Ann Bucklin leads new Ocean Decade Action: MetaZooGene

The UN Decade of Ocean Science for Sustainable Development 2021-2030 (see: has endorsed and approved a new project led by Ann Bucklin (UConn Marine Sciences) titled, MetaZooGene: Metabarcoding Zooplankton Diversity. The new project builds off an international Working Group of the same name, MetaZooGene (see:, sponsored by the Scientific Committee for Oceanic Research (SCOR WG157) and chaired by Bucklin. The new project will be attached to the Ocean Decade Program, Marine Life 2030 (see: and will work toward a global vision for integrative molecular – morphological taxonomic analysis of marine zooplankton, with overarching goals to promote and facilitate DNA barcoding and metabarcoding to characterize zooplankton species biodiversity and biogeography in ocean ecosystems.


Former DMS REU student Raul Flamenco on his next career plans

Reposted from UConn Today May, 17th

By Elaina Hancock. As a child, Raul Flamenco realized he was a biologist, always eager to share newly absorbed facts with his peers about birds, or lizards, or how cool tentacles are. He soon learned this zeal set him apart, which is something he was already grappling with as a Latinx student growing up in a predominantly white area of the Midwest.

Flamenco started to hide this part of himself to blend in more, which lead him to be unsure of what he wanted to do when he grew up. However, along his path in higher education and now working toward a PhD in Natural Resources, he has learned to embrace his true self and his love of studying nature.

Flamenco is a recent recipient of a National Science Foundation Graduate Research Fellowship, and of a member of UConn’s transdisciplinary training program in the Center of Biological Risk Team-TERRA.

He sat down with UConn Today to talk about his journey and his hopes for inspiring others experiencing a lack of representation.


Can you tell us how you rediscovered your love for animals and nature?

For a long time, I had no idea what I wanted to do. For school, I moved back to California, where I’m originally from, and I started taking classes at a community college to not spend an insane amount of money.

I knew I wanted to help people, so I started taking nursing classes, and I had to take a general biology class. I chose marine biology.

On the first day of class, the professor was so animated and passionate, and I kind of saw myself in him because he was Latino, too. It reinvigorated my love for animals, and I realized this is something that I can do, so, I changed my major to biology.

What helped you realize what you wanted to study ecotoxicology?

I was going to study marine biology because I really love invertebrates and I feel like they are underrepresented under undervalued organisms. Then I found out about ecotoxicology, which is the study of toxic chemicals and their impacts on ecosystems. Ecotoxicology is a unique union of different disciplines that benefits people and animals.

Two years before I decided to come to UConn for graduate school, I applied for a Research Experience for Undergraduates  (REU) with Penny Vlahos at Avery Point. I was selected, so I came out for 10 weeks and got to work on my own project looking at pesticides and mercury in harbor seal pup tissues to see if there was a relationship between the size of the pups compared with their pesticide or mercury contaminant burden.

What pieces of advice have been most helpful for you, and what do you tell others who may be unsure of what they want to do?

The advice that my mentors gave me was how important it is to choose the right advisor. Your advisor is the person that you are kind of stuck with, and having a good relationship with them is important to make grants or fellowships happen and to ensure that your research aligns with your interests.

I found my advisor, Jess Brandt after she had put out a call for students on Twitter. I reached out and we ended up having an interview that ended up being three and a half hours. It just kind of became a conversation and I thought that was a good indication that we’d get along and that it could be a good working relationship.

I ended up choosing UConn because of my advisor. Also having done the REU two summers prior at Avery Point, I already had an experience of Connecticut, I knew it’s not like the Midwest, it’s not like California, but somewhere in between.

I’m also a big advocate of community colleges. Through community college, I met that professor who was unforgivingly himself and seeing him talk so excitedly about what he was passionate about reminded me of how I get when I’m around the people I’m most comfortable around, I learned to not give that up.

Another difficulty in academia is imposter syndrome, and working through that has added another layer of self-discovery. I remember something that helped me in high school was a when a teacher said, “Fake it ’til you make it,” and I kind of stuck with that. Even if something’s difficult or challenging, I’ll do my best and just get through it. Now that I’m here, I’ve made it and I still feel like I’m faking it even though I’m doing research at this level and I received a prestigious NSF Fellowship sometimes I still feel like what am I really doing? Should I really be here? Based on conversations I’ve had with professors it seems like that never really goes away.

What has your experience been like as a member of Team-TERRA?

It is an interdisciplinary fellowship where we look at the risks to food, energy, water, and ecosystem services. The project is a chance for us to combine our expertise in a way that we wouldn’t normally. Two of us study birds, another studies wetlands, and I study the effects of contaminants.

We’re looking at how climate change can impact the release of contaminants into rivers through combined sewer overflows and other flooding events and how contaminants that get into rivers can then get into fish and shellfish that people are consuming.

We worked on a survey for anglers to figure out when and how much fish they eat, what species they catch. This project links things that I’m passionate about that in my normal research I’m not able to do as concretely — it’s linking contaminants to people.

That’s what interested me about ecotoxicology in the first place, I knew I wanted to help people and in this field I can help people and animals. Team-TERRA helped me bridge that gap.

What’s next?

I want to become a professor to serve as a mentor and role model for future generations of students. I am coming to understand myself better and knowing who I am and not giving in to what other people expect me to be or do. I always saw myself as kind of a chameleon, like I never really belonged anywhere, and I would just change who I was a little bit. That wasn’t so great for discovering my truest self.

Because of a professor just existing and being himself and knowing how few Latinos there are in academia, those are the driving reasons for why I want to become a professor, to become that representation that was important for me to help me get to where I am now.

I determined that getting my Ph.D. was the route that I have to take to get there and here I am.

Under Ocean Acidification, Embryos of a Key Forage Fish Struggle to Hatch

A potential ripple effect from carbon in the atmosphere could have severe impacts throughout the ocean ecosystem

This photo shows sand lance embryos that have and have not hatched. Sand lance have trouble hatching at future ocean CO2 levels (photo courtesy of Emma Cross).

By Elaina Hancock. Reposted from UConn Today, 7 April 2022

When carbon is emitted into the atmosphere, about a quarter of it is absorbed by the earth’s oceans. As the oceans serve as a massive ‘sink’ for carbon, there are changes to the water’s pH – a measure of how acidic or basic water is. As oceans absorb carbon, their water becomes more acidic, a process called ocean acidification (OA). For years, researchers have worked to understand what effect this could have on marine life.

While most research so far shows that fish are fairly resilient to OA, new research from UConn, the University of Washington, the National Oceanic and Atmospheric Administration (NOAA), and Southern Connecticut State University, shows that an important forage fish for the Northwest Atlantic called sand lance is very sensitive to OA, and that this could have considerable ecosystem impacts by 2100. The team’s findings have just been published in Marine Ecology Progress Series 687.

Sand lance spawn in the winter months in offshore environments that tend to have stable, low levels of CO2, explains UConn Department of Marine Sciences researcher and lead author Hannes Baumann.

“Marine organisms are not living in a uniform ocean,” Baumann says. “In near shore environments, large CO2 fluctuations between day and night and between seasons are the norm, and the fish and other organisms are adapted to this variability. When we stumbled upon sand lances we suspected they are different. We thought that a fish that lives in a more open-ocean offshore environment might be more sensitive than the near-shore fish because there’s just much less variability.”

The project was a collaboration with physical oceanographers, including Assistant Professor of Marine Sciences Samantha Siedlecki and Michael Alexander from NOAA’s Physical Sciences Laboratory in Boulder, Colorado, who modeled CO2 levels in 2050 and 2100 for a specific part of the Gulf of Maine where sand lance spawn. Then Baumann and his team reared sand lance embryos in the lab under experimentally higher CO2 levels matching the projected levels.

There are instances of direct fish mortality as result of elevated CO2, but they are rare, says Baumann. However, sand lance embryos proved to be exceptionally sensitive, and fewer embryos hatched under future oceanic CO2 conditions. The researchers repeated the experiments three more times to avoid jumping to conclusions but each time they observed the same result.

“We found that embryo survival-to-hatch decreased sharply with increasing CO2 levels in the water, concluding that this is one of the most CO2-sensitive fish species studied thus far,” Baumann says.

Sand lances are surely one of the most important forage fish here on the Northwest Atlantic shelf… The humpback whales, sharks, tuna, cod, shearwaters, terns — you name it — they are all relying on sand lance.

With this interdisciplinary approach combining model forecasts and serial experimentation the researchers arrived at a picture that is much more specific.

“We consequently applied principles of serial experimentation, which is a most timely and important topic in ocean acidification research right now,” Baumann says. “Because our findings are backed up by repeated independent evidence, they are more robust than many published ocean acidification studies to date.”

In addition to preventing many sand lance embryos from developing normally, the researchers document a second negative, and novel, response to elevated CO2. Higher CO2 levels appear to make it harder for embryos to hatch.

Baumann explains the lowered pH likely renders enzymes needed for successful hatching less effective, leaving the embryos unable to break through their eggshell (chorion) to hatch.

The results show that by 2100, due to acidification, sand lance hatching success could be reduced to 71% of today’s levels. Since sand lance are such a critical component of the food web of the Northwest Atlantic, this marked decrease in sand lance would have profound impacts throughout the ecosystem.

“Sand lances are surely one of the most important forage fish here on the Northwest Atlantic shelf,” Baumann says. “Their range spans from the Mid Atlantic Bight all the way to Greenland. Where we studied them, on Stellwagen Bank, they are called the backbone of the ecosystem. The humpback whales, sharks, tuna, cod, shearwaters, terns — you name it — they are all relying on sand lance, and if sand lance productivity goes down, we will see ripple effects to all these higher trophic animals. Even though we humans don’t fish for sand lance, we need to take care of the species because it has such a huge effect on everything else.”

Baumann says this study supports the hypothesis that offshore, high latitude marine organisms like the sand lance may be among the most vulnerable to OA. As a result, these organisms and food webs will likely be impacted first and soon, and we must act now.

Previous research has focused on opportunistically chosen species when testing their sensitivity for ocean acidification, says Baumann, but this should change.

“We need strategic thinking about what species we are testing next, because we cannot test every marine fish species, that’s an impossible task. We should concentrate on fish species that are likely the most vulnerable, and therefore the ones that are probably being affected first and this research makes a compelling argument that those are the fish species at higher latitudes and in more offshore than nearshore environments.”

DMS researchers contribute to study on copepod climate adaptation

One of the most difficult challenges facing scientists is predicting how organisms will respond to rapid global change. A collaboration between oceanographers at the University of Connecticut and evolutionary biologists at the University of Vermont is looking into how copepods (tiny crustaceans that rival insects as the most abundant animals on the planet) adapt to ocean warming and acidification. This requires understanding the underlying genomic mechanisms that allow these animals to adapt, and the constraints to adaptation. This study by Reid Brennan and collaborators is a lucid example of this approach, identifying sets of genes that are linked to copepod adaptation to stressful new environments, and showing that the ability of these animals to respond to changing conditions is challenged after prolonged adaptation. Therefore, there are limits to adaptation that can constrain the resilience of animal populations to environmental stress.


DMS faculty contributes textbook chapter on Fish Ecology

3rd March 2022. DMS faculty Hannes Baumann contributed a chapter to the new textbook Marine Biology: a functional approach to the oceans & their organisms (Taylor & Francis), which has just been published. The chapter is based on Baumann's long-running class "Ecology of Fishes" (MARN4018/5018), touching on a large variety topics including fish evolution, zoogeography, metabolism, growth, reproduction & basic concepts of fisheries science. The book is geared towards advanced undergraduate and graduate students, stimulating interest while encouraging readers to seek out further in-depth sources.

"With about 28,000 known species, fishes make up more than half of all known vertebrates (Helfman et al. 2009). Over the course of their long evolutionary history they radiated in every conceivable aquatic habitat, from the open ocean and deep-sea trenches to shelf seas, estuaries and lakes, to rivers and the smallest streams and ponds. They are found in subzero Antarctic waters, altitudes of over 4,000 m and even acidic desert springs of > 40°C (Moyle and Cech 2004). The fascinating adaptations to these habitats have produced a mind-bending diversity of form and function, a difference in size that spans more than three magnitudes (0.01 – 18 m), and a profusion of reproductive strategies. Apart from their diversity and unique evolutionary history, fishes are of intense scientific interest for economic reasons, because they comprise the nutritional foundation for a large part of humanity (Costanza et al. 1997) and their exploitation over time has led to thriving – and warring – civilizations. Today, the impetus of sustainable fish management at a time of rapid ecological re-organization due to man-made climate change has made the study of fish ecology and fish stock productivity as urgent and important as ever."

Fig.1: Origin, evolution, and systematics of fishes. A – Origin hypothesis. Early during chordate evolution, sessile arm feeders (pterobranchs) gave rise to gill feeders. In one line, free-swimming filter-feeding larvae lost their sessile stage and evolved into the first, gill-feeding vertebrates (redrawn after Romer and Parsons 1977). B – Evolution and relative abundance of major fish lines through time. Most of today’s fish groups originated in the Devonian; ray-finned fishes became the dominant fish group during the Meso- and Cenozoic (numbers refer to million year ago, Mya). C – Abridged overview of Actinopterygii systematics showing select major orders (-formes) and Perciform families (-idae) sorted top to bottom from ancestral to most derived groups. Most fishes are Teleosts, and within those, most belong to the Euteleosts. Acanthopterygii evolved fin spines; the most species-rich vertebrate order are the Perciformes (after Moyle and Cech 2004).

Ann Bucklin organizes special issue in the ICES Journal of Marine Science

Patterns of Biodiversity of Marine Zooplankton Based on Molecular Analysis is the latest themed set of articles from​ ICES Journal of Marine Science. (See ). This collection showcases the ongoing refinement of molecular approaches for analysis of zooplankton diversity.

ICES (International Council for the Exploration of the Sea) commissioned a cartoon by Bas Köhler and announced the publication (see:

The motivators for the special issue are members of the SCOR WG157 MetaZooGene (see: ), chaired by Ann Bucklin, who also authored the introductory paper, New insights into biodiversity, biogeography, ecology, and evolution of marine zooplankton based on molecular approaches (see with co-authors, Katja T.C.A. Peijnenburg (NL), Ksenia Kosobokova (RU), and Ryuji J. Machida (TW).

DMS post-doctoral researcher Emma Cross publishes new brachiopod research

15 April 2019. Dr. Emma Cross from the Baumann Lab just published her latest paper about brachiopod resilience to future ocean acidification in Environmental Science & Technology. The project involved long-term culturing of a polar and a temperate brachiopod under future ocean acidification and warming conditions during Emma’s PhD-research with the British Antarctic Survey. Substantial shell dissolution posed a threat to both species under ocean acidification, with more extensive dissolution occurring in the polar species.

Unexpectedly, however, the authors also discovered that brachiopods thicken their shell from the inner shell surface when extensive dissolution occurs at the outer shell surface under ocean acidification. This important finding furthers our understanding how predicted vulnerable marine calcifiers might cope under future environmental change.


Cross, E. L., Harper, E. M. and Peck, L. S. 2019. Thicker shells compensate extensive dissolution in brachiopods under future ocean acidification. Environmental Science & Technology (published online March 29, 2019).

Canadian Journal of Zoology publishes perspective on experimental OA research by DMS faculty

15 April 2019. Today, the Canadian Journal of Zoology published a perspective on the progress and challenges of experimental ocean acidification research, written by Hannes last year as an extension of keynote lectures on this topic given at the Annual meeting of the Canadian Zoological Society (St. John’s, NL, Canada) and the Gordon Research Symposium (Waterville Valley, NH). The perspective takes stock of the progress achieved in the field over past two decades in four key areas, hoping to inspire particularly new researchers to the field to build on this foundation.

Abstract: Experimental studies assessing the potential impacts of ocean acidification on marine organisms have rapidly expanded and produced a wealth of empirical data over the past decade. This perspective examines four key areas of transfor- mative developments in experimental approaches: (1) methodological advances; (2) advances in elucidating physiological and molecular mechanisms behind observed CO2 effects; (3) recognition of short-term CO2 variability as a likely modifier of species sensitivities (Ocean Variability Hypothesis); and (4) consensus on the multistressor nature of marine climate change where effect interactions are still challenging to anticipate. No single experiment allows predicting the fate of future populations. But sustaining the accumulation of empirical evidence is critical for more robust estimates of species reaction norms and thus for enabling better modeling approaches. Moreover, advanced experimental approaches are needed to address knowledge gaps including changes in species interactions and intraspecific variability in sensitivity and its importance for the adaptation potential of marine organisms to a high CO2 world.
Illustration of the Ocean Variability Hypothesis positing that the CO2 sensitivity of marine organisms is related to the magnitude of short-term CO2 fluctuations in their habitat (e.g., from nearshore to open ocean) and length of their early life stage durations. It suggests that the most CO2 tolerant marine organisms are those that develop fast and (or) in habitats with large contemporary CO2 fluctuations, whereas the potentially most vulnerable species are those that develop slowly in relatively stable open-ocean habitats.

New publication of mercury levels in aquatic wildlife and the atmosphere

17 April 2019. Rob Mason was a co-author of a recent publication in Science of the Total Environment (How closely do mercury trends in fish and other aquatic wildlife track those in the atmosphere? – Implications for evaluating the effectiveness of the Minamata Convention) that provided a review of the potential timescale and magnitude of response of fish in different ecosystems to changes in inputs of mercury to the atmosphere from anthropogenic activities. The paper is a synthesis of information gathered for the 2018 Global Mercury Assessment Report, published by the United Nations Environmental Program as part of the activities of the Minamata Convention on Mercury, a globally binding treaty that has been initiated to reduce anthropogenic mercury emissions to the biosphere.

    • Wang, F., Outridge, P.M., Feng, X., Meng, B., Heimbürger-Boavida, L.-E., and Mason, R.P. (2019)

How closely do mercury trends in fish and other aquatic wildlife track those in the atmosphere? – Implications for evaluating the effectiveness of the Minamata Convention
Science of The Total Environment 674:58-70