Journal Entries

Over the course of eight weeks, I studied the effects of fishing pressure on the reproductive biology of Halichoeres scapularis, a species of sex changing wrasse. This research was supported by my mentor, Mr. Abner Bucol of Silliman University and the principal investigators Dr. Dave Gauthier (Old Dominion University) and Dr. Chris Bird (Texas A&M Corpus Christi). The first four weeks were spent in Dumaguete, Philippines collecting data and the last four weeks the data was analyzed remotely.

Week 1

The day after we arrived in Dumaguete, we toured the Silliman University main campus and the Silliman University Marine Biological Laboratory. While in Dumaguete, the majority of my research will be done at the marine biological laboratory. Overall, I am excited to use these facilities as I begin my research project.

On Monday, I attended a lecture held on the main campus. Dr. Gauthier spoke to us about molecular biology, DNA extraction, PCR and microsatellites. I attended in order to gain insight into the work that some of my peers are doing and gain some knowledge in case I choose to help them with their projects or pursue a project that involves these kinds of techniques.

Tuesday brought my first experience with field work. I was brought along on a rotenone station. Rotenone is a piscicide which is applied underwater by scientifically trained SCUBA divers. As the rotenone is applied, the fish die, and float out of the reef. My job, as someone who is not trained in scientific diving to the appropriate level, was to snorkel above the SCUBA site and catch any fish that floated to the surface. This field work is in association with the PIRE project, an NSF funded study that aims to redo a biodiversity assessment done 50 years ago in order to see the impacts of human disturbance on fish biodiversity. The site we surveyed was in Siaton. When we arrived, there were windy and stormy conditions on the ocean. Unfortunately, the waves on the surface and the currents beneath the surface meant that the rotenone wasn’t as effective and there weren’t many fish caught or collected. No fish were seen on the surface, so we weren’t able to help out much on the surface. Afterwards, we went back to the marine lab to group and identify each fish caught. It was very exciting to learn about what scientific field work involves, especially since I have been interested in this kind of work for so long.

On Wednesday, I joined Jerome and Mikaela in going to the fish market. Jerome was looking for his species of blue swimming crab (Portunas pelagicus) in the markets, and I was searching for my own species of fish, Halichoeres scapularis. We easily managed to find Jerome’s species, as it is an important . Unfortunately, however, we only managed to find one sample (a singular fish) of my species. I was still excited about it though.

On Thursday, I was given the opportunity to help Karen with her field work in the mountains. For her project, Karen is surveying freshwater gobies in a river. We hiked through a forest for around 15 to 20 minutes until we reached the field site, where the traps set the night before were to be collected. The first trap had nothing in it, and the second trap had been stolen, so the trip was largely unsuccessful. We had an interesting discussion at the field site about pollution in waterways, and the potential reasons why Karen had found so much E. coli and other harmful bacteria in the river. After that we collected some invertebrate samples so Karen could use them to inform about the diet of freshwater gobies in the Philippines.

Friday was the prospectus symposium for Ph-IRES and PIRE researchers. I presented first, and it went pretty well. I was very impressed with everyone’s presentations, and I’m excited to see how everyone’s projects develop over the next 7 weeks and beyond.

Week 2

During the first week, I had mentioned to my mentor, Abner Bucol, that I was interested in exploring field work while in the Philippines. Abner was already planning on being on the island of Siquijor to help out with rotenone field work, so he decided that it would be beneficial if I joined the trip because he would be able to give me guidance on my own project, and I would have opportunities to help out with field work. Throughout the week, Mikaela, Jerome, Jordan, and some of the PIRE interns would also join to experience field work. I spent Monday preparing for the trip.

On Tuesday, we gathered all of the field and lab supplies for the week. We rode a boat to the island of Siquijor and then made our way from the harbor to a resort in San Juan. Once we arrived, we unloaded the truck and set up all the lab equipment on the porch of one of the rooms. We spent Tuesday going over field work protocol, and the plans for the next few days. We would leave the resort every morning at 7am and head down to the SCUBA shop where a boat had been rented for the week, and then head out to the field site. Afterwards we would grab lunch, and then head back to the resort to sort, ID, and photograph each fish. Once this was complete, I would dissect samples for my own research project. It was a busy week to say the least.

Wednesday we headed to our first field station. Because the research we were doing was to be compared with a past study, we needed to find the site based on the descriptions of the area and the coordinates, so it took a little while to find the location. We eventually found the site, a rocky outcrop in a shallow area (we could easily touch the bottom). The waves were rough this day, making the sample collection a lot more difficult because the fish would float away, and the rotenone was harder to distribute. We weren’t able to collect many samples as a result. During this field excursion I also had the opportunity to shadow a fisherman collecting samples for my project. He used a traditional fish trap called a palan-an with a bait of sea urchin to catch the fish. In the afternoon and evening, Abner taught me how to dissect the fish, determine the sex, and stage, and how to preserve the gonads.

Thursday, the conditions were much easier. We went to a site that was about a 30-minute boat ride away and it was much deeper than the last site at around 90 feet deep. Even though the reef was far below us as we snorkeled on the surface, we were surprised that we could see the dive team all the way at the bottom. We were able to collect a few fish from the surface, but most of the work was done by the SCUBA team.

Friday was our last field day. We went to a shallower reef and the conditions were very good. We collected the greatest number of samples on this day compared to the other two days. The reef was shallow enough that the snorkelers could dive down to the reef to help collect fish.

We spent Saturday exploring the island and jumping into waterfalls. On Sunday we packed the equipment and headed back to Dumaguete.

Week 3

Over the course of the third week, I continued with my dissections. I wasn’t able to finish dissecting all the fish caught in Siquijor while on site, so I finished those up this week, and then later in the week I received a lot fish from Buenavista, Bohol.

I also learned some new techniques this week. With the help of Jem, I learned how to extract the otoliths from the fish. I’m working with a smaller species of fish, so the otolith is really small (just a few millimeters long and wide), so it took a while to get a hang of it. Once I figured out which part of the skull the otolith was in, I was able to move relatively quickly in extracting them.

We also practiced mounting the otoliths on slides. I was hoping to include otolith data into my project because it would provide more information on the age at which each fish was changing sex, and I could compare between sites. Unfortunately, I only had one and a half weeks left in Dumaguete at the time I was starting to learn how to mount otoliths and the process is very time consuming, which means that it is not feasible. Abner is thinking that some students he is working with may be interested in collaborating and doing some work with the otoliths, but we’ll see.

Week 4

My last week in Dumaguete was spent at the Silliman marine laboratory finishing up as many dissections as I could. I ended up doing a total of 217 dissections. Because I was trying to dissect as many fish as possible before I left, it was a stressful week.

We ended the week with a bittersweet goodbye dinner with all the students and mentors. It was nice to get to say goodbye, but all of us students felt that we weren’t ready to leave Dumaguete quite yet. On Saturday, July 16th, we headed home.

Weeks 5-8

After recovering from some brutal jet lag, we jumped into our data analysis workshop during week 5. We started with R Studio. I had some previous experience with R Studio in a few statistics classes I took over the school year, so I was familiar with the platform, but the data analysis workshop dramatically improved my abilities in R. We learned how to use the Tidyverse package as well, which has a lot of practical uses in biological data analysis. We all practiced processing each other’s data so we would gain a well-rounded understanding of the ways we can use R Studio and the Tidyverse package to process data. We also learned how to create phylogenetic trees using Geneious.

Weeks 6, 7 and 8 were spent finishing up data analysis, creating a manuscript draft, and making a presentational for our end of the summer Ph-IRES symposium. The last day of our internship, we presented out work over zoom. I was so impressed with everyone’s projects. I feel so lucky to have had the opportunity to participate in the Ph-IRES internship. I learned so much, and I have gained a lot of confidence in myself as a scientist. I plan on continuing to work on this manuscript, and hopefully get it published at some point.

In October, I presented my research at the National Diversity in Stem Conference (NDiSTEM) in Puerto Rico.