Botany 2016 Workshops

A wide range of scientific and educational workshops will be presented during Botany 2016.  
Please register for the workshops of your choice - you will receive ticket(s) in your registration packet on site.
Pre-registration is required for all as seating is limited.  

All workshops will be presented on Sunday, July 31 in the Savannah International trade and Convention Center - Specific rooms will be on your ticket.


Subject to Change
Title Presenter Cost 
WS 1 8:00 AM - 5:00 PM Introduction to Next Generation Sequencing Shannon C.K. Straub $40.00
WS 2 8:00 AM - 5:00 PM IUCN Red List Assessment Training and Bioblitz Marian M. Chau $40.00
WS 3 8:00 AM - 5:00 PM Using Digitized Herbarium Data in Research: A Crash Course Pamela Soltis FREE
WS 20 8:00 AM - 5:00 PM Introduction to Botanical Drawing with Alice Tangerini Marilyn Garber
Alice Tangerini
WS 4 8:00 AM - 10:00 AM Constructing morphological character matrices from taxonomic descriptions using new  software approaches Lorena Endara  $10.00
WS 5 8:00 AM - 10:00 AM Using Visual Learning to Improve Comprehension Bruce Kirchoff $20.00
WS 6 8:00 AM - 10:00 AM Web-Based Retrieval Practice as a Self-Directed Study Tool for Students in Botany  and Plant Taxonomy Niels Proctor $10.00
WS 7 8:00 AM - 10:00 AM Assembly and analysis of genomic RADseq data using ipyrad Deren Eaton $10.00
WS 8 10:15 AM - 12:15 PM Planting Inquiry in Science Classrooms Gordon Uno
Marsh Sundberg
Catrina Adams
WS 9 10:15 AM - 12:15 PM We are All Plumbers Now: Toolboxes for Building Unconventional STEM Career Pipelines L. K. Tuominen
Kathryn Theiss 
WS 10 10:15 AM - 12:15 PM Tools for the International Botanist:  Navigating the Nagoya Protocol Rachel Meyer $10.00
WS 10A 10:15 AM - 12:15 PM

Integrating RNA-Seq Into Undergraduate Teaching

Stokes Baker and Bruce Cahoon $10.00
WS 11 1:00 PM - 3:00 PM

Applying to Graduate School: Tips for Success

Anna Monfils FREE
WS 12 1:00 PM - 5:00 PM Transcriptome analyses for non-model plants: phylogenomics and more Stephen Smith $10.00
WS 13 1:00 PM - 5:00 PM Making a Visual Key: A Lab Exercise  with Practical Consequences Bruce Kirchoff $20.00
WS 14 1:00 PM - 5:00 PM

Targeted next-gen sequencing for plant phylogenomics

Jennifer Mandel $10.00
WS 15 3:15 PM - 5:15 PM

Crafting an effective elevator speech and Communicating Broader Impacts of Your Work: A Workshop for Students and PostDocs.

Angela Mc Donnell and Rebecca Povilus $10.00
WS 16 5:15 PM - 7:00 PM


The U.S. Virtual Herbarium Project


Mary Barkworth Free



Introduction to Next Generation Sequencing

Next generation sequencing (NGS) describes technologies that produce billions of base pairs of sequence data per experiment. The low cost of these technologies (currently ca. 60 Mbp / dollar) allows an increasing number of biologists to incorporate genome-scale sequencing into their research. The goal of this workshop is to introduce participants to the essentials of NGS, so that they can develop and initiate their own projects in phylogenetics, population genetics, and gene expression using this technology. In the morning, we will describe the available technologies, applications, and protocols for sample preparation and sequencing. We will also describe options for computational infrastructure and analytical pipelines. In the afternoon, participants will then have an opportunity to work with data from the Illumina platform. Topics covered during the hands-on portion will include plastome sequence assembly and probe design for nuclear gene target enrichment (Hyb-Seq). A laptop computer is required. Fees will cover internet access, extension cords for laptops, a coffee break, and lunch.


IUCN Red List Assessment Training and Bioblitz

Become an official Red List Assessor for your specialty region or taxonomic group! George E. Schatz of the Missouri Botanical Garden/IUCN Species Survival Commission will provide training, and participating botanists will evaluate several plant species for Red List submission. The IUCN World Conservation Congress will be held in Honolulu in September 2016, which will be the first time the Congress is held in the United States. As botanists in the BSA and other national societies, we can participate in an important global biodiversity initiative and contribute to international conservation goals by conducting Red List assessments of the species that we know best. The IUCN Red List of Threatened Species is important because it allows us to evaluate the risk of extinction for any given species, providing open-source data that can be used for research, funding, and conservation prioritization - fitting for the Botany 2016 theme “Celebrating Our History, Conserving Our Future.” The workshop will be a full day. Prior to the workshop, participants will be required to complete online training in Red List assessment methodology, and come prepared with data on their species, including occurrences, population size, and threats. The morning session will include a review of terms, categories, criteria, concepts, and some examples. In the afternoon session, participants will assess species on their own or in small groups with assistance from the workshop leader. By the end of the workshop, each participant should have a Red List assessment ready to submit to IUCN. Brought to you by the BSA Public Policy Committee

Keywords:  conservation, assessment, biodiversity, endangered species 
Web Sites: The IUCN Red List of Threatened Species   ( Online IUCN Red List Training Course  (


Using Digitized Herbarium Data in Research: A Crash Course

Emerging cyber infrastructure and new data sources  provide unparalleled opportunities for mobilizing  and integrating massive amounts of information  from organismal biology, ecology, genetics,  climatology, and other disciplines. Key among  these data sources is the rapidly growing volume  of digitized specimen records from natural history  collections. With over 50 million specimen  records available online to date, an  ever-increasing number, these data provide  excellent information on species distributions,  changes in distributions over time, phenology,  morphology, and more. Particularly powerful is  the integration of phylogenies with specimen data,  enabling analyses of phylogenetic diversity in a  spatio-temporal context, the evolution of niche  space, and more. Beyond testing a priori  hypotheses, such data-driven synthetic analyses  may generate unexpected patterns, yielding new  hypotheses for further study. Ongoing efforts to  link and analyze diverse data are yielding new  platforms for comparative analyses of biodiversity data. However, the inundation of data and methods  can be overwhelming. In this full-day workshop,  we will provide hands-on instruction on ways to  access and download digitized herbarium data (from  GBIF, iDigBio, and other aggregators) and prepare  data sets for analysis.We will then offer a  series of modules on using georeferencing software  (GEOLocate), applying Maxent software to construct  ecological niche models and do paleoclimatic  modeling, linking specimen data to phylogenetic  trees, computing phylogenetic diversity measures,  reproducible science, and more. In addition to  learning how to use various software packages, we  will also discuss the assumptions of the analyses  and the interpretations of the results. We will  divide into groups based on participants’  experience, so novices and advanced users are all  welcome.  The workshop is free, and lunch is  included; sponsored by iDigBio (

Keywords:  digitized herbarium data, biodiversity, informatics, research applications, global change
Web Links:  iDigBio Homepage and Data Portal  (


Introduction to Botanical Drawing with Alice Tangerini

Join Alice Tangerini, Smithsonian Staff Illustrator, for this one day-long workshop on basic botanical drawing in pencil and pen and ink. This workshop will be a hands-on experience. Working from pressed plant material and digital prints of simple plants you will learn techniques used to create an accurate botanical plate.  No drawing experience necessary. 


Constructing morphological character matrices from taxonomic descriptions using new  software approaches

Phenotypic data is part of the evolutionary history of organisms and one of the only ways to integrate fossils into phylogenetic studies.  Additionally, this type of data can help researchers address scientific questions beyond Taxonomy and Systematics (e.g., studies of plasticity, adaptation, and evolutionary development). Yet phenotypic data can be challenging and time consuming to obtain. This workshop will teach scientists how to use a new semi-automated approach to extract large phenotypic datasets from taxonomic descriptions and transform them into characters useful for phylogenetic research. We will present the software pipeline used to extract phenotypic characters, and participants will work with a  sample dataset to learn the different applications  of the pipeline. A laptop computer is required.  We encourage participants that would like to analyze their own dataset to contact the organizers a few weeks in advance.

Keywords:  phenotypes, Taxonomic descriptions, morphological, characters, legacy literature, Natural Language,  Processing, phylogenetics
Web Links:  Text Parser - ETC (
MatrixConverter  (
AVAToL Phenomics project  (


Using Visual Learning to Improve Comprehension

Visual learning is a powerful modality that allows students to master complex material in a short amount of time. In the workshop you will learn to use free software to increase learning in your classes. The program, IQ, has been successfully used to improve student learning of plant life cycles, plant terminology, and organic chemistry functional groups. Results of the use of the program will be presented and discussed. IQ can be easily adapted to any knowledge domain where images play an important role. This includes the use of schematic images such as life cycles that summarize large amounts of information, and images that teach the proper use of terminology.  Participants will have the opportunity to work with the software during the workshop. A few weeks before the workshop you will be contacted with instructions on how to download the software and sample images for use in the workshop. The workshop will be even more meaningful if you bring your own images, but sample images will be provided. In order to use the software you will need to bring your own Mac or PC computer as these will not be provided.

Keywords: teaching, learning, education, visual learning, evaluation, life cycles, terminology


Web-Based Retrieval Practice as a Self-Directed Study Tool for Students in Botany  and Plant Taxonomy

Students who are learning to identify plants to family or species need a way to practice those  identification skills. Self-testing with collected plants carries the risk of learning the features of a particular specimen, rather than the diversity of the broader group. Self-testing with  unknown plants in a natural area provides no  feedback and carries the risk of learning a  misidentification. But widespread access to the internet and to high-quality digital cameras has now made it possible for instructors to provide a web-based study tool where students can practice  their identification skills. This workshop will look at web-based retrieval practice sites that have been used in undergraduate plant identification courses at the University of California at Davis and at the University of  Florida. We will look at student usage of those  sites and talk about how interface design  decisions affect usage patterns. We will also go over the steps involved in taking the necessary plant photos and building a new site for a particular course. Participants will have the chance to try using a botanical retrieval practice site and will receive a copy of the  HTML/javascript files for setting up their own  sites.

Keywords: Botany, Species Identification, Family, Recognition, Retrieval Practice


Assembly and analysis of genomic RADseq data using ipyrad

Restriction-site associated DNA sequencing (RADseq) and related methods (e.g., ddRAD, GBS) provide a simple and fast way to sample sequence data from thousands of genomic regions across many sampled individuals. The goal of this workshop is to introduce participants to the software ipyrad, which can be used to assemble and analyze RADseq data sets. We will begin with an introduction to what RADseq is, how the data are generated, and what the raw data look like. We will then learn the general workflow of ipyrad, and use it to assemble empirical test data sets. This will be followed by an introduction to more advanced Python scripting using the ipyrad API. We will end with methods for visualizing assembled data and analyzing results with population genetic summary statistics and tests for introgression. This workshop will be taught through the use of Jupyter Notebooks, with a goal of introducing participants to how this tool can be used to create  reproducible published bioinformatic workflows. No previous coding experience is required. Attendees will need a laptop running either mac or linux.

Keywords:  Genomics, Bioinformatics, Python, RADseq,  Reproducibility


Planting Inquiry in Science Classrooms

Science practices play prominent roles in the Next  Generation Science Standards, the revised AP  Biology Curriculum, and undergraduate teaching  reform efforts. In this interactive workshop, we  share simple yet effective techniques to help  students develop skills ranging from generating  questions based on observations of the usual and  unusual to exploring alternative explanations.  Leave with tested examples, ideas for using them  in your own classroom, and increased confidence to  up the ante on student-centered learning or  introduce inquiry into what you already do.  Workshop participants receive a print copy of Inquiring About Plants: A Practical Guide to  Engaging Science Practices. 

Keywords:  teaching, inquiry, student-centered learning, science practices


We are All Plumbers Now: Toolboxes for Building Unconventional STEM Career Pipelines

Research on the representation in academic science of women, people of color, and people who have experience(d) disability has shown a pattern of decreasing participation at every career level. This phenomenon, commonly known as the “leaky pipeline” effect, is familiar to most science educators, and multiple structural changes to institutional policies and training processes have been proposed to help improve retention of diverse scientists. In this workshop, we will move beyond the familiar data and common focus on institutional change to discover ways in which early career botanists, especially graduate students, postdoctoral researchers, and contingent faculty, can apply our problem-solving skills to address our current career challenges and continue towards satisfying science careers. While we will begin from the assumption that all present at the workshop are facing or have faced at least one challenge that has caused them to wonder, “Am I the Leaky Pipeline?”, such challenges need not be disclosed to other participants. Mentors seeking to support human diversity in botany are encouraged to participate.

The goals of this workshop are to:

    1. Identify several types of challenges that academic scientists face that may lead them to leave academic science,

  1. Share information about known institutional and professional resources geared towards fostering diversity within biology,
  2. Discuss science career pathways that diverge from the “linear pipeline” model, and
  3. Create personalized written plans to help address a challenge each participant faces at their current career stage by using multiple “plumbing tools.”

All participants will receive a workbook that will walk through a step-by-step process to address a current career challenge. An electronic copy of the workbook and online notes from workshop discussions will also be available to participants through the end of 2016.

 Keywords:  human diversity, leaky pipeline, nonacademic careers, contingent faculty, postdoctoral researchers, professional development, student mentorship


Tools for the International Botanist: Navigating the Nagoya Protocol

The Convention on Biological Diversity produced the Nagoya Protocol that has been ratified by 197  countries and dramatically changes the landscape  of botanical research abroad. The Protocol is a transparent legal document with a full name of  “The Nagoya Protocol on Access to Genetic  Resources and the Fair and Equitable Sharing of  Benefits Arising from their Utilization to the  Convention on Biological Diversity”. It is meant to help establish a fair framework for the  providers and users of genetic resources and to  protect providers of traditional knowledge by  requiring negotiations with appropriate parties to  ensure equitable benefits are given in exchange of  that knowledge. Many scientists fear the enforcement of this protocol, that in many ways is  focused on corporate utilization of genetic and  traditional knowledge resources for economic  benefit, will dramatically decrease basic science  research data and collections because of the  additional hurdles it creates. If you do international fieldwork or have international  collaborations, it is important to understand how  to adhere to the Protocol. Just as the Protocol creates new challenges and considerations, it also  provides a platform to leverage new opportunities,  such as lasting research partnerships and  increased intellectual collaboration. In this two-hour workshop, we break down the Protocol so  it becomes more interpretable and provide examples  of how researchers have met the new standards and  successfully completed projects that involved  sensitive genetic resources or traditional  knowledge. We also cover essentials for grant  proposal applications that now require language  about how the Protocol and other documents like the International Treaty will be followed.

Keywords: genetic resources, germplasm, economic botany, fieldwork, international research, ethnobotany, intellectual property, human rights, biodiversity


Integrating RNA-Seq Into Undergraduate Teaching

In recent years, next-generation sequencing (NGS) has become a mainstay of modern biology.  Two groups have been established to facilitate the integration of RNA-seq (i.e.,  whole transcriptome shotgun sequencing) data analysis into undergraduate biology curriculum, The Genome Consortium for Active Teaching: NextGen Sequencing Group (GCAT-SEEK;, and iPlant Collaborative’s DNA Subway (  In this workshop, resources developed by these two groups will be presented.  Workshop participants will learn about how to utilize RNA-seq data repositories and how to use freely available on-line and downloadable software tools to analyze RNA-seq data. Examples of instructional materials developed by the two presenters will also be presented.  Workshop participants will be required to bring a laptop with wireless Internet capabilities.  Since software will need to be loaded, the participants need administrative rights to their operating system.


Making a Visual Key: A Lab Exercise  with Practical Consequences

In this workshop you will make a completely visual key – a key a key based exclusively on images  – and learn about why these types of keys are  more effective than traditional text-based keys.  This will be a hands-on workshop in which everyone can participate. The procedure you learn can be easily adapted to the classroom and used, with the  appropriate modification, at any level from high  school through graduate school. Although illustrations have played an important role in identification keys and guides since the 18th century, their use has varied widely. Some keys lack all illustrations, while others are heavily  illustrated. Even within illustrated keys and guides the way in which images are used varies  considerably. During this workshop we will review some best practices for image use in keys, and  create a completely visual key. These types of keys have been made possible by advances in  digital imaging, which has allowed the rapid  collection of standardized photographs of plants.  Characters in visual keys are visually, not verbally defined. During the workshop participants will learn how to create a visual key, and will create a visual key to a group of taxa.

Keywords:  keys, visual learning, teaching, learning,  laboratory exercise, plant identification,  imaging, pictures, Quercus, Oaks, identification  guides 

Principles of Visual Key Construction  (
Image Use in Field Guides and Identification Keys  (


Applying to Graduate School: Tips for Success

 This workshop is a panel discussion designed to introduce undergraduate students to the specific requirements for applying to graduate programs in plant biology. Topics include considering a graduate degree, becoming a competitive applicant, establishing a timetable for application, picking a mentor, preparing a strong application, the  campus visit and funding options. Panelists will  include both current graduate students and faculty experienced in graduate admissions.


Transcriptome analyses for non-model plants: phylogenomics and more

Transcriptomic sequencing has become more common for non-model organisms as costs have lowered.  Often, however, the full utility of these data are  not realized because of barriers to data analysis.  In this workshop, we will examine many different uses for transcriptomes including phylogenomic  analyses, phyloGWAS, differential expression, and  more. Workshop participants will be given the  necessary scripts, instructions, and test data. No other special knowledge required. Instructions  and dependencies to install will be handed out for  participants to install and test before workshop.  For those who are not familiar with command line interface, additional tutorial instructions will  be provided. 

Keywords:  transcriptomes, phylogenomics, phyloGWAS, differential expression, phylogenetics, Genomics
Information Website:  (


Targeted next-gen sequencing for plant phylogenetics

Next-generation sequencing and phylogenomics hold  great promise for elucidating complex  relationships in plant lineages. In this workshop,  we will present an overview of the use of targeted  sequence capture and next-generation sequencing  for phylogenetics addressing questions like:

  • What  do I need to begin a phylogenomics project?
  • How do  I design capture probes in my group?
  • What hurdles  do I need to be ready for?
  • What kinds of questions  can I answer with any existing genomic data I  have?
  • How much does this cost?

We have  successfully implemented targeted capture of low  copy sequences followed by next-generation  sequencing on the Illumina platform in the large  and diverse angiosperm family Compositae  (Asteraceae). In this workshop, we will describe  the probe design process and the wet lab protocol  for performing sequence capture including helpful  information for designing similar experiments in  your own research system. Our method generates  nuclear data and chloroplast genomes (from  off-target capture reads) enabling the comparison  of nuclear and chloroplast genomes for  phylogenetic analyses. We also analyze multi-copy  nuclear genes in our data set using a clustering  method during orthology detection, and we apply a  network approach to these clusters—analyzing all  related locus copies. The organizers will  demonstrate the bioinformatic and phylogenetic  workflow, walk participants through the process,  and ample time will be provided for questions at  the end. As time allows at the end, materials and  software information will be distributed and  participants are encouraged to bring their laptops  to try out the bioinformatic workflow. Examples  will be given for implementing this method in the  Compositae and will generalizable to other species  groups. 


Crafting an effective elevator speech and Communicating Broader Impacts of Your Work: A Workshop for Students and PostDocs.

For each of us, a professional conference is an opportunity to develop skills as scientists and to communicate with an ever-growing network of colleagues. The “elevator speech” has received attention recently, particularly in the sciences as the need for effective science communication has increased due to a variety of factors. Whether we share our work with colleagues, at job interviews, or even your family, crafting an effective elevator speech requires us to think outside of our discipline and address the broader impacts of our work. This workshop will bring together students and post-doctoral fellows at different stages of their career to hone an elevator speech they have already prepared. Following a brief introduction with helpful tips for crafting your speech, we will have a breakout session to revise and modify our elevator speeches using tips from our keynote speaker. Finally, we will organize into groups to share these elevator speeches with each other. The social atmosphere of the event will contribute to opportunities for candid, constructive feedback and we encourage participants to use this interaction as practice toward pitching your elevator speech throughout the rest of your time at Botany 2016.


The U.S. Virtual Herbarium Project

The 2016 Annual Meeting of the U.S. Virtual Herbarium project will be held at 5:15 p.m., Sunday July 31.  It will last about an hour. The two main items on the agenda are:

  1. Status of herbarium digitization in the US and brief reports on new initiatives.
  2. Status of the U.S. National Vascular Plant Website.