Tag: Mariam Alsaid

Returning to the ocean with open ears

Mariam Alsaid, GEMM Lab Research Technician

It’s been three years since I last wrote a blog post for the GEMM Lab. At the time, I was wrapping up a wonderful summer filled with science, sun, and new friends and was eager to share all that I had learned and accomplished during my 10 weeks working on the Oregon coast as part of Hatfield Marine Science Center’s Research Experience for Undergraduates (REU). My love and concern for our oceans and its animals has always been the driving force of my academic pursuits. I am so thankful to this REU – funded by the US National Science Foundation – for introducing me to marine science research as a career path. 

Alongside the mentorship of Drs. Dawn Barlow and Leigh Torres, I investigated the occurrence of sei whales, an endangered species of baleen whale, offshore of Oregon. The sei whale’s global population is believed to have dropped by 80% due to whaling in the 19th and 20th centuries and little is known about their contemporary population status, especially in the Northeast Pacific (Horwood, 2018; Nieukirk et al., 2020). Sei whales have occasionally been observed by the GEMM Lab on research cruises and we were curious about when and how often they were in our neck of the woods. Despite being massive animals (the 3rd largest rorqual in the world!), these animals are challenging to study due to their low population densities and visual similarities to fin whales (Horwood, 2018, Reeves et al., 1998). Luckily, sei whales produce characteristic vocalizations that can help distinguish them from other baleen whales that call at similar frequency bandwidths (e.g. blue, fin, and humpback whales). 

Figure 1. Sei whale mom and calf (NOAA fisheries)

This is where bioacoustics – the study of sounds produced by living organisms – comes in. We are able to study this elusive species by deploying hydrophones (underwater microphones) offshore of Oregon and reviewing recorded data in search of sei whale calls. (See this blog post if you’re curious about our methods and findings!). 

Since 2021, the GEMM Lab and the  K. Lisa Yang Center for Conservation Bioacoustics at Cornell University have collaborated to deploy three hydrophones for continuous acoustic recording along the Newport Hydrographic Line as part of the Holistic Assessment of Living marine resources off Oregon (HALO) project. These hydrophones are bottom mounted to the seafloor and are deployed 20, 45, and 65 nautical miles offshore of Newport, OR. HALO cruises are scheduled to refurbish and redeploy these instruments every six months or so. These cruises are also an opportunity to conduct visual surveys of cetaceans and seabirds in between deployments.

Figure 2. Hydrophone deployments on one of our HALO cruises. Dr. Dawn Barlow pictured on the left and Marrissa Garcia pictured on the right.

I immediately fell in love with bioacoustics and was enraptured by the diversity of clicks, pulses, and moans made by marine animals that flood our oceans. Hydrophones are able to record sounds in locations and frequency ranges that we would never naturally get to experience. Baleen whales are especially fascinating because they tend to produce infrasonic calls (i.e., <20 Hz) to communicate over large distances. These calls occur at frequencies below our hearing range and are only audible when sped up. Listening to these recordings feels like a window into a secret world that few have ventured. 

Figure 3. Period of high vocal activity from blue whales (A, B, and D calls), fin whales (20 Hz pulses) , and rockfish (pulses). Audio was sped up by 5x.

After completing my undergraduate degree, I participated in a bioacoustics research fellowship hosted by the US Forest Service and Oak Ridge Institute for Science and Education. During this time, I explored the world of terrestrial acoustics by leading a research project on American pika occupancy in the Oregon and Washington Cascades. Forest soundscapes have a different beauty to them. While periods of quiet are rare in the ocean, this is even scarcer on the surface. Bird songs, insect buzzing, human chatter, rainfall, and highway noise constantly fill our soundscapes, sometimes simultaneously. This experience processing terrestrial sound gave me a newfound appreciation for the world around me and the sounds I’ve become so accustomed to hearing. Nevertheless, I found myself yearning for the ocean and its secrets.

Figure 3. The typical work setup of an acoustic analyst (headphones, extra hard drives, and coffee missing from photo)

I was invited back to the Marine Mammal Institute last fall as the GEMM Lab’s baleen whale acoustic analyst to continue working on the HALO project. I dove back into the data collected from our hydrophones, this time targeting blue, fin, and humpback whale calls in addition to sei whales. My efforts were also broadened to all five years of recording data instead of just one. Because manually reviewing large amounts of acoustic data can be cumbersome, I trained artificial intelligence classifiers using the BirdNET convolutional neural network to make acoustic data processing more efficient. After much iterative trial and error, I was able to develop a set of four classifiers, each specialized to detect one of our four target species. The first classifier was trained to target blue whale A, B, and D calls; the second targets fin whale 20 Hz and 40 Hz pulses; the third targets sei whale downsweeps; and the fourth targets humpback song and single non-song grunts. Once I evaluated that the classifiers were performing with high precision and recall rates, I used them to predict when calls occurred in the five years of recording data. I am currently in the process of validating the hundreds of thousands of predictions to generate detection histories of these species of baleen whales in this region. This information will be incorporated with various oceanographic datasets to get a better understanding of baleen whale distribution patterns and habitat preferences in the Northeast Pacific. 

I will be wrapping up my contract with the Marine Mammal Institute next month and I am endlessly grateful to the GEMM Lab for shaping me into the marine mammalogist I am today. I will look back on my time here fondly as I begin this next chapter of my life as a PhD student at the University of Washington’s School of Oceanography this fall. I am excited to share that I will continue to use acoustics to study baleen whales in the Northeast Pacific during my PhD! Although I dread the thought of having to say goodbye to Oregon and the Hatfield community, I thankfully won’t have to say goodbye to the whales. 

Works cited

Horwood, J. (2018). Sei Whale – Balaenoptera borealis. Encyclopedia of Marine Mammals 

(Third Edition), 845-847. https://doi.org/10.1016/B978-0-12-804327-1.00224-7

Nieukirk, S. L., Mellinger, D. K., Dziak, R. P., Matsumoto, H., & Klinck, H. (2020). Multi-year 

occurrence of sei whale calls in North Atlantic polar waters. The Journal of the 

Acoustical Society of America, 147(3), 1842-1850. https://doi.org/10.1121/10.0000931

Reeves, R. R., Silber, G. K., Payne, P. M. (1998). Draft recovery plan for the fin whale 

Balaenoptera physalus and sei whale Balaenoptera borealis. Office of Protected 

Resources, National Marine Fisheries Service, National Oceanic and Atmospheric 

Administration.

A Journey From Microbiology to Macrobiology

Mariam Alsaid, University of California Berkeley, GEMM Lab REU Intern

My name is Mariam Alsaid and I am currently a 5th year undergraduate transfer student at the University of California, Berkeley. Growing up on the small island of Bahrain, I was always minutes away from the water and was enraptured by the creatures that lie beneath the surface. Despite my long-standing interest in marine science, I never had the opportunity to explore it until just a few months ago. My professional background up until this point was predominantly in soil microbiology through my work with Lawrence Berkeley National Laboratory, and I was anxious about how I would switch directions and finally be able to pursue my main passion. For this reason, I was thrilled by my acceptance into the OSU Hatfield Marine Science Center’s REU program this year, which led to my exciting collaboration with the GEMM Lab. It was kind of a silly transition to go from studying bacteria, one of the smallest organisms on earth, to whales, who are the largest.

My project this summer focused on sei whale acoustic occurrence off the coast of Oregon. “What’s a sei whale?” is a question I heard a lot throughout the summer and is one that I had to Google myself several times before starting my internship. Believe it or not, sei whales are the third largest rorqual in the world but don’t get much publicity because of their small population sizes and secretive behavior. The commercial whaling industry of the 19th and 20th centuries did a number on sei whale populations globally, rendering them endangered. In consequence, little research has been conducted on their global range, habitat use, and behavior since the ban of commercial whaling in 1986 (Nieukirk et al. 2020). Additionally, sei whales are relatively challenging to study because of their physical similarities to the fin whale, and acoustic similarities to other rorqual vocalizations, most notably blue whale D-calls and fin whale 40 Hz calls. As of today, published literature indicates that sei whale acoustic presence in the Pacific Ocean is restricted to Antarctica, Chile, Hawaii, and possibly British Columbia, Canada (Mcdonald et al. 2005; Espanol-Jiminez et al. 2019; Rankin and Barlow, 2012; Burnham et al. 2019). The idea behind this research project was sparked by sparse visual sightings of sei whales by research cruises conducted by the Marine Mammal Institute (MMI) in recent years (Figure 1). This raised questions about if sei whales are really present in Oregon waters (and not just misidentified fin whales) and if so, how often?

Figure 1. Map of sei whale visual sightings off the coast of Oregon, colored by MMI Lab research cruise, and the location of the hydrophone at NH45 (white star).

A hydrophone, which is a fancy piece of equipment that records continuous underwater sound, was deployed 45 miles offshore of Newport, OR between October of 2021 and December of 2022. My role this summer was to use this acoustic data to determine whether sei whales are hanging out in Oregon or not. Acoustic data was analyzed using the software Raven Pro, which allowed me to visualize sound in the form of spectrograms (Fig. 2). From there, my task was to select signals that could potentially be sei whale calls. It was a hurdle familiarizing myself with sei whale vocalizations while also keeping in mind that other species (e.g., blue and fin whales) may produce similar sounding (and looking in the spectrograms) calls. For this reason, I decided to establish confidence levels based on published sei whale acoustic research that would help me classify calls with less bias. Vocalizations produced by sei whales are characterized by low frequency, broadband, downsweeps. Sei whales can be acoustically distinguished from other whales because of their tendency to produce uniform groups of calls (typically in doublets and triplets) in a short timeframe. This key finding allowed me to navigate the acoustic data with more ease.

The majority of the summer was spent slowly scanning through the months of data at 5-minute increments. As you can imagine, excitement varied by day. Some days I would find insanely clear signals of blue, fin, and humpback whales and other days I would find nothing. The major discovery and the light at the end of the tunnel was the SEI WHALES!!! I detected numerous high quality sei whale calls throughout the study period with peaks in October and November (but a significantly higher peak in occurrence in 2022 versus 2021). I also encountered a unique vocalization type in fall of 2022, consisting of a very long series of repeated calls that we called “multiplet”, rather than doublets or triplets that is more typical of sei whales (Fig. 3). Lastly, I found no significant diel pattern in sei whale vocalization, indicating that these animals call at any hour of the day. More research needs to go into this project to better estimate sei whale occurrence and understand their behavior in Oregon but this preliminary work provides a great baseline into what sei whales sound like in this part of the world. In the future, the GEMM lab intends on implementing more hydrophone data and work on developing an automated detection system that would identify sei whale calls automatically.

Figure 2. Spectrogram of typical sei whale calls detected in acoustic data
Figure 3. Spectrogram of unique sei whale multiplet call type
Figure 4. My first time conducting fieldwork! I spent a few mornings assisting Dr. Rachel Orben’s group in surveying murre and cormorant nests (thanks to my good friend Jacque McKay :))

My experience this summer was so formative for me. As someone who has been an aspiring marine biologist for so long, I am so grateful for my experience working with the GEMM Lab alongside incredible scientists who are equally passionate about studying the mysteries of the ocean. This experience has also piqued my interest in bioacoustics and I plan on searching for other opportunities to explore the field in the future. Aside from growing professionally, I learned that I am more capable of tackling and overcoming obstacles than I had thought. I was afraid of entering a field that I knew so little about and was worried about failing and not fitting in. My anxieties were overshadowed by the welcoming atmosphere at Hatfield and I could not have asked for better people to work with. As I was searching for sei whale calls this summer, I suppose that I was also unintentionally searching for my voice as a young scientist in a great, blue field.

Figure 5. My mentor, Dr. Dawn Barlow, and I with my research poster at the Hatfield Marine Science Center Coastal Intern Symposium

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References:

Nieukirk, S. L., Mellinger, D. K., Dziak, R. P., Matsumoto, H., & Klinck, H. (2020). Multi-year occurrence of sei whale calls in North Atlantic polar waters. The Journal of the Acoustical Society of America, 147(3), 1842–1850. https://doi.org/10.1121/10.0000931

McDonald, M. A., Calambokidis, J., Teranishi, A. M., & Hildebrand, J. A. (2001). The acoustic calls of blue whales off California with gender data. The Journal of the Acoustical Society of America, 109(4), 1728–1735. https://doi.org/10.1121/1.1353593

Español-Jiménez, S., Bahamonde, P. A., Chiang, G., & Häussermann, V. (2019). Discovering sounds in Patagonia: Characterizing sei whale (&lt;i&gt;Balaenoptera borealis&lt;/i&gt;) downsweeps in the south-eastern Pacific Ocean. Ocean Science, 15(1), 75–82. https://doi.org/10.5194/os-15-75-2019

Rankin, S., & Barlow, J. (2007). VOCALIZATIONS OF THE SEI WHALE BALAENOPTERA BOREALIS OFF THE HAWAIIAN ISLANDS. Bioacoustics, 16(2), 137–145. https://doi.org/10.1080/09524622.2007.9753572

Burnham, R. E., Duffus, D. A., & Mouy, X. (2019). The presence of large whale species in Clayoquot Sound and its offshore waters. Continental Shelf Research, 177, 15–23. https://doi.org/10.1016/j.csr.2019.03.004