Saltwater Semester Course Based Undergraduate Research Experience (Fall 2021, in-person)
In November 2021 I co-taught for Saltwater Semester at the University of Miami, an undergraduate research-intensive course, with Dr. Marjorie Oleksiak. Students were tasked with field work to collect Atherinomorus stipes, a small coastal mangrove fish, from different salinity environments followed by whole genome sequencing library preparation in September 2021. The goal of the Saltwater Semester is to engage undergraduate students in novel publishable research. To make this possible, because we were sequencing a non-model organism, I collaborated with Dr. Christopher Faulk at the University of Minnesota to assemble a genome for A. stipes using Oxford Nanopore long-read sequencing (manuscript in prep). After sequencing and genome assembly was completed students spent three weeks with Dr. Oleksiak and I learning to analyze genomic data. This included:
Linux command line operations
Remote supercomputing on the University of Miami high performance computer, Triton
Bash job scripting
RStudio and R Markdown for data visualization
Students went from learning basic command line operations to submitting jobs for raw sequence processing and relevant population genetics analyses. In the 3-week course we were able to calculate genotype likelihoods, ADMIXTURE, principal component analyses, Fst (genetic distance), and visualize the data. These analyses will be published in a manuscript detailing connectivity among coastal populations of A. stipes.
Introductory Marine Biology Laboratory (Fall 2020, hybrid in-person and online)
Undergraduate TA for Zoology/Animal Diversity Laboratory (Fall 2016 - Spring2018, in-person)
Undergraduates (and Dr. Oleksiak) show off their ADMIXTURE plots in the Saltwater Semester Marine Conservation Genomics course.
A school of Atherinomorus stipes near Broad Key, FL.
Photo taken by Dr. Evan D'Alessandro.