Biodiversity data wrangling: Linking large phylogenies with species traits and ecologies

Abstract

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 assessing trait history and evolutionary rate, ancestral niche reconstruction, trait-associated diversification, phylodiversity, 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.

Organizers

• Ryan A. Folk, Mississippi State University
• Carolina M. Siniscalchi, Mississippi State University
• Nicholas J. Engle-Wrye, Mississippi State University
• Robert P. Guralnick, University of Florida

Writing your CV and translating it into public-facing website

Abstract

Let's work together to create a comprehensive description of your career in a CV format and then create a website that will highlight those achievements for the world to see. We will first organize your skills and accomplishments in a CV that you can use for job, funding and nomination applications. Then we will use these highlights of your career history to design a website that can showcase your research, teaching, publications, speaking engagements and service. At the end of this workshop you will have the tools to write a well developed CV and to create your own website. You will also leave with a working draft of a CV and a basic academic website that you will be able to build up further in the weeks to come.

This workshop is for students and early career professionals. Please bring a draft of your current CV to edit in class, a computer and any previous attempts at making a website.

In this workshop, you will:
1. Learn the basic structure of a CV and best practices for writing it
2. Receive feedback on your CV from peers and instructors
3. Learn the steps to create your own website
     a. Why create a website? Define your audience and intentions for having a website
     b. Discover possible content to include and see good examples
     c. Create a structure for your personalized website content (using your CV as a starting point)
     d. Work together to build a free website

Organizers

• Ioana Anghel, University of California, Los Angeles
• Eli Hartung, Kansas State University

Using Digitized Herbarium Data in Research: Applications for Ecology, Phylogenetics, and Biogeography

Abstract

Emerging cyberinfrastructure 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 120 million specimen records available online, and growing, 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. 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 for novices and advanced users alike. In addition to training on the use of various software packages, we will also discuss the assumptions of the analyses and interpretations of results. We will divide into groups based on participants’ experience, so novices and advanced users are all welcome. Beginners will learn how to access and download digitized herbarium data (from GBIF, iDigBio, and other aggregators) and prepare data sets for analysis. We will offer a series of modules on using georeferencing software (GEOLocate) and applying Maxent software to construct ecological niche models, including paleoclimatic modeling. These modules will follow the successful training program we have used at past Botany meetings. For advanced users, we will provide new, innovative modules for linking specimen data to phylogenetic trees, computing phylogenetic diversity measures, conducting biogeographic analyses, and more. We will cover strategies to extract information from niche models, reconstruct ancestral niches, and test hypotheses about niche evolution. Participants will use new integrative software tools developed by the BiotaPhy Project that link occurrence data (through iDigBio), niche models, and ecological statistics calculated from the models, applying these to large trees in a desktop geospatial environment. Participants will learn how to conduct analyses that link species distributions to patterns of environmental sorting and the legacy of historical biogeography in a new phylogenetic framework called Meta-Community Phylogenetic Analysis or “MCPA”. Prepared datasets will be provided, but attendees may bring their own data. Beginners will need to bring a laptop (either Mac or Windows); advanced users should bring a computer with a UNIX-compatible operating system such as OS-X or Linux.

Organizers

• Pamela Soltis, Univ of Florida
• Douglas Soltis, Univ of Florida
• Shelly Gaynor, Univ of Florida
• Maria Cortez, Univ of Florida
• Makenzie Mabry, Univ of Florida
• Elizabeth White, Univ of Florida

Methodological advances in reticulate evolution

Abstract

The rapid development of phylogenetic network methods allows evolutionary biologists to infer reticulate relationships between species or their common ancestors. Given the notable levels of hybridization in plants relative to other groups, phylogenetic networks have the potential to elucidate complex evolutionary histories of speciation and trait evolution in addition to explaining historically contentious nodes in the Tree of Life despite increasing genomic data. This workshop will connect method developers with empirical botanists to discuss models, misconceptions, and best practices on network estimation and downstream applications. A combination of theoretical lectures and hands-on computational exercises will provide an overview of the field and exposure to cutting-edge tools. Workshop participants are encouraged to bring their own data as there will be opportunities for analysis and discussion with speakers outside of guided activities.

Specific topics include estimating networks using multi-locus nuclear data, evaluating the robustness of networks to different sources of error, and testing hypotheses of trait evolution on networks. Software used during the workshop includes FastNet, PhyNEST, PhyloNetworks, BPP, and PhyNetPy. This brief survey of the many existing methods will demonstrate a range of strategies that fit different data types and taxon sampling scenarios. The assumptions and limitations of various methods will be discussed. No prior experience is expected and speakers will be available to provide real-time guidance through exercises.

Organizers

• George Tiley, Royal Botanic Gardens Kew
• Claudia Solís-Lemus, University of Wisconsin-Madison

Planned Speakers

• Claudia Solís-Lemus, University of Wisconsin-Madison
• Lauren Frankel, University of Wisconsin-Madison
• Kevin Liu, Michigan State University
• Sungsik Kong, University of California San Diego
• George Tiley, Royal Botanic Gardens Kew
• Mark Kessler, Rice University
• Huw Ogilvie, Rice University

Supporting inclusive and sustainable research infrastructure for systematics (SISRIS) by connecting scientists and their specimens

Abstract

Scientific discoveries derived from biological collections depend on the people who create the infrastructure of preserved specimens. However, currently accepted metrics of professional success for taxonomists ignore the essential functions of collection, identification, and annotation of research specimens that support published research. This results in an incomplete picture of the contributions of those working in biological collections. Recently, web-based informatics tools have been developed to improve the attribution of specimens, so that collectors and determiners can track their contributions to subsequent research discoveries made using their work and receive greater professional recognition. In this workshop, participants will learn how to create an inclusive and sustainable research ecosystem for collections-based research by increasing the attribution of the people who create and identify herbarium specimens. This half-day workshop will comprise four hours of instruction about the structure and use of the web-based informatics tool Bionomia and the other software services that interact with this platform, including ORCID, GBIF, Wikidata, and Zenodo. The workshop will emphasize (1) how participants can use these tools as part of their collections-based research activities and (2) how increased attribution can be used as a means to effect community-level change in how taxonomic expertise is acknowledged. Participants will practice attributing specimens to historical collectors from underrepresented groups, which will directly increase the visibility of hidden figures in natural history collections. We encourage individuals from all career stages and institution types to attend the SISRIS workshop funded by the US National Science Foundation. Stipends for up to 30 in-person participants will be provided to defray the cost of attending, including dependent care. 
To be considered for participant support, please apply here For further details and application link: https://tinyurl.com/3jmaztfa. Email for questions: SISRIS2023@gmail.com

Organizers

• Shawn Krosnick, Tennessee Tech University, Department of Biology and Hollister Herbarium Cookeville TN 38505, USA
• Andrea Weeks, George Mason University, Department of Biology and Ted R. Bradley Herbarium Fairfax VA 22030, USA

Planned Speakers

• Deborah Paul, University of Illinois
• Zach Murrell, Appalachian State University, aweeks3@gmu.edu
• Shawn Krosnick, TN Tech University

Introduction to Phylogenetic Comparative Methods in R

Abstract

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 Introduction to Phylogenetic Comparative Methods in R 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 the 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.

Organizers

• John J. Schenk, Ohio University

Planned Speakers

• John J. Schenk, Ohio University
• Paige Fabre, Ohio University

A Working Group to Summarize Newly Described Vascular Plant Taxa in North America North of Mexico from 1995-2019

Abstract

In 1998 R.L. Hartman and B.E. Nelson published a comprehensive summary of newly described vascular plant taxa in North America (north of Mexico) covering the years 1975-1994. In so doing they helped illuminate the fact that many vascular plant taxa continue to be described, despite over 250 years of plant collecting and taxonomic research in this expansive and widely explored area. Not surprising to most taxonomists and systematists, new discoveries of vascular plant diversity have continued steadily since that time.

However, interest in (and even awareness of) taxonomy as a field of study, area of expertise, and career path continues its general decline, with increasingly fewer students acquiring basic skills in plant identification and fieldwork. This is unsurprising given that some universities under-prioritize offering taxonomic and systematics coursework and field opportunities, and the decline likely is further aggravated by the fact that the visibility of this work to the average student is minimal. In addition, easily found and digestible summaries of such work are difficult to find. A simple online search for plant species described in North America in 2020 yields only a few of the highlights considered interesting by popular science writers. Although it is satisfying to see some studies being highlighted, it is unhelpful that the bulk of the information remains obscured.

Our open workshop will bring together interested plant taxonomists and systematists to collaboratively create a Working Group with the goal of publishing a summary of new plant taxa described over the 25-year period of 1995-2019. The project will include analytics summarizing various aspects of taxonomic, geographic, and phylogenetic significance. We propose in concert the creation of useful online and interactive resources (perhaps hosted on ASPT or BSA websites) to allow interested users to explore the new taxa, where they occur, and other aspects of their biology, ecology, and phylogeny. The tentative goal will be to review the results at BOTANY 2024 and submit these as a publication soon thereafter.

Anticipated additional outcomes include raising the profile and importance of ongoing taxonomic work, biodiversity exploration, recruiting a diversity of new students to the field of taxonomy, and highlighting the project’s value to ongoing conservation efforts.

Organizers and Planned Speakers

• Dr. Neil Snow; Pittsburg State University
• Dr. Sarah Jacobs; California Academy of Sciences

Note: Most of the workshop will be discussion-oriented regarding the execution of the proposed project. However, the co-organizers (Snow and Jacobs) may allow additional speakers if we believe their viewpoints would be meritorious in the context of the Project's goals and outcomes.

Decolonizing Botany Discussion + Workshop

Abstract

The history of the botanical sciences is deeply intertwined with histories of colonization and resource extraction, which have resulted in the continuous disenfranchisement of peoples across the globe, especially Black and Indigenous peoples. This workshop will aim to discuss how this history and the assumptions embedded in the culture of the botanical sciences today engage with and perpetuate harms through colonization, and how we as researchers can critically examine our own work and how we can work to reduce, remove, and reverse colonial violence in our own work and the work of our institutions.

Aims of the workshop:

• Address questions from participants about what is colonization and decolonization, how botanical research perpetuates colonization, the scope of the impacts of colonization
• Brainstorm and share reading lists/resources on the subject, particularly as it relates to botany
• Discuss and share experiences and strategies of how researchers in our community have been working to address colonization and decolonization in their own work

Organizers

• Tabitha Faber, University of Wisconsin--Madison
• Louisa Bartkovich, University of Toronto
• Nick Koenig, University of Idaho
• Amy Wrobleski, Pennsylvania State University

Planned Speakers

• Dr. Az Klymiuk, University of Manitoba, az.klymiuk@umanitoba.ca

NSF Proposal Writing Workshop

Abstract

What makes a compelling, potentially-fundable grant proposal? In the first part of this workshop, NSF program officers will provide a quick overview of best practices and common pitfalls. In the second part, program officers will host mock proposal review panels in small groups, allowing participants to experience how proposals are evaluated and what makes a successful proposal. Participants will be provided with two proposals to review, along with instructions, ahead of the workshop. This workshop is limited to early-career researchers, e.g., postdocs, assistant professors, or equivalent.

Organizers

• Judy Stone, Division of Environmental Biology, National Science Foundation
• Shannon Fehlberg, Division of Environmental Biology, National Science Foundation

Planned Speakers

Program Officers from the Division of Environmental Biology, National Science Foundation

• Cathie Aime
• Shannon Fehlberg
• Matt Herron
• Kari Segraves
• Irv Forsyth
• Judy Stone

Navigating deep learning with digitized herbarium specimen image data

Abstract

The rapid increase in digitized herbarium specimens available in natural history collections has enabled us to study many aspects of plant biology, such as morphological comparisons, shifts in phenology, and changes in species distributions. Currently, tens of millions of herbarium specimen images are available via online databases, with more image data added every day. In recent years, machine learning methods have shown promise in efficiently extracting data from herbarium specimens. Deep learning analyses, such as convolutional neural networks, leverage computer vision to automate analyses of herbarium sheet images. Researchers can use deep learning methods to classify digitized herbarium specimens by species or other user-specified categories.

Even relatively simple neural networks can contain hundreds of billions of parameters and require the use of graphical processing units (GPUs), which can process multiple computations simultaneously. Accessing and interfacing with GPUs can represent a barrier to entry for some users. This workshop will help participants to vault past the initial technical challenges of using deep learning on herbarium sheets to conduct analyses for object detection, image segmentation, and taxonomic classification.

Participants will work with curated sets of images, or they can use their own datasets--although this will require some advance preparation by the participant to organize their images. The workshop will be conducted in Jupyter notebooks, and some knowledge of Python will be helpful, but not required. A laptop computer and a Google account will be required.

Organizers and Planned Speakers

• Richie Hodel, Smithsonian Institution
• Rebecca Dikow, Smithsonian Institution
• Jenna Ewkwealor, Smithsonian Institution
• Will Weaver, University of Michigan
• Sundre Winslow, Smithsonian Institution

3D Printing for Plant Science: Design to Optimize

Abstract

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 plant scientists. 3D printing facilitates the adoption of custom equipment that can increase the rate and quality of data collection.

3D printing in plant sciences is a relatively new subfield, but it is rapidly growing. Multiple peer-reviewed articles outlining potential uses of 3D printing in the sciences exist, but relatively few involve plant sciences.

• Microfluidics (https://doi.org/10.1016/j.addma.2018.10.028),
• microscopy (https://www.preprints.org/manuscript/202105.0352/v1),
• phenomics (https://doi.org/10.34133/2020/8640215), and
• education and outreach initiatives (https://doi.org/10.1016/j.revpalbo.2023.104860; https://doi.org/10.1016/j.addma.2018.10.028)  are all areas that have successfully demonstrated the potential impact of 3D printing.

To introduce and promote 3D printing in the plant 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 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 plant science 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.

Organizer:

• Mason McNair, Clemson University, mcnair5@clemson.edu

Rekindle your creativity: Unifying art and science for personal and professional wellbeing

Abstract

Are you curious about integrating art and science but not sure where to start? Do you love to create but feel intimidated by the gap between doodles and a completed project? Feeling isolated from your creative spark amidst academic pressure? Join us for panelist presentations, open-circle discussions, and guided activities on how art and science can strengthen each other in our professional and personal lives.
Throughout the workshop, we will explore our intrinsic motivations and celebrate bringing our whole selves to our work. Whether you are a veteran artist-scientist or new to the scene, we hope you’ll come out of this experience with a deeper connection to your creative process.
In the first portion of this workshop, we will see examples of projects that integrate art and science in teaching, research storytelling, personal growth, and more. Our invited panelists create diverse media for a range of audiences. They will bring us on a “behind the scenes” tour of their creative process, showing not just the final product but also the progress and pitfalls along the way. In the second portion of the workshop, we will embark on a guided exploration of how you personally approach art, from the emotional impetus to expression. We will also discuss our approaches and relationships to art with fellow attendees. This is a space to envision the role that creativity can play in your science and to develop ideas collaboratively.

Organizers and Planned Speakers

• Nicolette Sipperly, Stonybrook University, nicolette.sipperly@stonybrook.edu
• Patricia Chan, University of Wisconsin-Madison, pwchan@wisc.edu
• Rosemary Glos, University of Michigan, rglos@umich.edu
• Kasey Pham, University of Florida, kasey.pham@ufl.edu
• Ashley Hamersma, University of Florida, ahamersma@ufl.edu

What Makes Botanical Illustration Science

Accurate, quality botanical illustrations have been a primary component of floras, monographs, and descriptions of new species and infraspecific taxa for decades. The quality of illustrations is based upon the artistic ability of the illustrator, the standards used for illustration style, the specimens used as a basis for illustration, and the quality of the author’s work in the publication to be illustrated. In this two-hour workshop, botanical illustrator and Ph.D. botanist Linda Ann Vorobik presents standards she has used in her 30-plus years as an illustrator, followed by an open discussion as to what standards should be used for scientific illustration for publications in this century, as well as how to most effectively set up and edit illustrations. Examples of topics discussed are as follows. 1) Voucher specimens for illustrations make these illustrations science. 2) Parallel illustrations are as important as parallel key construction. 3) Use of photographic resources may present the problem of lens distortion and questionable reference to voucher specimens. 4) Simplified measurements for scale bars (ex multiples of 1, 2, and 5) more readily communicates the size of the subject illustrated. 5) Labelling within an illustration (as well as included in illustration caption) more readily communicates illustration information to the reader.          The workshop will conclude with a discussion of rates for illustration, copyright, limits to use of student illustration, and the ethics of illustration internship.

Organized by:

• Linda Ann Vorobik