Research News

[New publication] Brachiopods resilient to global change

Congratulations to Emma Cross to her new publication in Global Change Biology today!

The common brachiopod Calloria inconspicua (pink shells) in their natural environment in New Zealand. Photo credit: Dr Liz Harper.
Her study that was part of her PhD-research concludes that the brachiopod Calloria inconspicua, a common seafloor dwelling marine invertebrate from New Zealand, is more resilient to environmental change than expected.

Read the full press release by the British Antarctic Survey

[Research news] New NSF grant to study silverside genes!

We are overjoyed to announce that NSF is funding a new and collaborative research project to look at the genomic underpinning of local adaptation in the Atlantic silverside! Check out below for a first glimpse of the project website.


NSF-OCE #1756751 The genomic underpinnings of local adaptation despite gene flow along a coastal environmental cline (2018-2021)

Principal investigators


Nina Therkildsen (Cornell)



Hannes Baumann (UConn)



Anna Tigano (Cornell)

Graduate students


Maria Akopyan, Callie Concannon



Aryn Pearce-Wilder

Oceans are large, open habitats, where it was previously believed that the lack of obvious barriers to dispersal would result in extensive mixing, thereby preventing organisms from adapting genetically to particular habitats. It has recently become clear, however, that many marine species are subdivided into multiple populations that have evolved to thrive best under contrasting local environmental conditions. Nevertheless, we still know very little about the genomic mechanisms that enable divergent adaptations in the face of ongoing intermixing.

Learn more …

This project focuses on the Atlantic silverside (Menidia menidia), a small estuarine fish that exhibits a remarkable degree of local adaptation in growth rates and a suite of other traits tightly associated with a climatic gradient across latitudes. Decades of prior lab and field studies have made M. menidia one of the marine species for which we have the best understanding of evolutionary tradeoffs among traits and drivers of selection causing adaptive divergence. Yet, the underlying genomic basis is so far completely unknown.We will integrate whole genome sequencing data from wild fish sampled across the distribution range with breeding experiments in the laboratory to decipher these genomic underpinnings. This will provide one of the most comprehensive assessments of the genomic basis for local adaptation in the oceans to date, thereby generating insights that are urgently needed for better predictions about how species can respond to rapid environmental change. The project will provide interdisciplinary training for a postdoc as well as two graduate and several undergraduate students from underrepresented minorities. The findings will also be leveraged to develop engaging teaching and outreach materials (e.g. a video documentary and popular science articles) to promote a better understanding of ecology, evolution, and local adaptation among science students and the general public.

The project is organized into four interconnected components

Part 1 examines fine-scale spatial patterns of genomic differentiation along the cline to a) characterize the connectivity landscape, b) identify genomic regions under divergent selection, and c) deduce potential drivers and targets of selection by examining how allele frequencies vary in relation to environmental factors and biogeographic features.
Part 2 maps key locally adapted traits to the genome to dissect their underlying genomic basis.
Part 3 integrates patterns of variation in the wild (part 1) and the mapping of traits under controlled conditions (part 2) to a) examine how genomic architectures underlying local adaptation vary across gene flow regimes and b) elucidating the potential role of chromosomal rearrangements and other tight linkage among adaptive alleles in facilitating adaptation.
Part 4 examines dispersal – selection dynamics over seasonal time scales to a) infer how selection against migrants and their offspring maintains local adaptation despite homogenizing connectivity and b) validate candidate loci for local adaptation.


[Research feature] Our multistressor NSF project in the spotlight

This research feature makes the case for multistressor research to a broad general audience and introduces our NSF project and its participants. Download the feature by clicking on the pictures or the link below.


[Research news] Are sand lance embryos particularly sensitive to high CO2?

This article has been cross-posted at news sites of Connecticut SeaGrant, Stellwagen Bank National Marine Sanctuary, and the Early Life History Section of the American Fisheries Society.

By Hannes Baumann

On this dimly lit November afternoon, rain mercilessly drenched scientists and crew on board the R/V Auk as it slowly navigated the waters of Stellwagen Bank. A world like a wet sponge. Sky and ocean, indistinguishable.

Thanksgiving, the next day.

Despite the circumstances, the team’s mood was nothing short of elated. Our small beam trawl had just spilled hundreds of silvery fish on deck, wriggling like eels. They were Northern sand lance (Ammodytes dubius).

Running ripe adults.


Apparently, they like Thanksgiving, too.


As the ship docked back in the Scituate, Mass., harbor that day, the rain thinned to hazy darkness.

“Let’s get a coffee and then on the road,” mumbled Chris, who led the team, “the real work of the experiments has just begun.”

Chris RV Auk Sediment grab
Chris Murray, a member of the research team, checks the contents of a sediment grab for sand lance. Photo: Jacob Snyder / Red Skies Photography

The RV Auk in early morning, getting ready for another sand lance sampling trip to Stellwagen Bank. Photo: Hannes Baumann
Stellwagen Bank, the National Marine Sanctuary just north of Cape Cod, is a true hotspot for some of the Atlantic Ocean’s most iconic creatures: whales, seals, tuna and seabirds, who all share a particular appetite for this one fish – sand lance. Some experts in the sanctuary’s ecosystem call this species its “backbone.” Others consider it a classic forage fish, responsible for transferring massive amounts of energy from lower to upper levels on the food chain.

Sand lance have a few interesting and rare characteristics. They alternate between schooling and foraging in the upper water column and extended periods of being almost completely buried in sand. For that, they rely on sand of a particular grain size and with very little organic content. It’s the kind of sand that defines large areas of the Stellwagen Bank.

Surprisingly little is known about the ecology and ecosystem importance of this sand lance species, although research on its European relatives (A. tobianus, A. marinus) is more advanced. In particular, experiments on early life stages of Northern sand lance have been lacking, save for some pioneering work on rearing methods of the related A. americanus (Smigielski et al. 1984). One question that was of particular interest to our lab involved the potential sensitivity of this fish species to carbon dioxide (CO2). That’s due to two other interesting and rare characteristics of sand lance. They spawn in late fall and winter in cold (and still cooling) waters, which is why their eggs and larvae develop extremely slow compared to other, more typical spring and summer spawning species. In addition, the species is found not in nearshore, but offshore coastal waters, where smaller seasonal and daily CO2 fluctuations more closely resemble oceanic conditions. Could sand lance offspring be particularly sensitive to higher levels of oceanic carbon dioxide predicted during the next 100 to 300 years as climate change effects intensify?

Sand lance caught on Stellwagen Bank in November 2014
Adult sand lance, shown here, is the favorite food for whales, seals, tuna and seabirds. Photo: Hannes Baumann
Early results suggest that sand lance larva, shown in closeup, are particulary sensitive to higher levels of carbon dioxide. Photo courtesy of Hannes Baumann

Over the past two years (2016-17), we successfully found and sampled spawning ripe sand lance on Stellwagen Bank during a narrow window in late November. Eggs and sperm from adults were removed on board or after being transported live to our laboratory at UConn Avery Point. We reared newly fertilized embryos to hatch and to the feeding larval stage, under different sets of temperature and CO2 conditions, measuring survival and growth traits along the way.

Our experiments are still ongoing, and rearing protocols are being improved.

The preliminary findings, however, are stunning. Survival to hatch was dramatically reduced under elevated and high compared to baseline CO2 conditions. It was severely lowered at higher (10°C or 50°F) compared to lower temperatures (5°C or 41°F). Our second experiment this year appears to repeat this pattern. If these results continue, that would mean sand lance is one of the most CO2-sensitive species studied to date.

General interest in sand lance goes beyond its sensitivity to carbon dioxide. Given the species importance for the ecosystem and coastal economy, there are now increasing efforts to better understand sand lance feeding ecology, distribution and relationship to the rest of the food web. In this regard, funding of our project by the Northeast Sea Grant Consortium proved prescient and a seed for subsequent grants from MIT Sea Grant and the Bureau of Energy Management (BOEM) to continue the work. Surely, the groundswell of interest in sand lance is commensurate with its importance and will enable insights into better management strategies for sensitive ecosystems like those along the U.S. Atlantic coast.

This graphic shows survival to hatch rates of Northern sand lance embryos reared at three carbon dioxide levels and two temperatures. Graphic: Hannes Baumann

Collaborators on this project are: D. Wiley of the National Oceanic and Atmospheric Administration-Stellwagen Bank National Marine Sanctuary; P. Valentine of the U.S. Geological Survey; and S. Gallagher and J. Llopiz, both of the Woods Hole Oceanographic Institution.

[New publication] Mothers matter for the CO2 sensitivity of fish offspring

28 November 2017. The Journal of Experimental Marine Biology and Ecology just published the latest study by our group looking at differences in the CO2 sensitivity of Atlantic silverside offspring stemming from different mothers. Congratulations to Jacob Snyder for his first peer-reviewed publication.

Among the highlights of the study:

  • Offspring produced by different females varied in their sensitivity to high CO2 conditions.
  • Specific fatty acids in eggs were correlated to the log-transformed CO2 response ratio of embryo survival and hatch length.
  • Maternal provisioning might be an additional determinant of CO2 sensitivity in fish early life stages.


Snyder, J.T.*, Murray, C.S.*, and Baumann, H. (2018)
Potential for maternal effects on offspring CO2 sensitivities in the Atlantic silverside (Menidia menidia).
Journal of Experimental Marine Biology and Ecology 499:1-8

Fig2 - dancing men
M. menidia. Responses to high CO2 conditions among replicates within and among females: (A) embryo and larval survival; (B) overall survival; (C) SL at hatch; and (D) final SL (16 dph). Patterns of larval growth were nearly identical to panel D and are therefore omitted. Ambient and high CO2 treatments are denoted by red and blue colors, respectively. Small symbols depict replicate survival (A,B) or replicate average size (C,D), while large symbols depict CO2 treatment averages for each female. Black lines connect average response for each female. Asterisks represent significant differences (P < 0.05) between CO2 levels within offspring of each female (Bonferroni adjusted t-test). Letters denote to females A to E.

[Lab news] Baumann lab participates in Avery Point Open House Event

15 October 2017: All members of the Baumann lab – Hannes, Emma, Chris, Julie and Jake had fun at an Open House event at the Avery Point Campus as part of the 50th Anniversary celebrations. The whole department participated with a flurry of educational activities and fun exhibitions.
Our lab manned a table outside the Rankin Lab, telling people about the nearshore fish community, the phenomenon of ocean acidification and the measurement of pH in water. Everybody chipped in, thanks!
Hannes also premiered reciting Dr. Seuss’ “The Lorax” in front of young and old in the AP auditorium.

Check out some of the fun around the “Ocean Acidification and our fish” table:

There are fish!
Jake and Emma assist a little scientist in measuring the pH in our two demonstration tanks

Atlantic silversides from Mumford Cove, CT, swimming in our tanks. After the end of the demonstration, we released back into the wild.
Prof. Rob Mason taking briefly over our display. Emerging topic apparently – Mercury and ocean acidification

Fascinating sea life …

What an incredible creature a sea star is!

Hannes recited “The Lorax” – Dr. Seuss classic, comic-poetic tale of greed and environmental destruction

Julie manning our Ocean acidification outreach table at the Rankin Lab on 15 Oct 2017

[Lab news] Measuring juvenile silversides. Live.

10 October 2017. Today, Chris, Emma, and Julie measured over 400 juvenile Atlantic silversides for their length and weight. This time, however, we did not euthanize the fish before, but successfully measured them while still alive, only a little drowsy from the mild anesthetic we administered before.

Click on the video below to have a look for yourself.
Congratulations all, for a job well done!

[New publication] Nearshore pH and DO fluctuations across 16 US estuaries!

October, 2nd, 2017: Happy to announce that Estuaries and Coasts just published (online) our article that looked at unifying principles of pH and DO fluctuations across many US nearshore habitats. The datasets belongs to the US Nearshore Estuaries Research Reserves System (NERRS) and is one of the most extensive monitoring datasets in coastal aquatic habitats. In this case, we used 15 years of continuous monitoring data (> 5 million data points) from 16 different reserves across the US Atlantic, Caribbean, Gulf of Mexico, and Pacific coasts and analyzed short- to long-term variability in pH and DO fluctuations. Among the highlights:

  • Our analyses confirmed that large, metabolically driven fluctuations of pH and DO are a unifying feature of nearshore habitats. Even more so, we were able to show that across habitats, one can predict mean pH or mean diel pH fluctuations simply based on salinity and oxygen levels/fluctuations. This provided strong empirical evidence that common metabolic principles drive diel to seasonal pH/DO variations within as well as across a diversity of estuarine environments.
  • As expected, there were no interannual, monotonic trends in nearshore pH conditions; instead interannual fluctuations were of similar magnitude than the pH decrease predicted for the average surface ocean over the next three centuries.
  • By correlating weekly anomalies of pH, oxygen, and temperature, we found strong empirical support for the notion that coastal acidification — in addition to being driven by eutrophication and atmospheric CO2 increases — is exacerbated simply by warming, likely via increasing community respiration.

Citation and link:
Baumann, H. and Smith, E. (2017) Quantifying metabolically-driven pH and oxygen fluctuations in US nearshore habitats at diel to interannual time-scales Estuaries & Coasts (published online 2 Oct 2017)

Among many other aspects, the paper analyzed interannual trends in temperature (red bars), dissolved oxygen (%, blue bars), and pH (green bars) at 16 US Nearshore Ecological Research Reserves (NERRS), shown as yearly anomalies derived from averaging monthly anomalies for each variable, site, and year. Black trend lines were derived by LOESS smoothing.

[Lab news] Group effort – starting new silverside experiments in June 2017

It’s the beginning of June, and in the Baumann lab that means: high time for experimental research on the Atlantic Silverside, the famous forage fish and important model species! This year, we have several major objectives; our NSF-sponsored research examines the sensitivity of offspring to the individual and combined effects of high CO2 and low oxygen (Chris Murray), while in collaboration with our colleagues from Cornell University we rear several families for genetic and transcriptomic studies. Elle Parks, our REU student just started her work on the effects of CO2 and temperature on the starvation resistance of silverside larvae. As always, the days when new experiments start are a group effort, where everybody including many volunteers help. Thanks to Peter Morenus (UConn) for the coming down for documenting the activities!

This story is also featured on UConn Today.

[Field work] To Georgia and back in 48h – a special road trip for science

By H.B.

Somewhere after Richmond, VA, the sun sets and traffic on the I-95 begins moving better. At long last. The four people in the burgundy Dogde Challenger have all already cycled through their driving shifts once and dare an impatient glance at the time left. Still more than 8 hours. More than 8 hours to reach this very special location at the Atlantic coast – Jekyll Island, Georgia. In the trunk of the car a jumble of coolers and a beach seine, buckets, air pumps, and hoses topped with the crumpled witnesses of roadside dining. This is no ordinary road trip.

We, that are Aryn and Nicholas from the Therkildsen lab of Conservation Genetics lab at Cornell University and James and Hannes from the Fish Ecology Lab here at UConn; we went on this road trip to catch live, spawning ripe Atlantic silversides from the southern edge of the species distribution. We then intended to bring these fish back to UConn alive, sample another population from the south shore of Long Island (Patchogue, NY) and produce genetic crosses of these populations.

The broad goal of our expanding collaborative efforts with our geneticist friends from Cornell is the creation of an annotated genome of this species, which will be an important milestone in deepening or understanding of the molecular and genetic responses of organisms to local selection regimes and marine climate change. Given the Atlantic silverside’s ecological importance as an abundant forage fish along the American east coast and it’s rich history as a model organism in evolutionary and ecological studies, the annotated genome is the next logical step.

Even at hindsight, the plan still seems a little insane. But it worked. We indeed managed to catch spawning silversides at the Georgia site and then transported them immediately back to our Rankin Lab, which involved another 17 hours of driving back. After securing samples from Patchogue, we indeed managed to cross single parents from each site to produce full-sib crosses that will later be used to produce what geneticist call a linkage map. Other across and within-population crosses will be used to study gene expression at two different temperatures or raise adults for producing an F2 generation.

The silverside larvae are currently well, feeding, and growing up nicely. We all cross fingers for this enterprise to end in good samples and a step forward for genetic studies on a marine fish.