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Soltis, Pamela [1], Soltis, Douglas [2], Folk, Ryan [1].

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

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 100 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. 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 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, such as species occupancy in ecological space and niche breadth, reconstruct ancestral niches, and test hypotheses about niche evolution. Participants will use new integrative software tools developed by the BiotaPhy Project 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. 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". This analytical approach identifies links between species distributions, patterns of environmental sorting, and the legacy of historical biogeography in a phylogenetic framework that shows the relationship between phylogenetic breaks and barriers to dispersal.
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. To use the BiotaPhy/Lifemapper MCPA analysis tools, workshoppers will need QGIS installed and operating on a Windows, Mac OS, or Linux computer.
We anticipate that the workshop will be free and that lunch will be included; if selected by BSA, we will solicit funds to cover coffee breaks and lunch. Sponsored by NSF-funded iDigBio (www.idigbio.org) and BiotaPhy (www.biotaphy.org).
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Related Links:
iDigBio homepage
BiotaPhy homepage


1 - University Of Florida, Florida Museum Of Natural History, Po Box 117800, Gainesville, FL, 32611, United States
2 - University of Florida, Florida Museum of Natural History, PO Box 117800, Gainesville, FL, 32611, USA

Keywords:
digitized herbarium data
iDigBio
ecological niche modelling
georeferencing
phylogenetic diversity
spatial phylogenetics.

Presentation Type: Workshop
Session: W06, Using Digitized Herbarium Data in Research:  Applications for Ecology, Phylogenetics, and Biogeography
Location: Tucson C/Starr Pass
Date: Sunday, July 28th, 2019
Time: 8:00 AM
Number: W06001
Abstract ID:59
Candidate for Awards:None


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