Biodiversity and biogeography of Indo-Pacific octocorals

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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. This summer we will focus on (1) quantifying the diversity of octocorals collected from locations in the eastern and northern Indian Ocean, and (2) exploring how the species of symbiotic algae (zooxanthellae) that are found in these corals differ between species and locations. The work will involve extracting DNA from preserved specimens, PCR-amplifying and sequencing DNA barcode markers, and running a variety of statistical analyses to compare biodiversity and community composition among locations throughout the Indo-Pacific.


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

The focus of our research is quantification of biodiversity patterns in the ocean. As climate change increasingly impacts the survival and reproduction of those species that form the basis of coral reefs it is imperative that we better understand their biodiversity (numbers, abundance and geographic distributions). We focus on the development and application of molecular tools to identify species and quantify biodiversity. In addition to basic DNA barcoding (use of one or several well-defined gene sequences to discriminate species), we are also developing and applying genomic approaches (i.e., use of whole-genome sequencing methods) to distinguish species, and exploring the use of eDNA (environmental DNA, extracted from water samples) to census the diversity of corals in areas where collection of physical specimens is difficult or impossible. The work of students in the lab contributes to peer-reviewed publications, and most of the students who have worked in the lab for a summer have been (or will be) co-authors on those papers.

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

No specific background or skills are necessary for this project other than introductory biology (Bio52, 23).  Students from any of the Claremont Colleges are welcome to apply.

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

Basic molecular biology lab techniques (DNA isolation, polymerase chain reaction, gel electrophoresis, Sanger-sequencing), DNA sequence analysis, phylogenetic analyses and biodiversity statistics

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
3 sp. | 0 appl.
Hours per week
Summer - Full Time
Project categories