Submitted By: Emily Sessa
Life cycles are a fundamental aspect of organismal biology, and a cornerstone of most introductory biology and botany courses. Despite the importance of this topic and its ubiquity in the lab and lecture hall, plant life cycles can be a challenging subject to teach and students are often bewildered by the extensive terminology and unfamiliarity of the alternation of generations life cycle that plants undergo. During this workshop, the organizers and participants will share and discuss teaching methods for this topic, with the goal of providing everyone with a range of tools and approaches for tackling plant life cycles in their classes. We will discuss learning objectives, critical concepts, and assessment methods, and participants will be invited (if they wish) to share their own slides and/or other materials related to teaching plant life cycles, so that we can benefit from each other’s experiences. We will focus primarily on sexual reproduction and alternation of generations in land plants, but as time and participant interest permit, we may also discuss more advanced topics (e.g., selfing, apomixis) and/or additional life cycles (e.g., fungi). Students are very welcome to attend, and prior teaching experience is not necessary.
Emily Sessa, New York Botanical Garden
Jennifer Blake-Mahmud, Hope College
Eddie Watkins, Colgate University
Submitted By: John Schenk
Advances in phylogenetic comparative methods have allowed biologists to robustly and objectively test macroevolutionary hypotheses, leading to a greater understanding of the processes of species diversification. Although the potential to answer numerous hypotheses across clades has invigorated macroevolutionary studies, learning how to apply phylogenetic comparative methodology remains a significant impediment. The workshop will provide foundational knowledge of phylogenetic comparative methods and how to apply them using the statistical program R. Attendees will gain hands-on experience in applying methods, such as phylogenetic independent contrasts; phylogenetic generalized least squares; ancestral character estimations; constructing, fitting, and testing evolutionary models; fitting Brownian motion and Ornstein–Uhlenbeck models of evolution; lineage through time plots; and estimating phylogenetic signal in trait data. Participants will gain a theoretical understanding of phylogenetic comparative methodology and be able to apply even the most rigorous analyses to their own study systems. Prior experience applying phylogenetic comparative methods or using R is not expected or required. Early career scientists are especially encouraged to attend.
John J. Schenk, Ohio University
Paige Fabre, Ohio University
Johan Ling, Ohio University
Submitted By: Eduardo Charvel
Genome skimming (low-coverage shotgun-sequencing) approaches to evolution and population genetics offer flexible alternatives to traditional methods left to DNA (meta)barcoding, bypassing the need for PCR amplification of marker regions or by avoiding computationally expensive processes of assembly alignment (Bohmann et al. 2020). As the cost of shotgun-sequencing keeps decreasing, the potential use for these skimming methods in the study of genomic ecology is higher than ever. In this workshop, we will be looking at a low-coverage sequencing analysis pipeline with a variety of functions, including decontamination, genomic distance inference, phylogenetic placement, and estimation genome repetitiveness. The pipeline consists of a set of user-friendly command-line tools dedicated to analyzing low-coverage genome skims (https://github.com/smirarab/skimming_scripts).
Firstly we will be talking about CONSULT-II: a taxonomic identification tool that extracts k-mers from a query read and classifies them against k-mers in a reference database. In the context of the pipeline, we will be using it to remove reads that classify as bacterial contaminants, keeping reads that are specific to our organism of interest (Şapcı et al. 2022).
We will also be discussing Skmer, an alignment-free tool that estimates distances between genomes by looking at how many shared k-mers are found between sequences and outputs a distance matrix which you can use to create a phylogenetic tree (Sarmashghi et al 2019).
With a reference tree constructed by distance matrix generated from Skmer, we then use another tool APPLES for fast, alignment-free phylogenetic placement (Balaban et al 2020).
Finally, we will talk about RESPECT, a tool to accurately estimate properties like repetitiveness, genome length, sequencing coverage and error (Sarmashghi et al 2021).
This workshop will cover installation instructions, an overview discussion of how the methods function, and applying the suite of tools in your local computer and/or cluster. The workshop will work through a tutorial analyzing a small plant genome dataset.
Eduardo Charvel, UC San Diego
Siavash Mirarab, UC San Diego
Submitted By: Mason McNair
The methods used to collect data vary greatly between different research programs. Standardized equipment rarely accounts for nuances relating to study system or resource limitations, creating a need for inexpensive, custom solutions. Bespoke equipment has historically been limited to well-funded research programs, but advances in 3D printing are making it possible for nearly all labs to design and manufacture their own research tools using the current generation of inexpensive and reliable printers.
The goal of this workshop is to demonstrate the problem-solving potential of open-source hardware and 3D printing for scientists. 3D printing facilitates the adoption of custom equipment that can increase the rate and quality of data collection.
3D printing in most scientific fields is relatively new, but it is rapidly growing. Multiple peer-reviewed articles outlining potential uses of 3D printing in the sciences exist but adoption of this technology has been slow. For example, these are all areas that have successfully demonstrated the potential impact of 3D printing.
Education and outreach (https://doi.org/10.1016/j.revpalbo.2023.104860; https://doi.org/10.1016/j.addma.2018.10.028)
To introduce and promote 3D printing in the sciences, this workshop is part of a series of in-person and online workshops that guide researchers through the process of designing custom tools for their research questions, setting up and using 3D printers, and performing maintenance on their machines. While the organizers will not receive any financial benefits from 3D printing companies or suppliers through this workshop, we will be contacting 3D printing companies and suppliers to request discount codes, supplies, and assistance in creating workshop teaching materials to give to participants and offset workshop costs.
3D printing can positively impact scientific research and is worth adopting as part of your research methods. This workshop aims to provide participants with the knowledge needed to successfully incorporate 3D printing into their research.
Mason McNair, Clemson University
Submitted By: Sharon Bladholm
In this interactive workshop that merges art and science, we will begin with a short PowerPoint presentation about Seed Rain: Seed Bank, a large ceramic
installation I created and other seed inspired art. Participants will gain inspiration, working from a large collection of actual seeds ceramic seeds, and my enlarged seed sculptures, both from the Midwest and tropical regions. We will then move into a multifaceted afternoon (or day) of art making where we can slow down and appreciate the forms, colors and textures of these small packages that are imbued with so much potential. Power to the plants, Plants power the planet!
Participants will begin drawing with pencil to experientially understand these forms, simple and complex, add color with watercolors. The following investigation involves carving into small clay slabs, using brayer's to roll nontoxic ink on them and lastly burnishing rice paper over the slabs, creating a print. There is something exciting and transformative about this process where the unexpected can happen. The clay slabs used for printing are beautiful as well and can be taken home. The final option is to use the self hardening clay to create small seed inspired sculptures, adding color with paint.
Sharon is an artist inspired by the botanical realm in all its aspects, who loves to share her dual enthusiasm for seeds/plants and
art making. She has participated as artist on plant hunting expeditions with the Field Museum, Conservation International, and the Botanical Research Institute of Texas’s, Andes to Amazon Biodiversity Program. She has completed artistic residencies in other remote areas of the Peruvian and Ecuadorian Amazon with Project Amazonas and the Tiputini Biodiversity Station. Her traveling exhibition Soils, Seeds and Sprouts: Tropical and Temperate explores botany and soil microorganisms, using art as a conduit to inform the public on important issues regarding nature, science, conservation, and biodiversity. She often teaches workshops for a diverse audience.
Submitted By: Eli Hartung
R (www.r-project.org) is a free software environment for statistical computing and graphics. This workshop introduces basic concepts, syntax, and usage in R programming, statistical analysis, and visualization techniques for botanical data. This workshop is intended for anyone who is working to analyze their research data (including graduate students, early career faculty and researchers, undergraduate researchers) and would like to learn how to automate data processing and presentation using the R programming language. This workshop stands as the final installments of the Early Career and Development Committee Intro to R and Data Analysis workshop series and will combine and review the topics covered in previous workshops to produce highly communicative figures. Bring your own dataset and we will work through the complete process of data familiarization, cleaning, analysis, and visualization. In the first half of this workshop, we will provide an overview of R and its basic usage. We will cover basic information about R syntax, the RStudio interface, and move through how to import CSV files, the structure of data frames, how to manipulate data frames, how to calculate summary statistics from a data frame, and a brief introduction to plotting. In the second half of this workshop, we will discuss and perform statistical analyses and visualizations best suited to your dataset. We will also discuss different data visualizations to illustrate both good and bad applications of design and visualization principles. By the end of the course, you will have the essential skills of processing, manipulating and analyzing data of various types, creating advanced visualizations, generating reports, and documenting your codes. Attendees are asked to bring a computer with R and Rstudio installed and their own data in order to participate in this coding-based workshop.
In this workshop you will:
1. Become familiar with R and its applications
2. Perform a variety of statistical analyses for your dataset
3. Create publication ready figures
4. Be able to take these skills and apply them to your other projects
*Subject to Change*
Eli Hartung, Kansas State University
Josh Felton, Cornell University
Chistopher Krieg, University of Wisconsin-Madison
Min Ya, University of Connecticut
Miranda Sinnott-Armstrong, University of Colorado Boulder
Benjamin Blackman,University of California, Berkeley
Jill Spear, National Geographic
Submitted By: Ryan Folk
Botany has seen a massive growth in “big data” resources ranging from DNA to plant distributions and morphological traits. Databases like GenBank and GBIF have accordingly become household words among meeting attendees, reflecting the impact data resources have had on today’s research landscape. BSA has seen productive workshop series focused on each of these data streams in isolation, such as the popular iDigBio and phylogenomics workshops. Based on sheer data scale, we are at the threshold of using these data as platforms for assessing species traits and ecologies at the kinds of truly continental and global levels needed to test fundamental theories and to produce the applied outcomes needed for environmental action. Yet biodiversity researchers are only beginning to tap the potential that these datasets have when employed in synergy. Needed is a relatively new set of skills to perform analytical integration: bringing distributions and phylogenetic trees together, bringing traits and distributions together, and other typical yet challenging tasks. We propose a crash course in performing an essential component of integrative science—Data Wrangling—that meets the increasing needs of students and academics.
The purpose of this workshop is to showcase novel methods and applications of biodiversity data in a phylogenetic and spatial context, exposing attendees to several typical workflows and hopefully inspiring them with new ideas for their own scientific systems and datasets. We will cover diverse research topics representing the future of the field, and instructors will include early-career individuals. We will offer hands-on instruction in each analysis topic, including ancestral niche reconstruction, trait-associated diversification, spatial phylogenetics, measurements of phenology, and other popular topics. We will focus our coverage on strategies to test popular hypotheses using publicly available data. Advanced and novice users are both encouraged to attend and will be divided into separate working groups. We aim particularly for those who have or are in the process of acquiring datasets and looking for ideas for analytical applications, and we refer to other BSA workshops those attendees who primarily seek instruction in data acquisition. Prepared datasets will be used for this workshop; attendees who are able to bring their own diverse datasets are enthusiastically encouraged to do so, but should contact workshop leaders several days in advance of the workshop date to make the most of the workshop experience. Users should plan to bring a computer that is set up with an R environment. For previous attendees: this year we will present new tools in the afternoon session focused on ecological modeling accounting for phylogeny.
Ryan Folk, Mississippi State University
Robert Guralnick, University of Florida
Daijiang Li, Louisiana State University
Submitted By: Suneeti Jog
The workshop will teach participants to identify common species of trees and woody shrubs of the midwestern and eastern United States, with a special emphasis on distinguishing species of oaks in the winter. Participants will learn to use basic botanical features used for identification such as buds, twig characteristics, bark, and fruits. This will be a hands-on workshop where participants will be able to discern morphological characters, distinguish odors unique to certain taxa, and experience pertinent textures that will aid in species identification. In an increasingly ever-changing digital world, this back to basics, old-school and resilient approach using only winter attributes will be a refresher on plant identification of woody species.
Fresh as well as herbarium specimens of leafed out material will also be on display to compare with winter twigs, so that participants can associate dormant stages with active growth forms. The workshop will culminate with a keying exercise of unknown specimens of winter twigs. This workshop will be most beneficial to those who need field botany skills as well as international field botanists wishing to delve into winter botany.
Identifying tree species accurately is very important for ecological monitoring and for protecting and managing natural areas, in an ever changing, anthropogenically altering world.
Suneeti Jog, Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign
Matt Finzel, Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign
Submitted By: Muriel Poston
Science process and critical thinking skills play prominent roles in the revised Advanced Placement (AP) Biology curriculum, Vision and Change (AAAS, 2009, 2012, 2020) for undergraduate biology education, and other undergraduate teaching reform efforts e.g. Gordon Conference in Undergraduate Biology Education. In this interactive workshop, participants will engage in simple, yet effective, methods for instructors to help students develop their scientific literacy and science practice skills ranging from generating questions based on observations of the usual and unusual to exploring alternative explanations. Each person will leave the workshop with tested examples, ideas for using and adapting them in any science classroom, and increased confidence to promote student-centered learning and to introduce inquiry into an existing curriculum. The workshop has several major goals: 1) to demonstrate how to introduce inquiry instruction in a science classroom, to engage workshop participants in inquiry activities, and to work with participants to develop their own inquiry-based lessons; 2) to demonstrate the breadth of botanical examples that can be used to teach major biological concepts while using active learning; 3) to outline the key barriers to equity instruction in a science classroom and help workshop participants create activities that focus on scaffolded skills and concepts based on their own interests; 4) to illustrate the benefits and use of effective formative assessments in a science classroom and how instructors can create their own concept inventory questions; and 5) to identify methods for engaging a diversity of students in the study of science through an exchange of best practices and ideas among the entire workshop group.
Gordon Uno, University of Oklahoma
Anna Monfils, Central Michigan University
Muriel Poston, Pitzer College
Submitted By: Jacob Landis
The costs of generating a draft genome assembly for a study organism of choice are declining each year and more tools are becoming available to help in the endeavor. Recent advances in long-read sequencing technology (Nanopore Q20+ kits and the PacBio Revio) make generating the necessary read coverage feasible for most plant groups. However, generating the appropriate sequence data for assembly and phylogenomic/comparative analyses is not a trivial matter and the magnitude of tools available for analysis can be bewildering. The focus of this workshop is to go through the necessary steps for genome assembly and annotation, while also focusing on comparative analyses when a closely related reference genome is not available for the species of interest. The workshop will give an in-depth overview of assembling genomes using PacBio HiFi data and scaffolding assemblies with HiC data. Additionally, we will touch on other approaches and discuss scenarios where different methods may be more appropriate. Methods for extracting high-quality DNA suitable for sequencing and library preparation will be discussed, as many plant species possess secondary compounds which can be problematic for sequencing. Downstream evolutionary analyses that can be performed after assembly will be covered while highlighting that a perfect assembly is not necessary to answer many questions. These will include genome annotation, SNP identification, gene family evolution, and using single copy genes for phylogenomic analyses. Participants will get hands-on practice with all the necessary steps using either the supplied test data or their own data if previously generated.
Jacob Landis; Cornell University
Fay-Wei Li; Boyce Thompson Institue
Dylan Cohen; Chicago Botanic Garden
Haley Carter; Chicago Botanic Garden
Susan Strickler; Chicago Botanic Garden
Submitted By: Jessie Swimeley
Create Traditional Cyanotype prints with artist, Jessie Swimeley. Learn the history, chemistry, and artistry of this historic photographic contact printing process. Traditional Cyanotype printing and botany have a long history of making beautiful blue works of art together!
Bring fresh or pressed samples of your favorite botanicals to use to create your artwork. Plants with strong silhouettes work the best, but we can definitely try anything!
Jessie Swimeley- email@example.com
Submitted By: Matthew Kolp
Join us to draw your focus back to the fundamentals of collaboration across disciplines, a core concept of One Health research. In this 2-hour workshop, we will discuss and invite discussion from participants on productive, collaborative behavior in their fields. Then we will present our research in ethnobotany: how do native plants of Appalachia and their derived natural products compare for the purported medicinal, immunological, and phytopathogenic effects? How do plant endophytes and microbiome members contribute to these traits? We present our methods including but not limited to the application of HPTLC, mass spectrometry, and microbiome analyses; we also share our preliminary findings. We end our workshop with an outline of a review paper on Plant Microbiomes and Appalachian Folk Medicine and invite workshop participants to join as authors.
This workshop is for:
• Researchers and students at any stage of their career with no, some, or lots of expertise in topic areas (ethnobotany, plant endophytes, natural products, HPTLC and mass spec)
• Those interested in discussing the fundamentals of successful, productive, and collaborative behavior.
• Those interested in ethnobotany, phytopharmacology, plant chemistry, and/or endophytes.
• Those interested in collaborating with us to produce a One Health review paper on the intersection of ethnobotany, natural products, and microbiomes.
Folks that attend our workshop will:
• Create a list of productive, collaborative behavior to use in their research.
• Discuss their experiences of successful collaborative behavior.
• Gain knowledge of ethnobotany of Appalachia, the significance of natural products research, and plant endophytes as an abundant source of bioactive compounds.
• Consider committing to a collaboration with our group to produce a review paper and conduct empirical research on plant endophytes of ethnobotanically important natural products.
Matthew Kolp, Lincoln Memorial University, Richard A. Gillespie College of Veterinary Medicine
Marybeth Babos, Lincoln Memorial University, DeBusk College of Osteopathic Medicine
Noel Cawley, Lincoln Memorial University, School of Mathematics and Sciences, Cumberland Mountain Research Center
Lori McGrew, Lincoln Memorial University, DeBusk College of Osteopathic Medicine
Submitted By: Nina Lawrin
I propose a conversation around how ecological knowledge is preserved after immigration. It can include a portion where participants partake in the creation of a food/ culturally significant plant relationship to take home with them as well as a conversation around how we all can reconnect to ourselves through the land and preserve ecological knowledge while sharing in unity during these times of change.
In this pilot study I argue against the negative connotations of acculturation and acknowledge the fluidity, creativity, and adaptability of Ukrainian-American immigrants and their foodways. Ukrainian immigrants were able to assimilate to life within metro-Detroit while simultaneously preserving traditional foodways through celebratory foods. Through annual, familial holiday meals at Christmas, Easter and the occasional wedding, the matriarchal lineage has effectively preserved cultural keystone foods through language, use, and preparation. Community and schools also played a vital role in traditions and food preservation. First generation immigrants embraced transnational migrant identities which is reflective in their foodways. Second and third generations varied in frequency and seasonality as compared to first generation immigrants, although those who partook in annual Ukrainian celebratory foods were able to preserve key ecological food plant knowledge, usage, and language.
ethnobotanist Nina Lawrin with potential guest
Submitted By: Christopher Muir
Plant ecophysiological methods are becoming increasingly popular because of their ability to inform ecological and evolutionary processes across scales, e.g., at larger ecosystem-level and smaller genetics-level scales. One of the primary aspects of plant function is leaf gas-exchange (CO2 and water vapor) which can be used to understand plant water-use, productivity, stress tolerance, trait screening and phenotyping, adaptation, trait-genotype associations, and more. We propose a workshop focused on current and commonly requested techniques in leaf gas-exchange, led by experienced ecophysiologists from academia and industry. The major components of the workshop will include measurement theory, equipment operation, data analysis, and modeling. We propose a full-day workshop which we will divide into two half-day sessions. Part 1 will provide an introduction to measurement theory (e.g., responses to CO2) and focus on the basic operation of popular gas-exchange equipment. Part 2 will cover data analysis and modeling gas exchange using recently developed R packages. Participants can join either one or both sessions. This is similar to a workshop held at Botany 2022 but will be updated with new equipment and software advances.