Category: Article

Tags

Published: January 5, 2015

Bringing Collections to Life: Analysis of Specimen Data Using Modern Bioinformatics Tools

Stephanie Ware, Manager, Morphology Labs, SEM

Project Mentors: Dr. Robert Lücking (Adjunct Curator for Lichenized Fungi, Gantz Family Collections Center) and Dr. Mark Johnston (Geographic Information Manager, Action Science Center)

Project Description: The increasing number of digitized and georeferenced collections data provides an invaluable source of information for a variety of studies, ranging from plotting species distributions to mapping the effect of climate change using biological indicators. The Global Biodiversity Information Facility (GBIF) has already amassed over 500 million occurrence data corresponding to nearly 1.5 million species, with a sizable amount originating from the Field Museum's collections. One of the downsides of such data is the uncertainty of taxonomic identifications, and the lack of expertise available to critically revise these records. Fortunately, novel methods developed by Field Museum researchers allow for the remote assessment of the quality of taxonomic identifications, by using predictive ecogeographical mapping and collections metadata. The resulting high quality occurrence data can then be used for instance to analyze the phylogenetic composition of metacommunities. Collections data can also be used to provide novel, automated and rapid identification tools based on phylogenetic trees.

Research methods and techniques: The REU intern will be working on a specific group of lichen fungi, using three different methodological approaches based on collections data:

  1. Assemble a data set of confirmed, georeferenced records of a species (confirmed by molecular data and/or monographic revision), compute a predictive ecogeographical distribution model using ARCGIS and MAXENT, and compare existing GBIF occurrence data with the model to identify outliers as potential misidentifications.
  2. Use georeferenced occurrence and sequence data on species of a selected genus of lichen fungi to define metacommunities, and then analyze the phylogenetic composition of these metacommunities (whether phylogenetically clustered or dispersed) with PHYLOCOM.
  3. Assemble a phenotypic character matrix for collections of sequenced species to compile a novel, automated and rapid identification tool based on a phylogenetic tree using phylogenetic binning in RAXML.
Stephanie Ware
Manager, Morphology Labs

Stephanie started volunteering at the Field Museum in 1998, working with Curator John Bates in the Bird Division. In 1999, John Bates hired her as a research assistant. After that project finished in 2007, she went to work for Carl Dick in the Division of Insects helping him to complete his work on the museum's Bat Fly collection. She spent a great deal of time generating images for the Bat Fly portion of theDiptera Taxonomy Database. When Carl left for University of Kentucky in 2009, she continued her imaging work in the Insect Division. In the intervening years, she has imaged hundreds specimens, mostly types, from the rove beetle (Staphylinidae), ant and myriapoda collections.

Stephanie began working with the Chicago Peregrine Program in 2006.  Initially, she monitored the Metropolitan Correctional Center nest in downtown Chicago.  Over time, her duties have expanded to include other nests in the metro region, emphasizing the identification of nesting adults.  In March of 2007, Stephanie created a group called Midwest Peregrine Falcons on the photo sharing website Flickr with the goal of providing a place for photographers across the country to submit their photographs of peregrine sightings in the Midwestern United States. She also has many of her own peregrine photos on Flickr as well.

Related content,Check this out