Dr. Patrick J. Calie
- Ph.D., University of Tennessee
- M.S., University of Tennessee
- B.S., Rutgers University
- Department: Biological Sciences
- Office: Science Building 4222
- Mailing Address: Science Building 3238
- Email: email@example.com
- Phone: 859-622-1543
- Expert Areas: Phylogenetics and species biology of the Sarraceniaceae, and systematics of select sections of Carex and Rhyncospora (Cyperaceae); genomics and evolution of the Clavicipitaceae (Ascomycota)
Biology of New World Pitcher Plants
Since 2001 I have been involved with Dr. Rob Naczi, the Arthur G. Cronquist Curator of North American Botany of the New York Botanical Garden (http://www.nybg.org/science/scientist_profile.php?id_scientist=105) in a long-term study of the species biology and phylogeny of the New World carnivorous plant family Sarraceniaceae using nuclear, plastid and mitochondrial loci as molecular markers. A testable phylogeny of the group has been published (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039291. We continue to examine population-level variation within two common taxa using nucleotide sequence markers.
I am assisting Dr. Naczi in his investigations of several species complexes in the sedge genera Carex and Rhyncospora. My group’s role is to generate nucleotide sequence data that, when combined with Dr. Naczi’s morphological data, will assist in the systematics and phylogenetic reconstruction of these specific taxonomic groups.
Biology of symbiotic fungi
A collaboration was developed in 2010 with Dr. Chris Schardl (http://www.ca.uky.edu/agcollege/plantpathology/schardl/schardl.htm) of the Department of Plant Pathology at the University of Kentucky. Dr. Schardl’s lab has been examining the biology and evolution of fungal endophytes (Clavicipitaceae, Ascomycota) that infect members of the tribe Pooideae (Poaceae). These fungal mutualists produce a range of defensive alkaloid compounds, and provide a range of ecological benefits for their infected monocot hosts. My current efforts involve the genomics and biology of the epibiont Periglandula, a clavicipitaceous fungus that is endemic to select members of the Convolvulaceae (morning glories). An example of our investigations can be seen through the link http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003323
Fungal genome evolution
With Dr. Mark Farman (https://plantpathology.ca.uky.edu/person/mark-farman) in Plant Pathology and several colleagues in Computer Science (UK) I have been involved for five years in a summer training workshop focused on the analysis of NextGenerationSequencing data sets. Dr. Farman has recently received an NSF award (NSF -MCB #1716491) entitled “Role of telomeres in fungal genome evolution” funding the examination of the role(s) of fungal telomeres in generating accelerated sequence evolution in fungal-encoded host recognition (effector) genes. I am a co-P.I. on the award that involves several EKU undergraduates in data mining and software development activities.
Research mentoring: Mentors undergraduate students in research.