Biodiversity and Biogeography of Indo-Pacific Soft Corals

Throughout the Indo-Pacific region, octocorals (soft corals and sea fans) are the second-most abundant invertebrates found on coral reefs, where they compete for space with the dominant, reef-building stony corals. Changing ocean conditions appear to be shifting the dynamics between stony corals and octocorals in ways that will fundamentally alter the structure and function of reefs, as evidenced by Caribbean reef communities that are increasingly dominated by non-reef-building octocorals as stony corals have declined. Relative to the well-studied stony corals, however, little is currently known about the basic ecology of most octocorals, including how many and which species co-occur or how their populations vary over space and time, information that is necessary to determine which species may be imperiled by climate change and which may instead be benefitting. This lack of basic information is due in large part to the difficulty of distinguishing and correctly identifying octocoral species. Our lab is addressing this problem using molecular proxies (DNA "barcodes") to define species. This approach allows us to quantify species diversity, enabling the identification of geographic regions with high species richness, high endemicity or phylogenetically unique lineages that may merit special protection. Students will work with preserved museum specimens of corals to generate DNA barcodes and run analyses to quantify and compare species diversity between diverse locations in the Indian and Pacific oceans.

Essay prompt: What interests you about this project and what do you hope to gain from the research experience?

To complete your application for summer research in Biology, please contact me to discuss the project and submit this google form by Feb 28.

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

This project offers an excellent opportunity for students to apply the laboratory techniques learned in Bio23 to real-world research; little additional background or experience is required to contribute meaningfully to this NSF-funded project. The project blends hands-on laboratory research with computational analyses, and provides a good introduction to both areas for those who might not yet be sure where their interests and passions lie. Mastery of the basic molecular techniques we use provides an excellent background on which to build more advanced molecular biology skills. Experience with sequence analysis and the statistics platform 'R' likewise provide a stepping stone to more complex bioinformatic approaches.  

This project is part of an ongoing NSF-funded project that is a collaboration between HMC, the U.S. National Museum of Natural History (Smithsonian Inst.) and Tel Aviv University. Additional components of the project include application of next-generation sequencing approaches for species identification of soft corals; development of 'ancient DNA' protocols to extract and sequence DNA from museum specimens; and collection of additional specimens from poorly studied areas of the Indian Ocean. Students who participate in the initial DNA barcoding efforts will be given priority for future participation in these additional research activities. We strive to publish all of the work conducted in our laboratory, and students who contribute meaningfully to the work can expect to be co-authors on future publications.

Representative publication
Logistics Information:
Project categories
Student ranks applicable
Student qualifications

Bio23 (or basic familiarity with PCR and gel electrophoresis).  Some familiarity with 'R' helpful but not required.

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

DNA extraction; polymerase chain reaction (PCR); gel electrophoresis; DNA sequence analysis; phylogenetic and biodiversity statistical analyses

Contact Information:
Mentor name
Cathy McFadden
Mentor email
Mentor position
Principle Investigator
Name of project director or principal investigator
Cathy McFadden
Email address of project director or principal investigator
5 sp. | 15 appl.
Hours per week
Summer - Full Time
Project categories