Category: Blog


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, SEM

Stephanie Ware is currently a research assistant in the Division of Insects currently working with Dr. Petra Sierwald. She also works with Mary Hennen in the Division of Birds monitoring the Peregrine Falcon (Falco peregrinus) populations in Illinois.