Researchers at Cal Poly and Scripps Institute use tiny prey to track the largest animals on Earth
EASTERN PACIFIC REGION, Calif. (KEYT) – A research team of Cal Poly statisticians and marine biologists from UC San Diego have developed a new way to monitor local whale populations by measuring the abundance of the microorganisms they eat.
Traditionally, the presence of whales has been studied through visual confirmations, photo identification, satellite imagery, genomic matching, and acoustic monitoring.
But watching and listening for whales can only get you so much information for these marine mammals that travel vast distances in the open ocean.
Instead of that direct method of observation, a joint research team of marine biologists with UC San Diego's Scripps Institution of Oceanography and statisticians from Cal Poly decided to study the very small lifeforms that the largest animals on our planet eat.
"The concept of this project was to try and find an indirect signal that's based on ecological relationships in the microbial communities that are in the water and how they respond to macro-organisms, such as whales," explained Cal Poly assistant professor of statistics and a lead author of the study, Trevor Ruiz "We developed a tailored approach, and while our methods are not off the shelf, they remain transferrable to prediction from microbial data more broadly, and along with our scientific findings we have provided a portable software implementation of the methods to lower barriers to adoption for other researchers who might be interested in applying our approach to other problems."
Researchers analyzed the presence of microbial life that filter-feeding whales, also known as baleen whales, consumed between 2014 and 2020 from San Diego to Morro Bay and their findings were published earlier this month in the science journal PLOS One.
"Large baleen whales play a vital role in marine ecosystems by helping to regulate ecosystem processes. They are of conservation and management relevance as many populations are listed as threatened (Vulnerable, Endangered, or Critically Endangered) on the IUCN Red List of Threatened Species," opened Microbial and small zooplankton communities predict density of baleen whales in the southern California Current Ecosystem published on May 6, 2026 in PLOS One. "Each year, blue, fin, and humpback whales migrate to the productive waters of the California Current to feed on dense aggregations of krill and schooling fishes. Their foraging grounds and migratory corridors overlap with commercial shipping routes and areas of military activity, particularly in Southern California, making the ability to predict baleen whale distribution an important management directive in the region."
The overlap of migrating whales and shipping lanes led to the development of a decade-old vessel speed reduction partnership that aims to reduce emissions in the Santa Barbara Channel and mitigate whale strikes.
The Santa Barbara Channel's unique geography draws whales to the area as shown in the image below, courtesy of the Channel Islands National Park.
Those currents draw large numbers of microorganisms and of course, the filter-feeding whales that researchers want to keep track of, but the largest whales don't munch on their small pray the way we do.
Baleen whales don't have any teeth.
Instead they have hundreds of plates of long, flexible hairs made of keratin, which we find in our own hair and nails, embedded in their upper gums that they use to filter the food they want from the water they scoop into their mouths.
Once the mix of ocean water and microorganisms enters their mouths, baleen whales then use their tongues to push out the water and keep in their meal as shown in the images below, courtesy of the Center for Coastal Studies.
"Because large baleen whales are difficult to sample directly, yet are closely linked to their habitat and associated biota, we investigated whether microbial and small plankton communities could serve as proxies for predicting their density in the southern California Current Ecosystem," detailed the study. "We leveraged six years of ship-based marine mammal data coupled with data on the microbial and small-plankton community (hereafter planktonic communities) to predict seasonal and interannual baleen whale density."
Cross referencing the traditional methods of observing baleen whales with ocean water data about the amount of microorganisms present helped to create a model that predicted the density of whales 53 percent more accurately than current forecast models.
The interdisciplinary approach was something noted by Cal Poly statisticians.
"This project gave me valuable experience in data analysis and modeling," shared Nick Patrick, a 2025 Cal Poly statistics alumnus and coauthor of the study published this month. "It had many collaborators across different fields, from statistics to marine ecology to genomics, and seeing everyone from these disciplines coming together to form the final product was one of the most interesting aspects."
"Overall, our findings suggest that planktonic communities can serve as a predictor of baleen whale densities," concluded the study. "This study presents a reliable approach to predict baleen whale densities across long temporal (6 years) and spatial scales (over 200,000km2) using metabarcoding-derived communities of microbes and small plankton found in the water column. By demonstrating links between microbial community composition and large whale density, this work can be used to generate potential explanatory variables to predict cetacean density."
