Summer Undergraduate Research opportunity in fungal molecular phylogenetics

The Hibbett laboratory at Clark University seeks a talented undergraduate with interests in phylogenetic methods for a NSF-supported research experience associated with the Open Tree of Life Project (described below). Candidates should have experience in analytical methods for molecular systematics (sequence database searches, alignment, and phylogenetic analysis). Interest in fungi would be helpful, but is not essential.

OpToL“The Open Tree of Life Project seeks to develop tools to enable synthesis of phylogenetic trees and taxonomy into a comprehensive phylogeny of all life that can be updated by members of the systematics community. A key requirement of this project is that the source trees be available in electronic form. However, in a recent survey of fungal (and other) phylogenies, we found that only about 17% of published fungal phylogenetic studies have available trees. To address this situation, and to provide training in phylogenetic methods, we propose to have students supported with REU funds generate phylogenetic trees that correspond to important published studies in fungal systematics for which there are no treefiles available (i.e., following the Materials and Methods sections of published works, students will obtain and analyze data in an effort to regenerate published phylogenetic trees). These analyses will then be published in PLOS Currents Tree of Life, deposited in TreeBASE and Dryad, and integrated into the Open Tree phylogeny database using tools that the project has developed (currently, Phylografter is our tool for tree editing, taxon mapping, and integration, but it may be replaced by summer 2014). This work is important and necessary, because the vast majority of published phylogenies do not have trees available in electronic form, and many researchers who have been contacted have been unable to provide the trees. This work will provide the students with extensive experience in phylogenetic methods, and it will also demonstrate the importance of data archiving to achieve reproducibility in phylogenetic studies.”

Support is available for ten to twelve weeks, beginning as early as June 1, 2014. To apply, please send a single PDF file containing a cover letter (describing relevant experience, and stating dates of availability), resume, and contact information for two references to dhibbett@clarku.edu. This position is available for current undergraduates who are U.S. citizens, U.S. nationals, or permanent residents of the United States. Applications will be collected until March 26 (or until the position is filled).

 

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