Choose Your Own Adventure: The Tagging of the Horseshoe Crab

There’s already a UConn student shirtless and up to his waist in Long Island Sound when we tag our first horseshoe crab. The water is only 64 degrees Fahrenheit on this breezy June morning. Not everyone is so keen to get wet.

UConn’s Genome Ambassador Program and Sacred Heart University’s Project Limulus teamed up to tag horseshoe crabs crawling onto the beach in Stratford on June 16. Fortunately, the crabs are all over, scrabbling along the pebbled bank near the edge of the seagrass as well as four feet deep in the rising tide. Jo-Marie Kasinak, director of Project Limulus, describes finding horseshoe crabs as a “Choose Your Own Adventure” experience, in which you can get as wet and muddy as you (don’t) want. Some students start peeking into the large concrete reef balls high and dry on the beach, looking for horseshoe crabs that waited too long to swim out and got stuck inside during the last high tide.

“The males are smaller. They use their boxing gloves to latch onto the females to swim to shore for mating,” says Kasinak, referring to the specially shaped claws male horseshoe crabs have. She mentions that horseshoe crabs are not monogamous, and that in Delaware Bay one female was found with 19 males hanging onto her. It’s not quite that crazy out here in this salt marsh now managed by the Audubon Society. But we’ve already found one mating pair, and we’re looking for more.

Horseshoe crabs have scooted around Earth’s coastal waters for the last 450 million years. They existed before the dinosaurs, before any land animals at all. Which probably explains why they crawl onto beaches to mate and lay eggs; land predators weren’t a thing back then. Multiple epochs later, they still spend late spring and summer in and around the beaches and salt marches from Maine to Florida, then head out into deeper water for the colder months. Scientists don’t know too much about what they do out there.

Which is why we’re out here tagging them. Crabs tagged here in Stratford are most commonly reported along nearby beaches within a five-kilometer radius, although some have traveled as far south as Florida. The actual tagging process involves picking up a crab, driving an awl into its shell far enough from the edge to avoid it sticking off the side but close enough to the edge to avoid the brain, and then shoving a tag into the hole. It’s like an earring, or at least that’s how the researchers describe it.

When the awl goes in, most crabs bleed a little. Their blood is pale blue, and goes for more than $60,000 per gallon in the pharmaceutical industry. It’s used to test the cleanliness and sterility of vaccines and certain medical equipment, clotting immediately upon encountering the slightest contamination.

The crabs are picked up on mid-Atlantic beaches during mating season, bled, and then returned to the beaches weakened. Some of them manage to mate and lay eggs and survive, but some don’t, and the blood harvest is contributing to the decline in horseshoe crab numbers.

“There is a synthetic product made in yeast” to replace horseshoe crab blood, “but a lot of companies don’t trust it,” says Jay Podziewski ’27 (CLAS). The undergraduate molecular biology major is doing a Summer Undergraduate Research Fund (SURF) project this summer experimenting with how to grow horseshoe crab amoebocytes—the cells in the blood that clot to reveal bacterial contamination—in the lab. If scientists can figure out how to grow them in the lab instead of in a crab, they might be able to produce a product much closer to real horseshoe crab blood than the current yeast synthetic. “If we’re successful, it should have an easier time getting approved,” Podziewski says. And fewer crabs would need to be bled.

UConn marine genomicist Kate Castellano is Podziewski’s advisor on the project. She was on the team at UConn’s Institute for Systems Genomics that sequenced the horseshoe crab’s genetic code, publishing it in 2025.

“There are multiple factors in the horseshoe crab’s blood that cause the clotting,” Castellano says. Since the synthetic product produced by yeast was using only a single gene to produce a single clotting factor, “maybe it wasn’t working as well as it could because it was missing factors,” she says. Podziewski’s project will create a tool to better understand the biology of the cells, and see whether these other factors are required to make the test more sensitive.

One of the students manages to dig a small male horseshoe crab out of a reef pot, where he had buried himself to keep his gills moist during the last low tide. He is promptly tagged and released. Then two students walk over with a mating pair. The female is large. She has a hole in her shell, and is missing a few claws, but she’s carrying loads of eggs and has very light-colored eyes, a sign of relative health and youth. The researchers try to figure out if the hole in her shell is from a previous tagging or not.

“This seemed like a super cool way to experience field work in a different field,” says Jillian Taormina, taking a break from crab hunting. Taormina is doing a stint of post baccalaureate research on human genomics in Deborah Bolnick’s lab at UConn before moving on to graduate study at the University of Maine Farmington this fall. “It’s fascinating to see how different fields interact; I can definitely take some of this with me,” Taormina says.

The salt marsh we’re standing on was formerly owned by Remington Arms, which used it as a shooting range at one point. Later Dupont bought Remington, and tried to environmentally remediate the property, but reminders of the past still emerge from the muck on a regular basis. This writer found a piece of a clay pigeon, still painted safety orange. UConn multimedia specialist Syd Herdle picked up some shot casings as well as a discarded drone, a decidedly more modern piece of garbage.

It’s reassuring that even in this imperfectly repaired environment, the crabs still come and breed. All in all, the students tag 17 horseshoe crabs in two hours, and numerous other breeding pairs are spied but elude the researchers.

Other creatures come, too. A birder stopping by to catch glimpses of shorebirds walks over and asks what we’re doing, and whether she can help. Anyone can volunteer. The interested can check out Project Limulus or join in other UConn Genome Ambassador projects to learn more about horseshoe crabs, genetics and the scientific process.

Follow this link for the full UConn Today article by Kim Krieger and Sydney Herdle

heir fur might feel the same, but a mink in the Everglades is not the same as a mink from northern Florida, researchers from the University of Connecticut and Central Connecticut State University report in the April 20 issue of Nature Heredity, which also ran a podcast discussing the research. The scientists’ findings could justify greater protections for the Everglades mink.

Mink resemble semi-aquatic ferrets, and are found almost everywhere in North America where there is water except the dry southwest. But in Florida, a state filled with lakes and rivers, mink are found in only three places, and those three are isolated from each other.

“Mink are really difficult to study,” says Paul Hapeman, a conservation biologist at Central Connecticut State University. “They have low detection rates using established methods. Florida Fish and Wildlife had cameras set out for several years and only got a couple of photos. Recent efforts have been a little more successful.”

Hapeman had been studying the mink along with Florida Fish and Wildlife, looking at the genetics of the animals. Past research had tentatively suggested that the mink in the state had diverged into three subspecies in the salty waters along the coasts and seasonally flooded wetlands of south Florida. Mink in the Everglades seemed particularly distinct—and vulnerable. If conservationists could show undeniable genetic differences between the three subspecies, it would go a long way towards supporting protection for them.

The University of Connecticut’s Institute of Systems Genomics (ISG) reached out to Hapeman. They were looking for a project for a team of students, and though Hapeman’s work with mink and genetic novelty could benefit from the collaboration. UConn computational biologist Jill Wegrzyn’s team specializes in decoding complete genomes of threatened organisms.

Mink was an unusual choice for Wegrzyn’s lab, which more commonly focuses on trees or species of ecological concern. Mink, known scientifically as Neogale vison, are considered invasive in Europe, where they have escaped from fur farms and begun breeding in the wild.

And mink already had a reference genome—sequenced from a British mink presumably descended from a farm escapee. Creating another reference genome would be a lot of work.

In fact, Wegrzyn and Hapeman wanted to go further and create a pangenome, fully sequencing the genes of multiple mink from three locations in Florida and one in Louisiana. Such a thorough look would be the best way to make the case that the three groups of mink were genetically distinct. But that kind of effort would require a big team of researchers.

Fortunately Wegrzyn, evolutionary biologist Elizabeth Jockusch, and other scientists at UConn’s ISG had just the thing: funding from the National Science Foundation for a Research and Mentoring for Postbaccalaureates in Biological Sciences (RaMP) cohort.

RaMP grants were intended to give research experience to students who had undergraduate degrees but hadn’t had the chance to do much lab work. Wegrzyn, Jockusch, and their colleagues assembled a team of students for the RaMP cohort. They would be trained in bioinformatics, or how to assemble and analyze a genome, using the mink as their subject. Hapeman provided the students samples from six different minks—two from each of the three tentative N. vison subspecies in Florida and Louisiana. The genome of each mink was compared to the others to see which genes, or families of genes, were missing or different. Their results reinforced what biologists had already suspected: the samples represented three distinct subspecies.

Some of the samples came from Hapeman’s lab during cooperative research with state wildlife agencies in Florida and Louisiana, and some of them came from mink specimens archived at the Florida Museum of Natural History. In the past, archived specimens were often too degraded to get usable DNA. But the students, and newer techniques they trained on, proved that isn’t the case anymore.

“This study also supports the value of natural history collections for conservation genomics,” says Wegrzyn.

Mink from the Everglades (N. vison evergladensis) were genetically distinct from mink from northeastern Florida (N. vison lutensis) and mink from the northwestern Gulf coast (N. vison vulgivaga). Evergladensis mink had genetic differences related to reproduction and sensory systems, which makes sense; Everglades mink breed at a different time of year than other mink, likely due to seasonal flooding in the Everglades. Their genome also indicated a high level of inbreeding, as much as other mammals considered critically endangered, such as white rhinoceroses and lowland gorillas. This suggested a recent decline in their population, possibly associated with an outbreak of canine distemper in the late 1990s.

N. vison vulgivaga had genetic differences related to oxidative stress and adaptability, possibly due to the constantly shifting salinity of their marshy habitat. And N. vison lutensis, found in the tidal estuary of northeastern Florida, had genes enriched for neurological development. Mink of this subspecies also have a noticeably different skull shape. Genetic enrichment of this kind has been linked to learning and behavioral flexibility in other marine mammals such as otters and dolphins.

The team also compared the British mink reference genome to their team’s pangenome, and found the reference mink had genetic changes related to immunity, suggesting farmed mink in Europe are adapting to the overcrowding and disease common on fur farms.

“The approach of using genomic data to assess subspecies classifications has tremendous potential to assist with status assessments and protections,” says Hapeman.

Beyond the scientific findings, the study illustrates the value of the RaMP training model: three of the co-first authors from this cohort – Airianna McGuire, Mary Rutter (current and incoming Ph.D. students, respectively), and Kyle Paist – remain involved in mentoring the current group of RaMP fellows at UConn.

Follow this link for the full article from the UConn Today. 

Guide dogs help thousands of people with visual disabilities navigate daily life.

While guide dogs provide tremendous benefits, the current training program faces serious inefficiencies, since a large percentage never actually assist an owner. Only 60% of dogs evaluated for assistance work graduate from their training programs. This means a loss of more than $12,000 per dog unable to complete training. A dog that has completed the program costs up to $50,000, and people can wait years for a trained animal.

Most dogs that fail to complete guide dog training do so because of behavioral issues. This led Breno Fragomeni, associate professor of animal science in the College of Agriculture, Health and Natural Resources (CAHNR), to conduct an analysis of dogs’ genetics to see if there was a way to better predict which animals would be successful guide dogs.

“If we can tell before they are trained if they [will be successful], that saves a lot of time and a lot of money, and it will also increase the number of guide dogs out there to help people,” Fragomeni says.

This work was published in Genetics Selection Evolution.

Fragomeni looked at 17 traits taken from the International Working Dog Registry’s (IWDR) Behavior Checklist. Trainers working for organizations around the world use this checklist to quantify dogs’ fitness to work as guide dogs.

Fragomeni focused on the traits that are most associated with failure to graduate including jumping on people, biting, and reactivity to strangers or loud noises.

Fragomeni had access to IWDR’s pedigree information, which includes at least three generations, as well as complete genomic sequences for 1,100 Labrador retrievers, the most common breed of guide dog.

Using equations, he correlated this genetic information with the dogs’ performance according to their Behavior Checklist evaluations.

“If I have one dog with many puppies, and I look at the performance of those puppies, that performance would be a good indicator of the genetics of the father,” Fragomeni says.

With genomic data, Fragomeni was able to not only tell if certain parental genetics gave rise to puppies that were more likely to become guide dogs, but if individual animals are more likely to be successful. Fragomeni found that genomic data was a better predictor of a dog’s success for at least 11 of the 17 traits he studied when compared to traditional evaluations.

“If I have genomic data, I don’t need to wait for animals to have progeny to tell if they are going to be good [guide dogs],” Fragomeni says. “Just using genomic data, I can predict how well all those animals will perform.”

This information can inform “breeding values,” numbers IWDR assigns to give breeders a sense of the likelihood that a given dog’s offspring can be successfully trained as guide dogs.

“If we keep selecting them, we’re going to improve that population consistently over time,” Fragomeni says.

One major limitation of this study was the lack of animals with complete genomic data available. While people, including Fragomeni, have been using genomic information to help selectively breed livestock for decades, this was one of the first attempts to use it for guide dogs.

“The paper is very important for that reason, because now we have a working example in that specific population,” Fragomeni says. “It shows the potential of those tools, and we expect those numbers to increase much, much faster.”

While this study was confined to Labrador retrievers, Fragomeni says he plans to expand the work to other common guide dog breeds including German shepherds and golden retrievers. He is also working on a paper evaluating how selecting for one trait, like fear of strangers, could impact others, like harness sensitivity.

Fragomeni is also interested in using this work to predict common health issues within a breed. This could have applications beyond service animals.

“Eventually we want to come up with a way that people can genotype their pets and learn if they’re at a higher or lower risk of developing cancer,” Fragomeni says. “That will change how you treat them throughout their life and if you allow them to breed or not.”

Click to see original article on UConn Today.

The American Academy of Arts and Sciences (AMACAD) announced that Prof. Daniel Bolnick of the Department of Ecology and Evolutionary Biology is one of its newly-elected members. Prof. Bonick’s research in evolutionary ecology and evolutionary immunology “seeks to understand the evolutionary and ecological rules that promote genetic diversity within species: variation among individuals, and divergence between populations.” Prof. Bolnick is only the 8th member from UConn elected to AMACAD in the last 30 years, and the first since 2022

Researchers in the College of Agriculture, Health and Natural Resources have developed a novel line of bovine embryonic stem cells, which have significant potential for a variety of new innovations, from lab-grown meat to models for human tissue replacement.

This work, led by Xiuchun “Cindy” Tian, professor of biotechnology in the Department of Animal Science, and her former and current graduate students Yue Su, Jiaxi Liu, and Ruifeng Zhao, was published in Stem Cells.

Click here to read the full article from UConn Today.

Banka Rogina, M.S., Ph.D., of the UConn School of Medicine has been newly elected vice president of the Gerontological Society of America (GSA). Rogina will serve a 1-year term in this national leadership position, beginning January 2026.

Following the end of her vice president role, Rogina will assume the role of president of the GSA in 2027 and then chair of its Board of Directors in 2028.

The GSA is the nation’s oldest and largest interdisciplinary organization focused on aging with over 6,600 members from over 50 countries. GSA has six membership groups based on fields of interest including physicians, dentists, basic scientists, nurses, pharmacists, nutritionists, social workers, psychologists, sociologists, epidemiologists, policy makers, among others.

“I am honored to be selected for this prestigious leadership role,” shares Rogina whose tenure with the GSA has been longstanding.

Follow this link for the full UConn Today article.

BIODIVERSITY AND CONSERVATION GENOMICS PROGRAM