Deep Time: A Comprehensive Phylogenetic Tree of Living and Fossil Angiosperms

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Florida Meeting


Meeting Agenda

Friday, February 22 (Reitz Union Room 346-347
        8:00    Welcome
                    Overview of Deep Time
                    Summary of New Mexico meeting
                    Goals for Deep Time (projects, as discussed in NM)
                    Goals for this workshop
                    Announce support available
                    Date for future meetings
        8:30    Contributed Presentations by Deep Time Participants.
        8:30    USING PHYLOGENY TO INVESTIGATE THE HISTORY OF MORPHOLOGICAL EVOLUTION IN HETEROSPOROUS FERN
                        Kathleen Pryer, Harald Schneider, and Rick Lupia
        8:50    RATE HETEROGENEITY AMONG LINEAGES OF TRACHEOPHYTES: INTEGRATION OF MOLECULAR AND FOSSIL DATA AND EVIDENCE FOR MOLECULAR LIVING FOSSILS
                        Pamela S. Soltis, Douglas E. Soltis, Vincent Savolainen, Peter R. Crane, and Timothy G. Barraclough
        9:10    THE ROOT OF THE ANGIOSPERMS REVISITED
                        Michael J. Zanis, Douglas E. Soltis, and Pamela S. Soltis

        9:30-9:50    Coffee break

        9:50    COMBINING FAST EVOLVING CHLOROPLAST DNA SEQUENCES FOR PHYLOGENETIC ANALYSIS IN BASAL ANGIOSPERMS
                        Khidir W. Hilu, Thomas Borsch, and Kai Müller
        10:10    FAGALES OVERVIEW
                        Paul S. Manos
        10:30    PHYLOGENETIC ANALYSIS OF THE FAGALES USING FIVE GENES AND ONE DNA REGION FROM THREE GENOMES
                        Zhiduan Chen and Rui-Qi Li
        10:50   DIVERGENCE TIME INFERENCE IN THE BETULACEAE USING RDNA SEQUENCES AND MULTIPLE CALIBRATION POINTS FROM THE FOSSIL RECORD
                        Felix Forest, Peter Crane, Mark Chase, Vincent Savolainen,
                        and Anne Bruneau
        11:10    FUNCTIONAL FIELD ECOLOGY OF AMBORELLA AND ITA PLANTS
                        Taylor Field
       
        11:30-1:00    Lunch break

        1:00    Presentations by guests: 
                    PALEOBIOLOGY DATABASE     Hallie Sims
                    MORPHOBANK   Maureen O'Leary

        3:00    Coffee break
       
        3:30    Reports
                    Development of Deep Time website
                            Hongshan Wang
                    Virtual Fossil Project
                            Pat Herendeen/David Dilcher
                    Virtual Fossil data base development
                            Pat Herendeen/David Dilcher
                    Morphology database development for extant angiosperms
                            Walt Judd/Doug Soltis
        5:00    Adjourn

        6:30        Dinner at Soltis Home-2710 NW 26th Place
                        Catered Southern Barbecue

Saturday, February 23 (FLMNH)
        8:30    Resume
                   Discussion-Fagales as first "model"
       
        10:00-10:30    Coffee Break
   
        10:30-12:00    Discussion-Pursuing initial grant support for morphology data base

        12:00-1:00    Lunch-Box lunches from Heavenly Ham

        1:00    Discussion by project groups:
                    I.   Characterize and prioritize fossils:  D. Dilcher
                    II.  Correct time estimates:  P. Herendeen
                    III. Construction of a morphological matrix:  D. Soltis
                    IV. Calibration of branch points in cladogram/molecular evolution:  P. Soltis
                    V.  Integrating fossils into the angiosperm tree: Soltis/Soltis/Dilcher/Herendeen 

        3:00-3:30    Coffee Break

        3:30     Wrap-up and goals for next meeting
        4:30    Adjourn and travel to Powell Hall
                    (Florida Museum of Natural History Exhibit Hall)
        5:00-6:00    Private Viewing of Exhibit, "A T. rex Named Sue"

        7:00        Dinner at The Sovereign in downtown Gainesville, 12 SE 2nd Ave.


Meeting Summary

Gainesville, Florida, February 22~23, 2002

Major Discussion Items

  • Fagales. An informal working group was initiated to pursue Fagales as a model for the integration of fossils with a phylogenetic tree of extant taxa. Paul Manos assisted with and directed much of this discussion. Other investigators who expressed a willingness to help assist with work on Fagales include Steve Manchester, David Taylor, Jim Doyle, Pat Herendeen, and Felix Forest (working with Peter Crane).
  • Through our discussions the group decided (1) to begin to compile a list of morphological characters for use in the integration of fossils into a tree of living taxa, and (2) assemble a list of taxa for consideration (fossil and extant). Rui-Qi Li, our first recipient of a Deep time Graduate Student Training Award, may assist with the construction of the morphological data set.
  • The group established a two-month window to obtain some preliminary results for use in a Tree of Life proposal.
  • MorphoBank. Maureen O'Leary was one of two guest speakers on databasing. She provided an overview of the early version of MorphoBank that she and colleagues are developing. There was considerable enthusiasm and interest in the basic system they had developed. Their program contained many of the features that the Deep Time group considered important at the first meeting in New Mexico. Archiving of images is a major component of MorphoBank.
    • The central focus of the MorphoBank database is the data matrix; completed matrices from published analyses are to be archived. There was a great deal of discussion as to whether this approach is what we need for plants. It was generally agreed that the focus should not be at the level of a complete data matrix, but at the level of the character for a species, so that character states could be assigned as appropriate for a given level of analysis. Matrices could be provided by investigators if so desired. Not all participants agreed as to how a morphological database for angiosperms and other plants should operate. Some had a vision similar to GenBank, in which an individual character state could be retrieved for a specific taxon, whereas others envisioned assigned character states in defined matrices.
    • An important message from Maureen is that programmers could develop whatever system we want; the programming itself is not difficult. There was a general sense that flexibility with the system would be a good thing. It was agreed that a morphological data base system is needed and that we should be involved in the development and use of MorphoBank. Two groups agreed to test Maureen's system -- The Fagales working group headed by Paul Manos and a group at the University of Florida (D. Soltis, P. Soltis, W. Judd, S. Manchester).
  • Paleobotany database. Hallie Sims, the other guest speaker, provided an overview of the Paleobiology Data Base project. The project is based at UC Santa Barbara and initially involved marine invertebrates. It has expanded to include other groups, such as insects, plants, and vertebrates. The system is web-based and provides fossil locality, geographic location, age, and references. There was enthusiasm among participants for this system, but concern was expressed that the morphological data base system we initially discussed in New Mexico would include this information, plus more. It might be asking too much of investigators to load data into the PDB as well as a morphological database (e.g., MorphoBank). The importance of linking these two systems was noted.

Summary and Assignments

  • Fossil Priority List - David Dilcher and Pat Herendeen both presented lists of taxa for possible inclusion. Pat will take the lead in finalizing this list.
  • Fagales project - Paul Manos will lead.
  • Virtual Fossil - We need to start this and get a few templates on-line.
    David Dilcher and Pat Herendeen will work with Hongshan Wang to do this. They need to provide one or two fossils, data, literature, etc. so that templates can be placed on the web for others to consider.
  • Paleo-ranges: Constraining Age Estimates for Fossils- Rick Lupia will work on this.
  • Website - special access areas for fossil priority list working group and Fagales working group. Hongshan will develop these.
  • Tree of Life Proposal - Soltis will call NSF and obtain information. They will work with Pat, Kathleen, Paul and others to develop ideas.
  • Future Symposia - Pat Herendeen noted the importance of organizing symposia for Botany (BSA, ASPT) or SSB/Evolution meetings on integrating fossils into phylogenetic trees and calibration of branch points using molecules data.
  • Integrating Fossils - We should put examples from the literature on our web site and add a new heading, "Integrating fossils." We can begin with papers from the literature illustrating different approaches to this problem, eventually adding our own projects and work. Hongshan can begin to work on this with Doug and Pam.

Contributed Papers

USING PHYLOGENY TO INVESTIGATE THE HISTORY OF MORPHOLOGICAL EVOLUTION IN HETEROSPOROUS FERNS
Kathleen Pryer, Harald Schneider, Rick Lupia

ABSTRACT: Throughout the evolutionary history of plants on land there have been repeated re-invasions of aquatic environments by terrestrial plants from distantly related groups. In order to survive these very different physical conditions, these plants have had to dramatically modify their vegetative, reproductive, and dispersal systems. Few living ferns are aquatic, most are terrestrial and homosporous. The exceptions are heterosporous ferns, with morphologically distinct spores producing unisexual gametophytes. Heterosporous ferns are monophyletic and comprise two extant families, the semi-aquatic Marsileaceae and the aquatic Salviniaceae. Except for very recent interest in the relationships among the five extant heterosporous genera, these ferns have been largely ignored in systematic studies and infrageneric relationships are virtually unknown. Similarly, our knowledge of the history of the morphological character evolution that accompanied the transition of these ferns to their aquatic environments is limited. Heterosporous ferns are relative newcomers that diversified during the Cretaceous, at the same time as flowering plants, and the fossil record has preserved a rich history of these ferns, mostly in the form of microfossils with a remarkable diversity of ornamented spores. Together we are reconstructing a comprehensive phylogeny for the heterosporous aquatic ferns. Our study will be among the first to include both living and fossil members of a group, incorporating data from multiple genes, morphology, and developmental studies for the living taxa, and integrating ultrastructural morphological data from fossil taxa. Understanding the history of character evolution in these ferns requires integration of fossil taxa, necessarily using morphology pertinent to the spores. Understanding the development and structure of the spore wall, primarily through electron microscopy, is critical to this project because the character-rich spore wall is well preserved in fossils and will permit fossil taxa to be integrated into the phylogeny. We hope to understand better the morphological character state transitions associated with the ecological specialization of these ferns to aquatic habitats.

RATE HETEROGENEITY AMONG LINEAGES OF TRACHEOPHYTES: INTEGRATION OF MOLECULAR AND FOSSIL DATA AND EVIDENCE FOR MOLECULAR LIVING FOSSILS
Pamela S. Soltis, Douglas E. Soltis, Vincent Savolainen, Peter R. Crane, and Timothy G. Barraclough

ABSTRACT: Many efforts to date evolutionary divergences using a molecular clock have yielded age estimates that are grossly inconsistent with the paleontological evidence. Such discrepancies are often attributed to the inadequacy of the fossil record, but many potential sources of error can affect molecular-based estimates. In this study, we minimize the potential error due to inaccurate topology and uncertain calibration times by using a well-supported tree, multiple genes, and multiple well-substantiated dates to explore the correspondence between the fossil record and molecular-based age estimates for major clades of tracheophytes. Age estimates varied due to gene effects, codon position, lineage effects, method of inferring branch lengths, and whether or not rate constancy was assumed. However, even methods designed to ameliorate the effects of rate heterogeneity among lineages could not accommodate the substantially slower rates observed in Marattia + Angiopteris and in the tree ferns. Both of these clades of ferns have undergone dramatic decelerations in their rates of molecular evolution and are "molecular living fossils", consistent with their relative morphological stasis for the past 165-200 million years. Similar discrepancies between the fossil record and molecular-based age estimates noted in other studies may also be explained in part by violations of rate constancy among lineages.

THE ROOT OF THE ANGIOSPERMS REVISITED
Michael J. Zanis, Douglas E. Soltis, Pamela S. Soltis

ABSTRACT: Most recent phylogenetic analyses of basal angiosperms have converged upon the placement of Amborella as sister to all other extant angiosperms. However, certain recent studies suggested that Amborella and Nymphaeales (water lilies) form a clade sister to all remaining angiosperms or that Nymphaeales alone are the sister to the remaining angiosperms. We report here (i) maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses of 11 genes (> 15,000bp/taxon) for 16 taxa, (ii) maximum parsimony analysis for a subset of these genes for 104 taxa, and (iii) tests of alternative rootings using the non-parametric bootstrap and the likelihood ratio test using the parametric bootstrap. In addition, we use simulation analyses to examine the amount of bias that may be present in our methods of phylogeny estimation. Amborella continues to receive strong bootstrap support as the sister to all other extant angiosperms, and three of four tests reject alternative hypotheses of the angiosperm root. Although we cannot conclusively choose between Amborella vs. Amborella + Nymphaeales as sister to all other angiosperms, most analyses favor the former rooting.

COMBINING FAST EVOLVING CHLOROPLAST DNA SEQUENCES FOR PHYLOGENETIC ANALYSIS IN BASAL ANGIOSPERMS
Khidir W. Hilu 1, Thomas Borsch 2, Kai Müller 2
1 Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061.
2 Botanisches Institut und Botanischer Garten, Friedrich-Wilhelms-Universität Bonn, Germany.

ABSTRACT: Our understanding of flowering plant phylogeny has been enhanced considerably by recent information from gene sequences. A number of plastid, nuclear and mitochondrial genes have been used in deep level phylogenetic reconstruction. Emphasis has been placed on using slow evolving genes with the notion that levels of homoplasy will be kept at a minimum. We have been exploring the potential contribution of the plastid matK gene and the noncoding parts of the trnT-F-region, both evolving at higher rates than other genes used in angiosperm phylogenetic reconstruction. These two regions provide robust phylogenies for basal angiosperms that are congruent with each other and with recent angiosperm phylogenies based on combined data of gene sequences from the plastid and nuclear or from all three genomes (Soltis et al., 2000, Qiu et al., 1999, 2000). Analysis of the combined matK and trnT-F data sets resulted in a single most parsimonious tree. Statistical support for the majority of nodes substantially increased compared to previous analyses. The results of the present study point to the effectiveness of fast evolving DNA regions in providing strong historical signals that can recover a reliable and robust phylogeny for angiosperms.

FAGALES OVERVIEW
Paul S. Manos
Department of Botany
Duke University

PHYLOGENETIC ANALYSES OF FAGALES BASED ON MULTIPLE DNA SEQUENCES FROM THREE GENOMES
Rui-Qi Li, Zhi-Duan Chen, and An-ming Lu
Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, P. R. CHINA

ABSTRACT: Nucleotide sequences of five genes and one DNA region from three genomes were used to analyze the inter- and infra-familial relationships of Fagales. All 31 genera (excluding Ceuthostoma) were sampled representing eight families of the order. The parsimonious analyses of combined data set strongly supported the three major clades in the Fagales, i.e., Nothofagus, Fagaceae and core "higher" hamamelids as recognized by Manos and Steele (1997). Nothofagus is sister to all the other Fagales, and Fagaceae is sister to the core "higher" hamamelids. Two main subclades were resolved in the core "higher" hamamelids by the combined analysis, one being Myricaceae (Rhoipteleaceae (Juglandaceae)), the other Casuarinaceae (Ticodendraceae (Betulaceae)). The latter subclade is strongly supported, while the former is moderately supported although the positions of Myricaceae are quite different in each single-gene trees. Fagaceae, Betulaceae and Juglandaceae form their own clade with 100% bootstrap support, respectively.
Keywords: Fagales, "higher" hamamelids, Myricaceae, phylogeny, combined analysis

ESTIMATING TIME DIVERGENCE IN THE BIRCH FAMILY (BETULACEAE): RATE HETEROGENEITY, MULTIPLE CALIBRATION POINTS AND STEM LINEAGE-CROWN GROUP INTERVAL
Félix Forest, Vincent Savolainen, Mark W. Chase, Anne Bruneau, and Peter R. Crane

ABSTRACT: We present a phylogenetic analysis of the Betulaceae including at least one species of each subgeneric division (26 taxa) of the six genera (Betula, Alnus, Carpinus, Corylus, Ostrya, Ostryopsis). Parsimony analyses based on ribosomal DNA sequences of 5S gene spacers and ITS supported the monophyly of the subfamilies and all genera. Likelihood ratio tests showed rate heterogeneity across lineages, therefore we made the phylogenetic trees ultra-metric by transforming ML and MP branch lengths (HKY85 + gamma model of DNA evolution) using the non-parametric rate smoothing method of Sanderson. We estimated divergence times within the family using one of the six most parsimonious trees and eight calibration points from the extensive fossil record of Betulaceae. To assess the problem of using dates for stem lineages or crown groups in the calibration procedure, we calculated age estimates by placing each fossil on the stem lineage node and crown group node, creating an interval. The median value of those estimates was determined for each node. According to these results, the ages of the crown groups of the Betulaceae and subfamilies Coryloideae and Betuloideae are 97.7 Ma, 57.6 Ma and 89.8 Ma respectively. Taking into account the error estimates, these ages are similar to those inferred from the fossil record. Deceleration of rates of molecular evolution is observed in certain clades of the Betulaceae.

FUNCTIONAL FIELD ECOLOGY OF AMBORELLA AND ITA PLANTS
Taylor Feild

PALEOBOTANICAL DATA AND THE PALEOBIOLOGY DATABASE INITIATIVE
Hallie J. Sims

ABSTRACT: The Paleobotany Working Group (part of the Paleobiology Database; see http://www.paleodb.org/) has begun a project to compile locality-based occurrence data for Phanerozoic land plant localities, using a web-based, relational database. The database is structured around four tables: references, collections, occurrences, and taxa. Each collection record has the geographic coordinates and geologic age of the site, lithologic and paleoenvironmental context, and taphonomic modification of the remains. This is linked with a list or lists of taxon occurrences (and abundance data where available), including which plant parts are present. Taxonomic names are being linked to tables that allow taxonomic usage to be updated and plant parts to be associated, recording the opinions of different workers. Data are drawn from the primary literature, museum collections, and unpublished field work, and every datum entered is associated with a reference and an enterer. As a group of specialists (currently fifteen members), we are updating stratigraphic information and building a table of valid species, genera, and their synonyms. By making the data publicly available as a web-searchable database, the paleobotanical community will be invited (and perhaps incited?) to identify omissions and errors. The group has several scientific goals, including producing a sampling standardized plant diversity curve, assessing changes in within-community diversity over time, and exploring trends in morphological evolution. However, the lists of valid taxa and occurrence lists from well-constrained localities, vetted by specialists, can form building blocks for a wide range of research projects. We hope that this initiative will gain momentum within the community to maintain and contribute to a public repository of high-quality paleobotanical data.

MORPHOBANK
Maureen O'Leary


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