Workshops & Forums

Friday Morning (9am-12pm):

How to Navigate in Tree Space

Primary organizer: Dr. Nico Cellinese, Florida Museum of Natural History

Content: Integrating biological data with phylogenies has become a challenge, especially in view of the growing need for very large synthetic analyses. This is primarily due to the arbitrary approach we take to associate traditional names to tree nodes. In this workshop we will: 1) briefly introduce the rationale for generating clade names; 2) learn about the minimum requirements needed to generate the various types of phylogenetic definitions; and 3) learn how to generate a phyloreference (machine readable taxon concept).

Hands-On Learning with RevBayes

Primary organizer: Dr. April Wright, Southeastern Louisiana University

Content: This workshop will focus on using the phylogenetic estimation software RevBayes in an instructional setting. We will first introduce the graphical model framework used by the software. Graphical models can be used to introduce the fundamentals of probability, while also enabling transparent and flexible assembly of new phylogenetic models. Then, we will discuss using RevBayes in hands-on exercises for systematics and phylogenetics courses. Topics will include making use of the robust RevBayes tutorial library, tailoring pre-existing tutorials to your course, contributing your tutorials to the tutorial bank, using interactive computing notebooks, and integrating the software with R and Python.

Friday afternoon (1:30-5pm):

Using the Open Tree of Life for your Research

Primary organizer: Dr. Emily Jane McTavish, University of California (UC) Merced

Content: The Open Tree of Life project is a phylogenetic resource that offers a synthetic tree summarizing evolutionary relationships across 2.6 million taxa. OpenTree (as of September 2019) also provides access to 4,168 published studies comprising 9,367 trees, and the database is growing weekly. The tips of these trees are mapped to taxonomic identifiers that link across taxonomic and informatics databases such as NCBI and The Global Biodiversity Information Facility (GBIF). The website also provides user-friendly resources for bulk reconciliation of taxonomic names to these standardized identifiers. Together these resources offer a formidable suite of tools and data for taxonomic name reconciliation and phylogenetic comparisons and analyses.

This workshop will cover how to understand, access and apply these data resources from the Open Tree of Life project to your research questions. Topics will include accessing phylogenetic relationships for arbitrary sets of taxa, applying date estimates to these trees, linking phylogenetic and geographic information, assessing conflict between phylogenetic estimates, and incorporating your own phylogenetic estimates into the OpenTree of Life project.

The workshop will include interactive browser based exercises, demonstrations of how to access OpenTree data through the API, and tutorials in R and Python. Experience using a command line interface, R or Python will be helpful, but is not required.

State-dependent Diversification Models via Graphical Models and RevBayes

Primary organizer: Dr. Rosana Zenil-Ferguson, University of Hawaii Manoa

Content: SSE models such as BiSSE and MuSSE are powerful approaches for testing the association of a character with diversification rate heterogeneity. However, they have been shown to be prone to falsely identifying a positive association when diversification rate shifts are correlated with a character not included in the model. One approach to reduce the possibility of falsely associating a character with diversification rate heterogeneity is to incorporate a second, unobserved character into the model (i.e., a Hidden State-Dependent Speciation and Extinction (HiSSE) model. This workshop will discuss hidden state models and their uses in evolutionary biology, and participants will use RevBayes to set up such a model and use it to test some basic questions about trait associations.

Friday whole day (9am-5pm):

Software School for Phylogenomics

Primary organizer: Dr. Tandy Warnow, University of Illinois Urbana-Champaign

Content: This workshop provides hands-on training in numerous software tools for phylogenetics and phylogenomics, including PASTA, UPP, ASTRAL, Phylonet, TIPP, and SVDquartets. Participants will learn about methods for estimating large multiple sequence alignments and trees, and how to estimate species trees in the presence of gene tree incongruence using genome-scale data. This workshop was offered very successfully at a previous SSB Standalone (in 2015), and will be updated to address new challenges and approaches for its 2020 offering.

Monday morning (9am-12pm):

Broader Impacts and Science Communication

Primary organizer: Sadie Mills, Florida Museum of Natural History

Content: The goals of this workshop are to broaden participants’ perspectives on conducting in-person and digital science communication, to help them craft and tailor a message for both in-person and online delivery, and to educate participants on how to best connect outreach to broader impact goals.

Diversity statement: The facilitators of this workshop are from multiple organizations across the University of Florida campus, including staff from the Florida Museum, iDigBio, and the Thompson Earth Systems Institute. Facilitators range in career stage and educational and demographic backgrounds.

Phylogenic Comparative Analysis of Integrated Anatomical Traits

Primary organizer: Dr. Josef Uyeda, Virginia Tech

Content: Attendees will learn how to use R packages such as RPhenoscape to access a knowledgebase of ontology-linked phenotypes, build character matrices that take anatomical dependencies into account, and use these to construct stochastic character maps on a phylogeny. The course will also include a practical introduction to community ontologies for biodiversity domain knowledge (anatomy, taxonomy, phenotypic quality).

Monday afternoon (1:30-5pm):

Posterior Predictive Simulation with P2C2M

Primary organizer: Dr. Bryan Carstens, Ohio State University

Content: This workshop will introduce students to posterior predictive simulation, an approach to evaluating the fit of statistical models used in a Bayesian framework. In addition to the theoretical background, students will be introduced to P2C2M, an R package that enables users to test the fit of the multispecies coalescent to their sequence or SNP data.

Monday whole day (9am-5pm):

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

Primary organizer: Dr. Pamela Soltis, Florida Museum of Natural History

Content: This workshop provides hands-on instructions on how to link and analyze diverse data types from organismal biology, ecology, genetics, climatology, and other disciplines, including information on phylogenetic diversity, species distributions, changes in distributions over time, phenology, morphology, and more. Participants will divide into groups based on experience. For beginners, we will cover 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) and applying Maxent software to construct ecological niche models and do paleoclimatic modeling. 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, such as species occupancy in ecological space and niche breadth, and link them to phylogenetic trees to test hypotheses about niche evolution, such as ancestral niche reconstruction. Participants will use new integrative software tools developed by the BiotaPhy Project (www.biotaphy.org) in collaboration with the Lifemapper 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 using the QGIS GIS application. Prepared datasets will be provided, but attendees may bring their own data.

Analysis of Target Enrichment Data

Primary organizer: Dr. Keith Barker, University of Minnesota

Content: This workshop will focus on issues that can arise when raw genomic data are assembled using different methods, with resulting differences or biases in quality that can affect downstream interpretation and analysis. The workshop will use available avian UCE data and will walk participants through contig assembly, alignment, filtering, and concatenation using Phyluce, providing all necessary code but with "precooked" versions of each step available, especially where run times are prohibitive (e.g., assemblies). Participants will then generate post assembly and alignment summaries and conduct analyses of gene tree estimation (RAxML/MrBayes), species tree estimation (Astral/SVDquartets), node assessment (via locus bootstrapping, ICA values in RAxML, and gene and site metrics in IQ-tree), and possibly evaluation of hybridization hypotheses (BUCKy and SNaQ) if time allows.