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Smithsonian Botanical Symposium 2012 — Presented by the Smithsonian's National Museum of Natural History Department of Botany in collaboration with the United States Botanic Garden with support from the Cuatrecasas Family Foundation:

"Transforming 21st Century Comparative Biology using Evolutionary Trees"

Over the last 20 years great progress has been made toward assembling a phylogeny of life on Earth and our expanding knowledge of evolutionary relationships is transforming 21st century biology. This is especially true in comparative biology where phylogenetic methods and trees - usually based on molecular data which is increasingly of genomics scale - are proving effective tools to reveal new and often unexpected insights into how organisms evolve and adapt to their environments. These advances span new important questions and enable a fresh look at old questions that include: diversification, role of extinction, response to climate change, co-evolution, the influence of genetic architecture on morphological evolution, and patterns of community assembly and interaction.

The 10th Smithsonian Botanical Symposium, hosted by the Department of Botany and the United States Botanic Garden, will address the question: How do we put the knowledge of evolutionary relationships to work to better describe and understand the diversification of life on Earth? The invited speakers will cover a wide range of organisms and topics to illuminate how molecular phylogenetics can be used to understand evolutionary and ecological processes.

Program and Schedule

Friday, April 20, Evening Events
The United States Botanic Garden

6:00 p.m. Opening Reception, The United States Botanic Garden, Washington, DC.

Saturday, April 21
Morning Session
NMNH Baird Auditorium

9:00 a.m. Registration and Coffee, Evans Gallery (enter through Constitution Avenue Lobby)

9:30 a.m. Opening Remarks, Warren L. Wagner, Chair of Botany, Smithsonian Institution, and Jonathan Coddington, Associate Director for Research and Collections, National Museum of Natural History, Smithsonian Institution. Presentation of the José Cuatrecasas Medal for Excellence in Tropical Botany, Laurence J. Dorr, Department of Botany, Smithsonian Institution.

Symposium Convener: Kenneth Wurdack, Department of Botany, Smithsonian Institution

10:00 a.m. Scott V. Edwards, Harvard University, “Resolving the Tree of Life through phylogenomics and the multispecies coalescent model”

10:45 a.m. Coffee Break, Upper Level of the Museum Rotunda

11:15 a.m. Charles F. Delwiche, University of Maryland, “Illuminating the origin of land plants with algal genomes”

12:00 p.m. James W. Horn, Department of Botany, Smithsonian Institution, “Diversification and structural innovation in Euphorbia”

12:45 p.m. Boxed Lunch, Upper Level of the Museum Rotunda

Afternoon Session
NMNH Baird Auditorium

2:30 p.m. Karen Osborn, Department of Invertebrate Zoology, Smithsonian Institution, “Discoveries in the deep and their usefulness for studies of invertebrate evolution”

3:15 p.m. David D. Ackerly, University of California, Berkeley, “Traits, communities, and history: what do we learn from phylogenies?”

4:00 p.m. Coffee Break, Upper Level of the Museum Rotunda

4:30 p.m. Richard Ree, The Field Museum, “Phylogeny and the evolution of floral diversity in Pedicularis (Orobanchaceae)”

5:15 p.m. Michael Donoghue, Yale University, “Adventures in plant phylogeny and prospects for the future”

Evening Events
NMNH Rotunda and Exhibits

6:15 p.m. Reception

7:15 p.m. Symposium Dinner, Museum Rotunda

Abstracts

Resolving the Tree of Life through Phylogenomics and the Multispecies Coalescent Model
Scott V. Edwards, Harvard University, U.S.A.

As phylogenomics makes available ever-increasing numbers of loci for phylogenetic analysis, the diversity of gene histories due to incomplete lineage sorting and other factors increases as well. Concatenation of multilocus data sets into supermatrices has proven an effective way of increasing phylogenetic signal for the Tree of Life. However, when analyzed by standard methods that ignore gene tree heterogeneity, theory suggests that concatenation yields inconsistent estimates of phylogenetic relationships when gene tree heterogeneity is high. Here I illustrate an empirical example of this inconsistency using phylogenomic data from 447 loci and 37 species of placental mammals and outgroups. Remarkably, these loci yield 440 topologically distinct gene trees, indicating that virtually every locus has a distinct phylogenetic history. As expected, standard Bayesian and maximum likelihood analysis of these loci yields a tree with full support on every node, yet, unexpectedly, analysis of concatenated subsamples of the data yield equally strong relationships that often conflict with each other. By contrast, analysis of complete and subsampled data sets using so-called “species tree” methods – a family of methods that accommodates gene tree heterogeneity through the multispecies coalescent model – yields trees with consistent and increasing support with increasing numbers of loci. Additional examples from birds confirm that gene tree heterogeneity is not confined to recently radiating clades, but is also present at deeper phylogenetic levels. Species tree methods invariably require more loci to achieve significance than concatenation, but they appear to be consistent and less erratic with genome-scale data sets.

Scott Edwards is Alexander Agassiz Professor of Zoology and Curator of Ornithology in the Museum of Comparative Zoology at Harvard University. He came to Harvard in December 2003 after serving as a faculty for nine years in the Zoology Department and the Burke Museum at the University of Washington, Seattle. Edwards got his undergraduate degree from Harvard in 1986 and his PhD from the Department of Zoology, University of California, Berkeley, in 1992, and conducted postdoctoral research in avian immunogenetics at the University of Florida, Gainesville. He has conducted fieldwork throughout the U.S., Australia and the Pacific region, and has interests in many aspects of avian biology, including evolutionary history and phylogeography, genome evolution, disease ecology and population genetics. He has served on the National Geographic’s Committee for Research and Exploration, the Comparative Genomics Working Group of the National Human Genome Research Institute of the NIH, the Senior Advisory Board of the National Evolutionary Synthesis Center (NESCent) and is on the Board of Directors of the Cornell Lab of Ornithology and the National Museum of Natural History. He oversees a program funded by the National Science Foundation to increase the diversity of undergraduates in evolutionary biology and biodiversity science.

Illuminating the Origin of Land Plants with Algal Genomes
Charles F. Delwiche, University of Maryland, U.S.A.

The close relationship between green algae and land plants (embryophytes) was recognized prior to Linnaeus, and by the end of the 19th century it was understood that the land plants are younger than, and probably derived from, green algae. Ultrastructural studies in the second half of the 20th century refined the problem, revealing two great lineages of green algae, the true chlorophytes and the charophytes, the latter including land plants. However, it was only with the rise of molecular systematics at the end of the millennium that the relationships among these organisms could be fully appreciated. Paleobotanical studies indicate that green algae originated deep in the Precambrian, probably on the order of 2 ba, while land plants arose late in the Ordovician, about 450 ma, and diversified through the Silurian and Devonian. Consistent with the evidence from the fossil record, in molecular analyses land plants are deeply embedded in green algal biodiversity, and the individual lineages of charophytes (traditionally classified as orders) are each comparable in age to the land plants. This illustrates the vast, understudied biological diversity found not only in green algae, but throughout the basal lineages of eukaryotes (the “protists”). By applying state-of-the-art DNA sequencing technologies we have been able to identify in charophyte algae components of fundamental biological processes that were previously believed to be unique to land plants. Studies targeted on the basis of evolutionary relationships hold the promise of shedding new light on the origin, evolution, and function of fundamental plant processes.

Charles F. Delwiche is a Professor of Cell Biology and Molecular Genetics at the University of Maryland. He received a classical training in Botany at the University of California, Berkeley (A.B., 1984) and the University of Wisconsin, Madison (Ph.D., 1990) before adopting molecular methods during postdoctoral studies at U.W. Madison and Indiana University. He has been on the Faculty of the University of Maryland since 1996, and uses a combination of classical and genomic techniques to study algal biodiversity, the origin of land plants, and the endosymbiotic origin of chloroplasts. He was awarded an Alfred P. Sloan Foundation Young Investigator award for Molecular Studies in Evolution, has been a Kavli Fellow, and received the 2006 BSA Darbaker Award for study of microalgae.

Diversification and Structural Innovation in Euphorbia
James W. Horn, National Museum of Natural History, Smithsonian Institution, U.S.A.

Euphorbia—with over 2,000 recognized species of protean habit, and with a nearly global distribution—has long been considered one of the most challenging clades of flowering plants to untangle. Yet manifest in these complexities is the potential of Euphorbia as a system to address fundamental issues in plant evolutionary biology. A newly developed and robustly supported molecular phylogeny for the genus provides a framework with which we are achieving a synthesis of structural evolution, evolutionary tempo, and diversification in Euphorbia. Outstanding are the many examples of extreme parallelism in trait evolution, including at least 14 origins of xeromorphic growth forms. The evolution of growth form and inflorescence position is significantly correlated, and a pathway of evolutionary transitions is supported that has implications for the evolution of Euphorbia CAM xerophytes of large stature. Such xerophytes total more than 400 species and are dominants of vegetation types throughout much of arid Africa and Madagascar. Divergence dating estimates indicate these xerophyte lineages rapidly radiated in the late Miocene to early Pliocene (~8–4 Ma), subsequent to aridification of these regions and lowered atmospheric CO2 levels. We test these and other traits as correlates of diversification in Euphorbia to shed further light on the evolution of this remarkable angiosperm clade.

James Horn is currently a Postdoctoral Research Fellow in the Department of Botany at the Smithsonian Institution. He grew up in the greater Chicago area, and on family vacations to northern Wisconsin he developed a strong interest in botanical diversity. Horn earned a B.S. in Plant Science from Cornell University, and went on to study for an M.S. degree at the University of North Carolina at Chapel Hill. His dissertation research at Duke University, under Paul Manos, focused on the molecular systematics and evolution of the phylogenetically key family Dilleniaceae. Prior to his residence at the Smithsonian, Horn was a Postdoctoral Research Associate at Fairchild Tropical Botanic Garden, where he worked with on a project culminating with the publication of the Anatomy of Palms. His current research is on the phylogenetics and evolution of Euphorbia, Hawaiian Metrosideros, and Dilleniaceae, with an emphasis on using phylogenies to understand plant structural evolution.

Discoveries in the Deep and Their Usefulness for Studies of Invertebrate Evolution
Karen Osborn, National Museum of Natural History, Smithsonian Institution, U.S.A.

The deep, open ocean is the largest habitat on earth by volume and supports a huge diversity and biomass of invertebrates. Most animal groups have representatives living in the open ocean but many of these pelagic animals have dramatically different morphology, behavior and ecology in relation to their closest relatives. By studying the differences between these animals and their relatives in shallow water or on the sea floor, we learn how the pelagic environment changes and shapes the many animals that survive there. Additionally, we learn about the constraints and possibilities for various animals groups and how open ocean communities functions. Because of the difficulty studying this habitat, the delicate nature of many of the animals, new ways to explore this habitat, and molecular tools exciting discoveries and new understanding of the evolutionary history of numerous invertebrate groups are now possible. I will introduce a recent discoveries and talk about how they are useful in study of the evolution of pelagic invertebrates and the communities those animal are part of. 

Karen Osborn is a Curator of Marine Invertebrates at the Smithsonian's National Museum of Natural History and studies the evolution of life in the deep, open ocean. She is interested in evolutionary processed taking place in open water, including adaptations to this unique habitat and diversification processes in a habitat considered to have minimal dispersal barriers. Osborn recently arrived at the Smithsonian after completing her dissertation at University of California, Berkeley and the Monterey Bay Aquarium Research Institute, followed by a postdoctoral position at Scripps Institution of Oceanography. She spends a lot of time at sea using remotely operated vehicles to explore and study the deep, open ocean invertebrates.

Traits, Communities, and History: What Do We Learn from Phylogenies?
David D. Ackerly, University of California, Berkeley, U.S.A.

The use of phylogenetics as a tool and a conceptual framework reflects a significant shift in ecology thinking in recent years. I will highlight three aspects of this synthesis, and specifically ask, what has ecology learned from phylogenetics? 1) In community ecology, phylogenetic approaches are widely used to test hypotheses about the role of abiotic and biotic influences on community assembly. The key question is: if we knew all the traits of species in a community, and the mechanisms of interaction, would phylogenetics still be useful? 2) At a larger scale, phylogenetic methods provide unique insights into the influence of biogeographic and bioclimatic history on patterns of regional and local diversity. The deep history of many lineages is evident in the environmental tolerances and traits of organisms observed in modern-day communities, yet the underlying ecological and evolutionary processes remain obscure. 3) Comparative methods provide a phylogenetic approach to examine the tempo and mode of evolution. The bulk of evidence suggests that ecological traits exhibit modest, but not strong, phylogenetic signal, based on patterns of similarity among close relatives. Increased understanding of the evolutionary fate of lineages with extreme-trait values (e.g., the tallest trees or the smallest seeds) will be critical to distinguish among alternative evolutionary models. Drawing on these three areas, I will identify research priorities to fill major gaps in the continuing synthesis of phylogenetics and ecology.

David Ackerly received his B.A. in Biology from Yale University and Ph.D. in Organismic and Evolutionary Biology from Harvard University. He held postdoctoral positions at the Arnold Arboretum and Harvard University Herbaria, and then moved to Stanford University in 1996 as an Assistant Professor, and to the University of California, Berkeley in 2005 as Associate Professor. He holds the Gill Chair in Natural History in the Department of Integrative Biology and is an Associate Curator of the Jepson Herbarium. His research focuses on ecology and evolution of plant functional traits, the use of phylogenetics to study trait evolution, and trait-based approaches to community assembly. Recent research addresses climatic and spatial heterogeneity, its influences on plant distributions, and the implications for conservation strategies in the face of climate change. He has conducted field work in Japan, Brazil, Mexico, New England and California, and just completed a year as a Fulbright Fellow in South Africa researching microclimates and plant distributions on Table Mountain, Cape Town.

Phylogeny and the Evolution of Floral Diversity in Pedicularis (Orobanchaceae)
Richard Ree, The Field Museum, U.S.A.

In China's Hengduan Mountains, over 350 species of Pedicularis exhibit spectacular variation in floral form and color, and often co-occur and flower synchronously. However, all are pollinated solely by bumblebees. Phylogenetic analysis of trait evolution and community structure reveals evidence that a geographic mosaic of pervasive reproductive interference between co-occurring species of Pedicularis may accelerate the evolution of floral traits and elevate rates of both speciation and extinction, and explain the preponderance of species in the Hengduan hotspot. These results motivate finer-scale analysis of Pedicularis phylogeny at and below the species level, and I will present some preliminary results on how reduced-representation genomic tools can be used not only to confidently infer relationships, but also reveal patterns of historical introgression.

Richard Ree received his PhD in 2001 from Harvard University, where he was advised by Michael Donoghue and David Baum. He first became interested in the large genus Pedicularis on a field trip to China in 1997, and focused his dissertation work on its phylogeny and floral evolution. After postdoctoral research stints at the University of California, Davis and the University of British Columbia, in 2003 he joined the Field Museum as a curator in the Botany Department. In addition to Pedicularis, Ree has worked on other plant clades with similar biogeographic patterns, such as Corydalis. He also pursues theoretical research on comparative methods for macroevolution and biogeography, and on issues relating to large-scale synthesis of phylogeny.

Adventures in Plant Phylogeny and Prospects for the Future
Michael Donoghue, Yale University, U.S.A.

Progress in understanding plant phylogeny has exceeded our wildest dreams, but there is still much to be done. I will briefly review some of the most extraordinary advances of the last few decades and the corresponding insights into plant evolution. Having established a solid phylogenetic backbone, the next step will be to fill in the details. But, far from being a pedestrian exercise, I predict that the most important findings are yet to come. As I hope to illustrate with concrete examples from Viburnum, a more comprehensive coverage will enable truly compelling analyses of character evolution, biogeography, and diversification.

Michael Donoghue joined Yale in 2000 as the G. Evelyn Hutchinson Professor of Ecology and Evolutionary Biology. He served as Chair of Ecology and Evolutionary Biology in 2001-2002, and as Director of the Peabody Museum of Natural History from 2003-2008. From 2008-2010 he served as Yale’s inaugural Vice President for West Campus Planning and Program Development, and in 2011 he was named Sterling Professor of Ecology and Evolutionary Biology. Donoghue earned his B.S. from Michigan State University in 1976 and his Ph.D. in Biology from Harvard University in 1982. He served on the faculty of San Diego State University (1982-1985), the University of Arizona (1985-1992), and Harvard University (1992-2000). He was the Director of the Harvard University Herbaria from 1995-1999, and President of the Society of Systematic Biologists from 1994-1995. He was elected as a Fellow of the American Association for the Advancement of Science in 1997, as a Member of the U. S. National Academy of Sciences in 2005, and as a Fellow of the American Academy of Arts and Sciences in 2008. Donoghue's research focuses on understanding the diversity and evolutionary history of plants. He has mentored 25 postdoctoral associates and 22 graduate students.

Sponsors

United States Botanic Garden of Washington DC

Cuatrecasas Family Foundation

Office of the Associate Director for Research and Collections, NMNH

Hosted by the Department of Botany of the Smithsonian Institution.

Contact the symposium coordinator at sbs@si.edu.