01 May 2022

Potential Graduate Student Projects

If you are interested in joining the lab as a Ph.D. or Master’s student, please look over the following projects. These are projects for which funding or data currently exists, and are also a way to help focus your research interest statement when applying to graduate school. These projects are not set in stone - I will work with all students to develop research questions matching their interests.

Use the Google form here to express your interest in joining the lab. I will review potential graduate student applications in October, and will invite the best candidates to apply to work in my lab before December 1, for fall admission the following year. You can find more information about applying at the TTU Graduate School and the TTU Department of Biological Sciences websites.

Project 1: Functional Genomics of Bryum argenteum

Bryum argenteum is a moss found on all seven continents, including Antartica! However, it is a bit of a nuisance on golf courses in North America, where it is referred to as “silvery threaded moss.” We have a collaboration with a bryophyte physiology lab at the University of Nevada Las Vegas (Lloyd Stark) and the Davey Tree Company (Zane Raudenbush) to help control the moss infestations on putting greens. Interestingly, the mosses on the putting greens have a distinct growth pattern and are always female. We have samples collected from across North America and a promising graduate student project could be to identify local adaptation and/or differential gene expression associated with mosses on putting greens.

Work on this project would involve bioinformatics, phylogenomics, RNA and DNA sequencing, and managing moss tissue cultures.

Project 2: Cryptic Speciation in Physcomitrium pyriforme

The moss Physcomitrium pyriforme is a widespread species, common in eastern North America. Our recent results from targeted DNA sequencing suggest that there may be cryptic taxa within P. pyriforme resulting from autopolyploidy, allopolyploidy, and subtle morphological variation. A graduate student could lead a project testing whether individuals from phylogenetically distinct populations are reproductively isolated. We will conduct experimental crosses and test for hybrids using PCR and DNA fingerprinting. Further assessment of introgression between the distinct populations will use targeted DNA sequencing and hybridization analysis.

Work on this project would involve bioinformatics, targeted DNA sequencing, and managing moss tissue cultures.

Project 3: Phylogenetic Systematics in Flowering Plants

The phylogenomic toolkit Angiosperms353 has made phylogeny inference from hundreds of genes tractable for flowering plant groups with few genomic resources. Targeted DNA sequencing with Angiosperms353 is especially well suited for herbarium specimens, as degraded DNA can be recovered, reducing the need for expensive field work. The E.L. Reed Herbarium is well suited to host graduate students interested in phylogenetic systematics of flowering plants of the southwest United States, especially Texas and New Mexico. Examples of possible taxa to work on include Haplopappus, Cryptantha, Egrostris, and Bouteloua. Students would work with me to develop phylogenetic systematics projects.

Work on this project would involve herbarium curation, bioinformatics, targeted DNA sequencing, and taxonomic revisions using phylogenetic and morphological data. Possible field work and/or travel to other herbaria to collect new specimens.

Project 4: Phylogenomic Methods Development

Our lab has worked on the development of new bioinformatics workflows in non-model plants, including HybPiper, Homologizer, a variant call pipeline for target sequence data, and helpful visualizations for bipartition analysis. We have also made progress in laboratory methods, especially in reducing per-sample costs, enabling studies with dense sampling and wider access to genome-scale approaches.

Students interested in methods development could help move the field forward through innovations in bioinformatics and/or lab procedures. For example, a student could lead development of targeted single-molecule approaches (i.e. Oxford Nanopore) for phylogenetics in plants. Or, a student could contribute to the development of HybPiper, for example to improve the ability to detect and use paralogs in phylogenetic analysis.