Sunday, June 16th - All Day 8:00 am - 5:00 pm

Fees, where indicated, include coffee breaks and a shared buffet lunch

Sold Out - Introduction to Phylogenetic Comparative Methods in R

Organized by:  John Schenk
Free

Data Analysis and Visualization In R

Organized by:  Eli Hartung, Josh Felton, Gregory Pec, and Malu Ore-Rengifo
Free

Sold Out - SNPs, genes, genomes: using assembled genomes for answering evolutionary questions

Organized by:  Jacob Landis
$50.00

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

Organized by:  Ryan Folk
$50.00

Sold Out - Common methods in leaf gas-exchange research: an introduction to measurements, theory, and data analysis

Organized by:  Christopher Muir, Christopher Krieg and Richard Vath
Free

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Workshop Descriptions

Introduction to Phylogenetic Comparative Methods in R

Submitted By: John Schenk

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 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.

Planned Speakers

John J. Schenk, Ohio University
Paige Fabre, Ohio University
Johan Ling, Ohio University

Data Analysis and Visualization In R

Submitted By:  Eli Hartung, Josh Felton, Gregory Pec, and Malu Ore-Rengifo

Abstract

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

Planned Speakers

*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

SNPs, genes, genomes: using assembled genomes for answering evolutionary questions

Submitted By:  Jacob Landis

Abstract

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.

Planned Speakers

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

Sold OutBiodiversity data wrangling: Linking large phylogenies with species traits and ecologies

Organized 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.

Common methods in leaf gas-exchange research: an introduction to measurements, theory, and data analysis

Submitted By:  Christopher Muir

Abstract

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. 

Planned Speakers:

Christopher Muir
Christopher Krieg
Richard Vath