Bio 450 Applied Research Class

at Cabrillo College, Aptos CA

We are linking Cabrillo College students to the One People One Reef Program by involving them in research opportunities. We chose to work with them on genetic projects, because these help build skills that students from a wide variety of science related fields need: 1) lab etiquette, 2) learn and understand the basis of techniques of DNA extraction, PCR, electrophoresis, 3) keeping a good notebook journal, 4) handling chemicals and samples that require cleanliness and preventing contamination, 5) understanding and analyzing DNA sequence data, 6) learn and discuss evolutionary, taxonomic and ecological concepts, 7) develop critical thinking, 8) present results using blogs and powerpoint presentations

In Fall 2016, we started with a small cohort of students, that extracted coral DNA to build a next-generation sequencing library. The coral project was to understand the mode of dispersal of Montipora, an aggressive, weedy species that is overgrowing entire reefs and converting them in monospecific stands in Ulithi atoll. The aim was to understand if typhoon Maysak facilitated coral dispersal, and get a grasp on the population genetic structure of this coral on the island. This is an ongoing project, thus far we have found that recent, smaller coral colonies are product of breakage from larger colonies, supporting the idea that the typhoon had a role in dispersing these corals. We have also found strong genetic structure within the atoll, and had informed the Ulithian communities of these results. We will continue studying the evolutionary history of this coral.

In Spring and Fall 2017, we have been working on a different project. The communities of Ulithi atoll have been collecting fisheries catch data since 2012. There has been a strong effort to match the names in Ulithian with the scientific names. One single species can have different names matching different color morphs, maturity or sexual stages. During their collections, they have been taking small pieces of fish tissue (fins), to preserve for genetic analysis. At Cabrillo college, we are barcoding the species collected, to create a genetic database of the fishes from Ulithi atoll, validate the fisheries database, and compare with conspecifics from other places in the world, in order to identify potential cryptic species. During the Spring of 2017, we found that the species that were reportedly collected match those barcoded, and to our surprise, we found a signature that indicates the presence of a new species. The project is ongoing in the class of Fall 2017.

This is an amazing opportunity for community college students to gain experience, skills and knowledge in an undergraduate setting!

Future projects include population genetics of sea cucumbers of the Yap outer islands, and to continue with the Montipora project, to reveal its evolutionary history and past population expansions and reductions.

Besides involving Cabrillo College students with One People One Reef research projects, they have an opportunity to participate on our Youth Action Program. In this program, students visit Ulithi atoll, meet and work with the local youth in community service projects and take data for field research projects, as well as the opportunity to experience the field side involved with collecting the samples used for genetics. Also, students are allowed to retake the class, or become teaching assistants to continue learning and doing research. We are also open for them to use the lab as a platform for their own projects, as long as they have taken the class once.

What we did (written by Daniel Alexander)

  • We did DNA Barcoding of fish samples collected on Ulithi atoll for the One People One Reef Project.
  • DNA barcoding lets you identify a sample by species using the mitochondrial CO1 gene.
  • In class we extracted DNA, amplified using PCR, checked the success of the PCR using gel electrophoresis, did troubleshooting for our amplification issues, varied the PCR protocol, sent samples to UC Berkeley for DNA sequencing, and finally analyzed results using the programs R and Geneious.

Results – what we found (written by Shannon Scott)

  • From 120 DNA extractions we got 45 successful sequences, which we identified as 15 species of fish.
  • The results helped confirm the quality of the fisheries database, and also helped identify a fish that the project had previously only identified to genus level.
  • One of our phylogenetic trees showed an anomalous result, which suggests we could possibly have found a new species. (Ulithian Variola albimarginata, sister species of Variola louti, appears more closely related to some V. louti than they are to an outgroup of other V. louti)
  • Another of our phylogenetic trees revealed a misidentified species from the published literature. We notified the paper’s authors and they have corrected their mistake!

Students who took the class (written by Vanessa Howland)

  • A diverse group of 14 students took the class. This included students working towards transferring to biology and medical programs, or who have now transferred, students preparing to apply to grad school, and a high school student taking classes at Cabrillo.

Things we gained (written by Matthew Lutz)

  • Problem solving – we got into unexpected challenges
  • Use of current research tools – programs like R and Geneious
  • Insight into what research is like – can be tedious, can be frustrating, but very exciting when it finally works! Can help students decide if research is what they really want to do
  • Makes student CV stand out/ research experience for those preparing for grad school
  • UCSC connection – lab visit, lectures from UCSC professor, networking opportunity
  • How this class differs from ACCESS: No limits on who can take it- except some class requirements. Happens during the semester, not summer

Fall 2017 Bio 80S Class Presentation PDF