Standing your ground: Understanding plant defense from molecules to morphology

Submitted By:  Gaurav Moghe

Plants are intricately connected with their natural biotic world, continuously interacting with pollinators, above and below ground herbivores, as well as various pathogens. These interactions are mediated through the language of chemistry, however, plants have also evolved various physiological and developmental mechanisms for these purposes. These include specialized morphologies such as thorns, trichomes and laticifers, physiology-altering hormonal signaling cascades and phenological patterns of growth and flowering. Understanding the links between physiology, development, genetics and chemistry offers points of intervention to utilize and engineer plant defensive mechanisms. This symposium will highlight how plants stand their ground against an assemblage of aggressors as they encounter new environments through dispersal and/or climate change. This integrative topic is timely given that climate change is also projected to increase the frequency of plant diseases along with other stressors, and that new strategies to strengthen our plants’ defenses worldwide are urgently needed.

Our symposium will highlight senior as well as early career faculty. The selected speakers represent a diverse range of viewpoints and expertise, and will span the range from molecular and genetic to ecological and evolutionary aspects of plant-herbivore and plant-microbe interactions. This diffusion of expertise and ideas across plant biology is in the theme of One World - where a shared passion for understanding biological phenomena trumps and builds upon the diversity of viewpoints.

Planned Speakers:

• Gaurav Moghe/Kira Tiedge Topic: "Introduction: Standing your ground: Understanding plant defense from molecules to morphology"
• Annika Nelson, Postdoctoral Researcher, Virginia Tech, USA. Topic: "Seed defenses and ant-seed dispersal mutualisms"
• Vivian Irish, Professor, Yale University, USA. Topic: “The evolution and development of thorns”.
• Pablo Vera, Professor, Instituto de Biología Molecular y Celular de Plantas, Spain . Topic: “The role of laticifers in the co-evolutionary arms race between plants and their enemies”
• Dan Kliebenstein, Professor, UC-Davis, USA. Topic: “Plant-Botrytis warfare across core Eudicots”
• Ashish Ranjan, Research Assistant Professor, University of Minnesota Twin Cities, USA . Topic: “Mechanisms of plant defense against pathogenic soil fungi”
• Maggie Wagner, Assistant Professor, University of Kansas, USA. Topic: “The complex ecology of glucosinolate variation in a wild perennial mustard”

Standing Seeing the network for the trees: Methodological and empirical advances in reticulate evolution

Submitted By:  George Tiley

Methods to reconstruct phylogenetic networks are becoming increasingly popular given the widespread evidence of reticulate evolution in the Tree of Life. At the same time, genomic or large multi-locus nuclear datasets are becoming increasingly available across all plant groups. Given contentious nodes persist in many plant phylogenomic studies and the propensity for cross-species gene flow within some plant lineages, there is now an opportunity for botanists to characterize reticulate evolution within difficult species complexes and along the backbone of major groups. This symposium will include topics related to the development of novel methods for reconstructing phylogenetic networks and highlight case studies where networks have been transformative in our understanding of plant or fungal evolution. Among the specific topics, the symposium will include a description of novel phylogenetic network reconstruction methods. Speakers will cover introductory background material on methods that leverage results from graph theory, algebraic geometry, and coalescent theory. In addition, speakers will discuss robustness studies on the accuracy and applicability of existing network methods on a variety of in silico or real data in-plant applications. Furthermore, we will present novel mathematical insights on the space of phylogenetic networks and discuss the limitations of existing tools and data.  Several talks will highlight empirical case studies where network methods have been successfully used to answer questions related to the evolution and adaptation of plants and fungi. As a whole, the symposium will offer an overview of our current understanding of network models, tools, and insights.

Planned Speakers:

• Claudia Solís-Lemus, University of Wisconsin-Madison, Overview of phylogenetic networks
• Diego Morales-Briones, Ludwig Maximilian University of Munich, Exploring the possible role of hybridization in the evolution of photosynthetic pathways in Flaveria (Asteraceae), the prime model of C4 photosynthesis evolution 
• Sungsik Kong, Ohio State University, Topological Incongruence between Median-Joining Networks and Bayesian Inference of Phylogenies 
• Sylvia Kinosian, University of Arizona, Evaluating the effect of missing data in evolutionary networks with simulated and empirical RADseq data 
• Kevin Liu, Michigan State University, The Impact of Multiple Sequence Alignment Error on Summary-based Phylogenetic Network Estimation 
• Cécile Ané, University of Wisconsin-Madison, Accounting for intraspecific variation in continuous trait evolution on a reticulate phylogeny 

The ploid thickens: Methodological developments, empirical advances, and remaining challenges in polyploid phylogenetics

Submitted By:  Jenna Ekwealor

Polyploidy, the state of having more than two full genomic complements in the sporophytic generation, is ubiquitous across plants: it is a major component of plant diversity patterns (e.g., c. one-third of extant vascular plants are newly formed polyploids) and polyploidization is an important process generating that diversity (it’s a mechanism of “instantaneous” speciation). Genomic approaches have revolutionized our ability to study many aspects of polyploid evolution. However, the phylogenetic study of polyploidy has lagged behind due to the combined challenges of data generation and analysis. Polyploids are often avoided or omitted from phylogenetic study due to the difficulties posed by their large genome sizes and because, once sequence data are produced, there remains the issue of accurately inferring the sequences of each of the distinct homoeologous gene copies (many polyploids contain subgenomes from multiple independent lineages—they are “‘allopolyploids”), which can be particularly difficult in short-read datasets such as often characterize genomic approaches. Then, once the appropriate data are generated, significant analysis challenges remain, including the fact that classic bifurcating-tree models are inappropriate for allopolyploids. This symposium will highlight significant recent developments in both of these areas—generating sequence data from polyploids and the application of those data to phylogenetic inference—and demonstrate how biologists can now include polyploids in phylogenetic analysis and approach previously inaccessible questions relating to the systematics and macroevolution of polyploids. Speakers will span taxonomic breadth including mosses, ferns, and angiosperms, and present on topics ranging from novel methodologies and workflows to examples of cutting-edge empirical study.

Planned Speakers:  

• Carl Rothfels and Jenna Ekwealor, Utah State University, and Smithsonian Institution, Introduction to recent methodological developments in “polyploid phylogenetics” and their application in Syntrichia (bryophyte)
• Erin Sigel, University of New Hampshire, Albion Hodgdon Herbarium, Assembling and phasing Salvinia target-capture data using the SORTER pipeline to reconstruct relationships and identify hybrid progenitors (fern)
• Mike Barker, University of Arizona, Phylogenetic simulations support inferences of multiple rounds of WGDs in flowering plants despite high turnover of polyploid species (angiosperms)
• Sarah Jacobs, California Academy of Sciences, How to accommodate polyploidy when setting up population-level sampling design, data collection, and analysis in Castilleja (angiosperm)
• Jacob Landis, Cornell University, Phylogenomics of the model allopolyploid system Glycine (angiosperm)
• George Tiley, Royal Botanic Gardens Kew, The software PATÉ for phasing target-capture reads, now with the ability to estimate site frequency spectra for mixed ploidy populations (method)

From theory to practice: New innovations and their application in conservation biology

Submitted By:  Christopher Krieg

Plant species are facing unprecedented challenges to their survival, growth, and reproduction due to numerous threats, including anthropogenic factors such as land use change, habitat destruction, climate change, and illegal poaching. The most urgent threats vary by region and species; thus, addressing individual threats to species survival worldwide will require a broad knowledge of plant organismal function, ecology, and evolution and the creation of innovative, targeted tools and applications. This symposium will feature new techniques and approaches across multiple disciplines (from physiology to evolution) and scales of inquiry (from individual plants to global perspectives), with a central focus on the development and dissemination of new methods in conservation biology. The invited speakers will present current work on the development and application of cutting-edge tools and software that link plant organismal function, ecology, and evolution to provide unique and effective conservation risk assessments and solutions. This symposium will present a balanced view of conservation biology across the diversity of vascular plants and across fields of study (physiological, ecological, and evolutionary biology), highlighting advances in techniques from modeling to ground-tested methods in conservation biology. In this way, this symposium is specifically intended to cross multiple BSA sections including Genetics, Systematics, Ecology, Physiology, and Pteridological, and draw interest from other societies such as the American Society of Plant Taxonomists, the American Fern Society, and the Natural Areas Association.

•  Jeannine Cavender-Bares, Professor (University of Minnesota), remote sensing and global ecology
•  Lauren Trotta, Research Scientist (Institute for Regional Conservation), community ecology
• Michele Pfab, Conservation Biologist (South African National Biodiversity Institute), forensic tracking
• Randal Long, Visiting Assistant Professor (Lewis & Clark College), ecophysiology
• Kaylee Rosenberger, PhD student (UC Boulder), genetics
• Bethany Zumwalde, PhD student (University of Florida), genetics

Whole genome duplications and impact on angiosperm character evolution

Submitted By:  Hong Ma

Whole genome duplications (WGDs, often also referred to as polyploidization events) generate many thousands of gene duplicates and are detected throughout the evolutionary history of angiosperms, with at least two WGDs shared by all extant angiosperms and multiple events occurred during the early diversification of major mesangiosperm clades (monocots, eudicots, magnoliids, and others). Numerous WGDs have been revealed over the past decade by phylogenomic and/or phylotranscriptomic analyses and localized to specific phylogenetic nodes. Specifically, a number of lineage-specific WGDs have been identified, including those unique to certain orders (e.g. Caryophyllales, Ericales, Poales, and Lamiales), and large families, such as Asteraceae, Brassicaceae, Poaceae, Cucurbitaceae, Fabaceae, Solanaceae, and Orchidaceae. Also, some clades within families, such as subfamilies and tribes, are now known to have their own WGDs at various time-scales. WGDs, therefore, are considered major genomic events that shape plant evolution, including the evolution of many important characters crucial for adaptation and agriculture. WGDs have been proposed to increase the ability of plants to survive major catastrophic events and adapt to other stressful environmental conditions. One of the effects of WGDs is subgenome-biased gene expression, such that one subgenome maintains a higher global expression level over other(s). An important question is how environmental conditions experienced by recently formed polyploids might play a role in shaping such differential gene expression. For example, maize and its close relatives share a recent WGD, but have different degree of tolerance to flooding. The differences among these species in retention and expression of genes from the subgenomes could be relevant to their adaptive capacity. In addition, the hypothesized contribution of additional gene copy to functional divergence and morphological innovation has been supported by analyses of character evolution, including origins of tendrils in Cucurbitaceae, pome fruits in Rosaceae, and other characters in Asteraceae, Fabaceae, and Poaceae. These physiological and morphological changes are thought to contribute to species divergence by enhancing environmental adaptation and/or reproductive success. Many WGDs occurred prior to the origin of phenotypic novelty and/or morphological changes and species diversification, suggesting that functional divergence of duplicated genes might require sufficient time and suitable environmental changes that select for those species that have experience innovation. This session will present six talks investigating WGDs and their impact on character evolution in various angiosperms.

Planned Speakers: 

• Andre Chanderbali, University of Florida - Whole genome duplication in Ericales 
• Ya Yang, University of Minnesota - Whole genome duplications in Caryophyllales and other angiosperms
• Brittany Sutherland, Michigan State University - Environmental influence on subgenome expression dominance in the aviation biofuel crop, Camelina sativa
• Yuannian Jiao, Institute of Botany, CAS - Evolutionary contribution of polyploidization events in Triticeae
• Santosh Deb, University of Alabama - Evolution of flooding tolerance in maize relatives
• Lin Zhang, Henan Agricultural University - Phylogeomic detection of WGD events and evolution of horticulturally important traits

Global Change and Plant Reproductive Failure: Beyond Climate Change Effects

An Annals of Botany Sponsored Symposium at Botany 2023

Organizers: Mauricio Quesada, Johanne Brunet, Rowan F. Sage

Abstract:  One of the great threats to the integrity of the future biosphere is disruption of plant reproduction by global change drivers – the human activities which scale in magnitude to impact the global biosphere. Major global change drivers include climate change, direct effects of rising atmospheric CO2, biotic invasions, alteration of biogeochemical cycles, species overexploitation and land transformation.  This proposed symposium will address how global change drivers impact plant reproduction beyond the often considered direct effects of climate warming on flowering and plant reproduction. Our line-up of topics includes an opening talk by Rowan Sage which will introduce the broader aspects of plant reproduction and global change, highlighting global change wildcard effects which can create surprising and often unpredictable consequences.  We have invited but not yet confirmed Dr Amy Iler to present a talk on impacts of invasive species on plant pollinator mutualisms, while Professor Joy Ward will address how elevated atmospheric CO2 directly interacts with the flowering process. Professor Mauricio Quesada will examine land use change effects, such as habitat fragmentation on reproductive fitness. Professor David Green has agreed to discuss his work showing how increased fire activity is modifying composition of the western US forests by favoring serotinous pines, whose reproduction is triggered by the heat of fire.  The symposium closes with a talk by Professor Haldre Rogers who will discuss her work on how seed dispersal and pollination success is being impacted by widespread faunal decline across the earth. 

Symposium Speakers and Titles: 

Introduction:  Johanne Brunet   

• Rowan Sage (University of Toronto): Global change wildcards and plant reproduction. 
• Haldre Rogers (Virginia Tech University): Cascading impacts of defaunation on seed dispersal and pollination
• David Green (Humboldt State University): Increasing fire frequency and species compositional change in forests of the Western US
• Megan DeMarche (University of Georgia) Consequences of earlier flowering in a warming world.
• Joy Ward (Chase Western University, Cleveland): Atmospheric CO₂  variation and flowering: genetic controls.
• Sara Good (University of Winnipeg) Internal and external factors associated with plant family species richness: the importance of considering the impact of global change on self-incompatible taxa
• Mauricio Quesada (UNAM): Effects of global land use change on female and male reproduction in angiosperms