Building an eDNA reference library as a tool for deepwater exploration

Are you interested in the project below? Awesome! PLEASE DO NOT APPLY THROUGH THE URO SITE. Instead, follow this link [https://forms.gle/hrbnmY5Dz9ZoW1bj8] to send in your application by Feb. 20th.

Environmental DNA sampling, or eDNA, is a technique in which DNA is isolated from an environmental sample, such as water or soil. DNA is then sequenced using a high throughput metabarcoding approach and bioinformatics are used to match the DNA to reference databases in order to identify the organisms that live in the environment. All of this can be done from taking just one environmental sample. We are currently testing eDNA techniques to help characterize coral ecosystems in the deep Gulf of Mexico. This project will entail building reference DNA barcode database libraries of species known to occur in mesophotic and deepwater coral habitats. Students will gather existing data from online databases and then help fill in the database gaps through assembling mitochondrial genomes and other barcode markers using bioinformatic techniques. Phylogenetic analysis will also be performed on particular groups of taxa. This work will be conducted virtually at both Harvey Mudd College and the Smithsonian National Museum of Natural History.

Name of research group, project, or lab
Coral Lab (McFadden) (virtual)
Why join this research group or lab?

In the NMNH (National Museum of Natural History) coral lab, we are passionate about understanding the ecological and evolutionary processes that shape patterns in marine biodiversity. Our group primarily studies corals and their relatives because they are some of the most important metazoans on Earth: these animals provide habitat, refuge, and food for many other species from shallow waters to the deep abyss. 

By determining the drivers of diversity across multiple scales of space (e.g, reefs to ocean basins) and time (e.g. geological to ecological), we seek to understand how these animals and the ecosystems they support are impacted by one of the greatest threats to our society: global ocean change. 

Through our location at the NMNH and by access to its collections, we are able to utilize a fully integrative approach— employing morphological, genomic, ecological, and bioinformatic methods— in our study of the coral tree of life.

Logistics Information:
Project categories
Biology
Student ranks applicable
First-year
Sophomore
Junior
Student qualifications

Introductory biology and CS5 are the only background requirements.

Time commitment
Summer - Full Time
Compensation
Paid Research
Number of openings
1
Techniques learned

Basic bioinformatic methods including genome assembly and annotation, sequence alignment and phylogenetic reconstruction

Contact Information:
Mentor name
Cathy McFadden
Mentor email
mcfadden@hmc.edu
Mentor position
Principle Investigator
Name of project director or principal investigator
Cathy McFadden and Andrea Quattrini
Email address of project director or principal investigator
mcfadden@g.hmc.edu
1 sp. | 0 appl.
Hours per week
Summer - Full Time
Project categories
Biology