fields. Most importantly, the proposed coordination activities
are extensive and can best be implemented by dividing the responsibilities
among a small number of dedicated organizers.
Each of the
four PIs will lead one of the Focus Groups; this will involve setting
priorities and coordinating activities for the group, enhancing
communication within the group, monitoring the progress of the group,
and organizing a workshop for the participants in the Focus Group.
The PI, D.
Soltis, will oversee all aspects of the project: he will facilitate
communication among the five Focus Groups, organize the annual meeting
of the RCN, serve as the leader for Focus Group III, and supervise
the development and maintenance of the website.
Co-PI D. Dilcher
will be the leader for Focus Group I and will coordinate discussions
and facilitate the assembly of the fossil priority list.
Co-PI P. Herendeen
will oversee the assembly of the Virtual Fossil Collection and will
also be the leader for Focus Group II.
Co-PI P. Soltis
will be the leader for Focus Groups IV and V, coordinate the training
activities and funding opportunites for students and postdocs, and
work with the Botanical Society of America's Education Committee
(of which she is a member) in K-12 outreach (see below).
leadership of the Focus Groups among the PIs will result in focused
and sustained effort on all objectives simultaneously. This concentrated
effort within Focus Groups, combined with effective communication
among Focus Groups, will produce an active and interactive network
of researchers. Rather than a hindrance, we feel that having coPIs
enhances our chances of success.
structure may be an exception among RCNs, it is the best organizational
plan for this network. [Note that the Green Plant Phylogeny Research
Coordination Group ("Deep Green") also had multiple PIs. This structure
was particularly effective in bringing together algal systematists
(led by PI M. Buchheim and co-PI R. Chapman) and land plant systematists
(led by co-PI B. Mishler); no single PI could have brought these
groups of researchers together.]
will be modelled on the successful structure of the Deep Green consortium
and on the PIs' experience on the Executive Committee of the Botanical
Society of America, a professional society of nearly 3000 members
(D. Soltis, current President; P. Soltis, current Secretary; D.
Dilcher, former Program Director, President, and Secretary).
Organization: Membership in the network is open to all interested
scientists in the fields of paleobotany, plant morphology, phylogenetics,
and geology. Because many of the issues we plan to address (e.g.,
the integration of fossils into phylogenetic analysis, dating of
divergence times) are not restricted to plants, we will involve
theoreticians, paleontologists, and phylogeneticists who work on
other groups of organisms.
To date, the
PIs have identified and contacted a number of investigators who,
based on their past research, seem likely to be interested in participating
in the proposed RCN. Those who responded positively are listed as
Core Participants or as interested in particpating.
broader participation in the future, the PIs will send letters of
invitation to the first annual meeting to key researchers and those
identified by the Core Participants as likely to be interested,
and information on the meeting will be posted on the RCN's website
and the websites of other relevant groups and societies. Similar
procedures will be followed in subsequent years; through this process,
we hope to encourage the participation of all interested individuals.
efforts will be implemented and supervised by an Executive Committee
(EC) composed of six regular members and two student/postdoctoral
members (initially M. Zanis and S. Magallón-Puebla). The
PI and co-PIs will serve on the EC for the duration of the funding
period (5 years), and W. Judd and J. Doyle will each serve initial
three-year terms, rotating off after three years, with two new members
rotating in for three-year terms.
At the end
of the funding period, two of the PIs will rotate off and be replaced
by two new members. After two additional years, two new members
will replace the last two PIs still on the EC. From that point on,
additional EC members will serve three-year terms, with two members
rotating off each year. This long-term strategy is important given
that we see the mission of Deep Time extending beyond the five-year
period of this grant.
members will serve two-year terms. The composition of the EC will
maintain a balance of research expertise, gender, ethnicity, geography,
and age, to the extent possible. Terms of the EC will begin and
end with the annual meeting of the entire RCN membership, generally
in conjunction with the annual meeting of the Botanical Society
The PI (D.
Soltis) will serve as Chair of the EC and act as website coordinator/supervisor.
He will supervise the efforts of the webmaster and coordinate the
dissemination of information from the EC to the membership. The
website coordinator/supervisor will serve a role much like that
of an editor of a society-sponsored journal and will report to and
work with the EC.
The EC will
have the responsibility for all fiscal decisions. Most of the funding
requested is to support the participation of members at meetings
and workshops. Funding will be on a reimbursement basis only. Rather
than providing full funding for participants to meetings and workshops,
we prefer to provide partial support to a larger number of participants.
We will provide additional funds, if needed, to new investigators
and/or to participants located in remote or distant areas from the
meeting sites to ensure maximum participation.
above, we will also provide travel support and research training
opportunities to post-docs and students. Co-PI P. Soltis will coordinate
the training activities and funding opportunities for post-docs
and graduate and undergraduate students. Regular announcements describing
upcoming travel awards to meetings and cross-training opportunities
in other labs will be posted on the RCN's website and other relevant
websites and disseminated via e-mail to all RCN members.
Awards Committee, chaired by P. Soltis, will establish selection
criteria for each award, review applications, and make funding recommendations
to the EC, which will make the final decisions. P. Soltis served
on the Deep Green committee for student travel awards and has extensive
experience in this area, having chaired the American Society of
Plant Taxonomists' Honors and Awards Committee and Washington State
University's Department of Botany Graduate Student Advisory Committee.
Each of the
research themes described above will be the topic of a Focus Group.
Members of the RCN may participate in one or more of these Focus
Groups, and additional Focus Groups may be established throughout
the course of the funding period. Each Focus Group will be facilitated
by a Leader (or co-Leaders). Initial Leaders have been selected,
but these Leaders of the Focus Groups may change throughout the
course of the funding period; new Leaders will be selected by participants
in the respective Focus Groups.
of Management Activities
in each Focus Group will communicate via e-mail, plus other avenues
devised by the Group. Leaders of the Focus Groups will meet monthly
via conference calls to discuss progress, upcoming workshops, etc.
The EC will also meet monthly via conference call to monitor progress
and plan future events. All participants will meet annually, most
likely in association with the annual meeting of the Botanical Society
of America. The EC will also meet at this time. The PI will meet
annually with the PIs of other RCNs, as specified by NSF.
of Research Coordination Activities
first few months of funding, the EC will set a series of goals,
with estimated times for completion, for the group as a whole. These
goals will be discussed by the entire membership at the first annual
meeting and modified as considered appropriate. For example, target
dates for completing a list of morphological characters and how
they should be coded and for prioritizing a list of fossil materials
for possible inclusion will be set by the EC and evaluated by all
participants. At the conclusion of each workshop, symposium, meeting,
or other group event, a questionnaire will be distributed to all
participants to gauge their satisfaction with the operation and
productivity of the session.
The PI and
co-PI P. Soltis will work with the Social and Economic Sciences
Research Center at Washington State University, a nationally-regarded
research survey and polling center, to develop an appropriate questionnaire.
The EC will consider the suggestions reported in the survey and
make appropriate changes in the operation of future meetings. The
PI will have ultimate responsibility for assessing the progress
of the RCN.Based
on our participation in Deep Green, we are very hopeful that this
will be a positive and productive experience for all participants.
RCN will interface with Deep Green and with another proposed RCN
(B. Mishler, PI) on the integration of plant phylogenetics and plant
genomics. The Soltises are involved in all three efforts: P. Soltis
is a member of the Deep Green Executive Committee, and both D. Soltis
and P. Soltis are Core Participants in the proposed phylogenetics/genomics
RCN, as is Y.-L. Qiu. We will therefore be able to keep abreast
of the activities and progress of all three groups.
correspondence and meetings of the leadership of all three networks
will maintain communication and lead to joint sponsorships of workshops
and colloquia (e.g., a joint workshop on phylogenetics for molecular
biologists and paleobotanists). Through coordination among these
RCNs, the network of interacting scientists will expand to include
geologists, paleobotanists, morphologists, phylogeneticists, and
because the PIs of this RCN are active in their respective professional
societies, they will be able to coordinate symposia and workshops
sponsored by the RCN with the scientific programs of the societies'
annual meetings. Information and Material Sharing: Part of the success
of Deep Green is undoubtedly the clear and repeated commitment by
the organizers to individual ownership of data prior to publication
and proper attribution of contributions by collaborators. We will
therefore model the proposed RCN on this commitment.
on the RCN website we will present "Data Availability Matrices"
(DAMs) rather than "data matrices" to protect the data of individual
investigators. The DAMs will indicate what data have been collected,
by whom, and the relevant citation for published data. These DAMs
will prevent duplication of research effort and suggest possible
collaborations by reporting who is doing what. Contribution of data
to collaborative analyses is not required by participants in the
RCN, although we anticipate that those who participate will be interested
in exploring such collaborations.
Virtual Fossil Collection will be a product of the RCN's activities,
but credit for its construction will be given to those individuals
who develop it. Each image will be labelled with the contributor's
name and the RCN label. Likewise, any methodologies or software
for the joint analysis of fossils and extant taxa or for dating
divergences will be credited to the developers.
RCN welcomes participation by a diverse array of scientists and
will encourage participation by under-represented groups and those
individuals in diverse types of institutions. As noted above, the
composition of the EC will maintain a balance of research expertise,
gender, ethnicity, geography, and age, to the extent possible.
The best way
to increase the participation of under-represented groups in science
is through public outreach and opportunities for students. The proposed
Virtual Fossil Collection will be a valuable teaching tool, at the
graduate and undergraduate levels as well as for advanced high school
students. We will develop a series of exercises to guide students
through the collection, raise questions, and encourage additional
A select bibliography
will also be provided. We will publicize the collection and accompanying
exercises through the Botanical Society of America's award-winning
website (www.botany.org) and link it to the BSA's Botanical Image
Collection, a collection of nearly 1000 images available through
the BSA site. We will also work with the BSA's very active Education
Committee (David Kramer, Ohio State University--Mansfield, Chair)
to publicize the site and exercises (including a demo) at the annual
meetings of the National Association of Science Teachers and the
National Biology Teachers Association.
the site and exercises will be sent to biology and science departments
at colleges and universities across the country, including minority-serving
institutions. While these activities will result in few direct associations
with the RCN, they will increase the visibility of exciting science
to all potential future scientists, including those in under-represented
groups. Core Participants in the RCN will be encouraged to visit
nearby minority-serving institutions to talk about their research
and about travel and training opportunities through the RCN.
encouragement of under-represented groups will be through Minority
Student Travel Awards and Minority Student Research Training Awards.
In each competition for student awards, a portion will be reserved
for deserving women and ethnic minority students. (If an insufficient
number of such students apply, these awards will revert to the "open"
Diversity of Institutional Settings
The Core Participants
reside in diverse types of institutions: research universities,
teaching institutions, museums, and botanical gardens. In fact,
the PIs themselves reflect this diversity: research universities
(Soltises), natural history museums (Dilcher), and primarily teaching
institutions (Herendeen). Members of these different types of institutions
bring different perspectives and resources, which will strengthen
these institutions have different constituencies, and the research
and training activities of the RCN will have broader impact through
the participation of scientists and students from different types
of institutions. We will encourage the participation of individuals
from institutions other than research universities by ear-marking
some Student Travel Awards and Student Research Training Awards
for these students. In addition, if needed, additional funds, beyond
those typically allocated, will be available to support travel and
participation by faculty of small, primarily teaching institutions.
Opportunities for Students, Post-docs, and New Researchers
above, the RCN is committed to providing training opportunities
for students at the undergraduate, graduate, and post-doctoral levels.
This commitment to undergraduate training in particular is a reflection
of the Soltises' work with undergraduate students. During the 1999-2000
academic year, the Soltises supervised seven undergraduates in their
lab. Two of these students presented posters at the International
Botanical Congress in 1999, and one will give a presentation and
another will present a poster at the annual meeting of the Botanical
Society of America in August, 2000. Athough the focus of the Student
Travel Awards and the Student Research Training Awards will be graduate
students, qualified undergraduates and post-docs will also be supported.
new researchers may lack the funding needed to participate in meetings
and workshops, additional funds, beyond those typically allocated,
will be available to support travel and participation by new researchers.
for increasing diversity are extensions of the networking and training
opportunities of the proposed RCN. The goal of these plans is to
maximize participation by all groups in the RCN. Selection of students
of under-represented groups and from institutions other than research
universities will be conducted by the Travel/Training Awards Committee
chaired by P. Soltis. Allocation of additional funds for faculty
in need, including new researchers, will be made by the Executive
products will result from this RCN.
- We will
help develop and expand a new research area at the interface of
systematics, phylogeny reconstruction, paleobotany, and geology
and provide students and postdocs with the opportunity for interdisciplinary
- In developing
this area of research, we will put into place a methodology and
conceptual strategy that can be applied to other groups of organisms.
If all proceeds well, we anticipate the development of software
for such analyses.
- We will
facilitate the development of a morphological data matrix for
extant angiosperms. This matrix will be a critical underpinning
for the integration of fossils into a comprehensive phylogenetic
tree and will be of great value for the investigation of living
angiosperms. For example, it can be used in combination with molecular
data sets to provide additional resolution within some portions
of the angiosperm tree (see Nandi et al., 1998) and for reconstructing
the history of morphological features across a molecular-based
tree. This matrix will be made readily available to other researchers
and will be periodically updated, as needed.
- This RCN
will facilitate better characterization of early angiosperm fossils
and develop a list of high-priority fossils for future research.
collaborations with geologists, the RCN will apply more accurate
dating of early fossils, concomitantly permitting more accurate
dating of divergence times.
dating of divergences will provide new opportunities for estimating
rates of diversification of clades, structures, and gene sequences.
- The Virtual
Fossil Collection will be valuable for both research and education,
promoting a greater awareness and appreciation of paleobotany
and early angiosperm fossil remains.
- The website
will serve as an effective resource for research and teaching.
This RCN will enhance communication among researchers in different
disciplines, a goal that is already being realized through the
establishment of an initial network of investigators to formulate
a research strategy. The coordination we propose with other phylogenetic
networks, such as Deep Green and Deep Gene, and our links to both
Tree of Life and TreeBASE will augment the scope of this single
RCN and broaden its impact.
fossils into phylogenetic trees of living taxa remains essential
for understanding the origin of extant angiosperms and the origins
of morphological features. However, attempts at such integrations
have been rare, not only for angiosperms, but for any group of organisms.
With the rapid developments in angiosperm phylogenetics and paleobotany,
the timing is now excellent for integration of the fields.
of Deep Time is to explore the ways in which angiosperm fossils
can be appropriately integrated into the phylogenetic framework
for extant taxa, with the ultimate goal of forming a comprehensive
phylogenetic tree of living and fossil angiosperms.
Deep Time will
develop and expand a new research area at the interface of paleobotany,
systematics, phylogenetics, and geology. Using our collective expertise
on Cretaceous angiosperms and angiosperm phylogeny and morphology,
we will develop a paradigm for integrating paleontology and phylogenetics.
theory, and principles that we develop for integrating fossils into
a phylogenetic tree will have broad applicability to other groups
of organisms. Through workshops, training grants, and Focus Groups,
this RCN will essentially develop a new area of interdisciplinary
research and provide students and postdocs with the opportunity
for interdisciplinary training.