Publications & Presentations

[Lab news] Hannes & colleagues organize a Virtual Town Hall

23 June 2020. It’s been a remarkable day. A remarkable few months of preparation. But on this Tuesday in June, more than 250 people from all over the world logged in to a UConn WebEx Event organized by Hannes Baumann, Eric Schultz, Jacqueline Webb, Paul Anderson and Jon Hare. The event, billed as the “1st Virtual Larval Fish Science Town Hall” was of course a product of the strange and challenging times we live in right now. A consequence of almost a year of painstaking preparations for the 44th Larval Fish Conference in Mystic, CT … eclipsed by the COVID-19 pandemic that made having a physical science conference impossible.

Number of attendees per minute throughout the day. Science sessions were followed by 120-170 attendees worldwide.
Network Mentors

The Virtual Town Hall gave 16 speakers from around the world the opportunity to communicate their science, while providing a forum for the community to interact. The Early Career Committee of the AFS Early Life History Section contributed as well, organizing a round table discussion led by Kelsey Swieca with Chris Chambers, Jackie Webb, and Peter Konstantidinis. Individual networking meetings – although hobbled initially by technology – were held after the meeting between senior and early career researchers.

And best of all – more than 40 people participated in a picture contest, contributing stunning images of larval fish or larval fish science.

For more information, speaker bios’s, talk titles, abstracts and even some video please visit the event website

Some of our personal favorites among the best larval fish picture submissions

Mike Bartick | Ribbon fish
Irene Middleton | A diver checks out a juvenile flying fish at the Poor Knights Islands in New Zealand
Suzan Meldonian | Cyclopsetta fimbriata, photographed in situ along Gulf Stream Current, SE Florida
Winner – Kerryn Parkinson | Mola sp – a larval sunfish collected off New South Wales, Australia.
Gabriel Monteiro | Caulolatilus chrysops larvae cleared and stained. This specimen belongs to ColBIO USP biological collection.
Harvey Walsh | Bothus larvae sorted at sea from a bongo net tow collected during the summer of 2017 aboard the NOAA Ship Gordon Gunter.
Chris Murray | Wild Pacific herring spawn from Skagit Bay, WA (~72 h old). Note the flat edge of the egg where it was adhered to sea grass.
Henrique Grande | Post-larval reef fish Acanthurus coeruleus Bloch & Schneider, 1801 collected in 2015 using light traps in the Bay of Tamandaré, Brazil.

[New Publication] Fish and Fisheries publishes review of sand lance!

20 March 2020. We are happy to announce that the prestigious journal Fish & Fisheries just published a comprehensive review about the role of sand lance in the Northwest Atlantic Shelf ecosystem. The article, which came out of a workshop on this topic three years ago, reviews the the current state of knowledge about these enigmatic and important forage fish and urges continued efforts to better understand their role in the ecosystem and sensitivity to climate stressors.

SL beam trawl_credit HB
Sand lance caught on Stellwagen Bank in November 2014

The publication of this article was featured by UConn Today on 24 March 2020.

This work represents the first comprehensive assessment of this important forage fish in the Northwest Atlantic, though similar efforts have been carried out in the Pacific Northwest and Europe. In the Atlantic, sand lance are observed to be a significant food source for the federally endangered Roseate tern, Atlantic sturgeon and cod, Harbor and Grey seals and Minke and Humpback whales. “This paper is a call to our peers and colleagues that there is a big gap in knowledge, and to bring more attention to these species as unmanaged forage fish,” says Staudinger.

Staudinger, M., Goyert, H., Suca, J., Coleman, K., Welch, L., Llopiz, J., Wiley, D., Altman, I., Applegate, A., Auster, P., Baumann, H., Beaty, J., Boelke, D., Kaufman, L., Loring, P., Moxley, J., Paton, S., Powers, K., Richardson, D.E., Robbins, J., Runge, J., Smith, B.E., Spiegel, C., and Steinmetz, H. (2020)
The role of sand lances (Ammodytes sp.) in the Northwest Atlantic Ecosystem: a synthesis of current knowledge with implications for conservation and management
Fish and Fisheries (published online 20 March 2020)

[New Publication] MEPS publishes Julie’s Ms research on silverside otoliths

12 December 2019. We are happy to announce that Marine Ecology Progress Series just published our latest paper on Atlantic silversides, but this time not an experimental but a field study! During her time in our lab, Julie Pringle investigated the otolith microstructure of young-of-year silversides, finding intriguing patterns about differential growth in males and females that likely result in sex-selective survival during their growing season. Congratulations, Julie, well done!

Pringle, J.W. and Baumann, H. (2019) Otolith-based growth reconstructions in young-of-year Atlantic silversides (Menidia menidia) and their implications for sex-selective survival. Marine Ecology Progress Series 632:193-204

This graph shows reconstructed hatch distributions of male and female Atlantic silversides sampled in fall 2015. Counting daily otolith increments, young-of-year fish caught in October could be reliably aged, whereas those from November and December where likely underaged because water temperatures had already decreased below their growth threshold. This graph compbines previous knowledge, environmental monitoring and results of otolith microstructure analysis.

From the abstract:

“We examined the utility of otolith microstructure analysis in young-of-year (YoY) Atlantic silversides Menidia menidia, an important annual forage fish species along the North American Atlantic coast. We first compared the known hatch window of a local population (Long Island Sound, USA) to otolith-derived hatch distributions, finding that YoY collected in October were reliably aged whereas survivors from November and December were progressively under- aged, likely due to the onset of winter ring formation. In all collections, males outnumbered fe- males, and both sexes had bimodal size distributions. However, while small and large females were almost evenly represented (~60 and ~40%, respectively), over 94% of all males belonged to the small size group. We then examined increment widths as proxies for somatic growth, which suggested that bimodal size distributions resulted from 2 distinct slow- and fast-growing YoY phe- notypes. Length back-calculations of October YoY confirmed this, because fast- and slow-growing phenotypes arose within common bi-weekly hatch intervals. We concluded that the partial sexual size dimorphism in this population resulted largely from sex-specific growth differences and not primarily from earlier female than male hatch dates, as predicted by the well-studied phenome- non of temperature-dependent sex determination (TSD) in this species. Furthermore, observed sex ratios were considerably less male-biased than reconstructed thermal histories and published laboratory TSD values predicted. Assuming that selective mortality is generally biased against slower growing individuals, this process would predominantly remove male silversides from the population and explain the more balanced sex ratios at the end of the growing season.”

[New Publication] IUCN published ocean deoxygenation report!

9 December 2019. During the COP25 summit in Madrid, the International Union for Conservation of Nature (IUCN) released its latest comprehensive report titled “Ocean deoxygenation: everyone’s problem” that compiles the current evidence for the ongoing, man-made decline in the oceans oxygen levels. The 588 page, 11 chapter wake-up call to these detrimental changes was produced by leading experts in the field. We are happy to announce that Hannes is one of the many authors of this document, co-authoring chapter 6 “Multiple stressors – forces that combine to worsen deoxygenation and its effects“.

From the executive summary:

“The equilibrium state of the ocean-atmosphere system has been perturbed these last few decades with the ocean becoming a source of oxygen for the atmosphere even though its oxygen inventory is only ~0.6% of that of the atmosphere. Different analyses conclude that the global ocean oxygen content has decreased by 1-2% since the middle of the 20th century. Global warming is expected to have contributed to this decrease, directly because the solubility of oxygen in warmer waters decreases, and indirectly through changes in the physical and biogeochemical dynamics.”

From the summary of chapter 6:

  • Human activities have altered not only the oxygen content of the coastal and open ocean, but also a variety of other physical, chemical and biological conditions that can have negative effects on physiological and ecological processes. As a result, marine systems are under intense and increasing pressure from multiple stressors.
  • The combined effects of ‘stressors’ can be greater than, less than, or different from the sum of each stressor alone, and there are large uncertainties surrounding their combined effects.
  • Warming, acidification, disease, and fisheries mortality are important common stressors that can have negative effects in combination with low oxygen.
  • Warming, deoxygenation, and acidification commonly co-occur because they share common causes. Increasing carbon dioxide (CO2) emissions simultaneously warm, deoxygenate, and acidify marine systems, and nutrient pollution increases the severity of deoxygenation and acidification.
  • A better understanding of the effects of multiple stressors on ocean ecosystems should improve the development of effective strategies to reduce the problem of deoxygenation and aid in identifying adaptive strategies to protect species and processes threatened by oxygen decline.


Access the full report from

[New Publication] Scientific Reports publishes fluctuating CO2 x O2 paper!


3 December 2019. We are happy and proud to share that Scientific Reports has published our latest research on the effects of fluctuating CO2 × O2 environments on the early life stages of Atlantic Silversides. The paper synthesizes findings of two years and four separate experiments – all conducted in our automated larval fish rearing system – to answer the question how current and future diel and tidal fluctuations in CO2 and O2 affect the survival and growth of silverside embryos and larvae.

The paper is a great demonstration of the vast capabilities of our system to simulate non-static conditions, which is a frontier in climate change research. Congrats to Emma Cross for pulling all the complex data together!

Cross, E.L., Murray, C.S., and Baumann, H. (2019)
Diel and tidal pCO2 × O2 fluctuations provide physiological refuge to a coastal forage fish
Scientific Reports 9:18146


From the Abstract:

“Static low DO conditions severely decreased embryo survival, larval survival, time to 50% hatch, size at hatch and post-larval growth rates. Static elevated pco2 did not affect most response traits, however, a synergistic negative effect did occur on embryo survival under hypoxic conditions (3.0 mg L−1). Cycling CO2 × DO, however, reduced these negative effects of static conditions on all response traits with the magnitude of fluctuations influencing the extent of this reduction. This indicates that fluctuations in pco2 and DO may benefit coastal organisms by providing periodic physiological refuge from stressful conditions, which could promote species adaptability to climate change.”

The source data for this publication are openly available (and citable) from the BCO-DMO database. Head to Products -> Research Data to access them!

[New Publication] Conservation Physiology publishes our first sand lance paper!

21 November 2019. We are excited to announce the Chris Murray‘s paper on the unusual, high sensitivity of early life Northern sand lance to acidification and warming has just been published in the journal of Conservation Physiology! This is the first publication of our extensive work on this enigmatic species.

Sand lance species play a key ecological role in most temperate to polar shelf ecosystems of the northern hemisphere, but they have remained unstudied with respect to their sensitivity to predicted future CO2 levels in the ocean. For the past three years (2016 – 2018), we have sampled and spawned with northern sand lance (Ammodytes dubius) from Stellwagen Bank National Marine Sanctuary and subsequently reared their embryos under factorial CO2 x temperature conditions to hatch and early larval stages. Our results were striking, in all years, high CO2 conditions severely reduced embryo survival up to 20-fold over controls, with strong synergistic reductions under combined high CO2 and temperature conditions. High CO2 also delayed hatching, reduced remaining endogenous energy reserves at hatch, and in combination with higher temperatures, reduced embryonic growth.

Indeed, given the observed effect sizes, northern sand lance might be the most CO2 sensitive fish species tested to date.

[Presentation] Callie presents research at the Graduate Climate Conference

Callie presenting her poster to other graduate students
November 8, 2019. Callie Concannon joined other graduate students of the Department of Marine Sciences to present her thesis research at the Graduate Climate Conference in Woods Hole, MA. She presented a poster entitled “Long-term CO2 and temperature effects on fecundity and oocyte recruitment in the Atlantic silverside
Her preliminary findings can be summarized as:

Warmer, more acidic environments impact reproductive output in the Atlantic silverside

The participants of the Graduate Climate Change conference in November 2019


[Presentation] Hannes gives first NECAN webinar on sand lance CO2 sensitivity

10 September 2019. Hannes started of the new 2019 NECAN Sea Grant Webinar Series with a presentation of our past years of research on the sensitivity of Northern sand lance (Ammodytes dubius) to ocean acidification and warming. The purpose of this webinar series is to highlight four projects funded through NOAA Sea Grant following the release of the NECAN paper published in Oceanography Magazine in 2015, “Ocean and Coastal Acidification off New England and Nova Scotia.”

Thanks to the more than 50 people who attended the webinar. If you have missed it, it’s accessible for free online. See below.

[New publication] Science publishes our silverside genetic study!

Fishing changes silverside genes
1 August 2019. We are overjoyed that our paper on genetic changes in experimental silverside populations subjected to strong size-selective fishing has just been published by Science!

Therkildsen, N.O., Wilder, A.P., Conover, D.O., Munch, S.B., Baumann, H., and Palumbi, S.R. (2019)
Contrasting genomic shifts underlie parallel phenotypic evolution in response to fishing
Science 365:487-490
Related perspective: Fishing for answers Science 365: 443-444 | Cornell Press release | UConn Press release

Over recent decades, many commercially harvested fish have grown slower and matured earlier, which can translate into lower yields. Scientists have long suspected that rapid evolutionary change in fish caused by intense harvest pressure is the culprit.

Now, for the first time, researchers have unraveled genome-wide changes that prompted by fisheries – changes that previously had been invisible, according to a study published in Science by a team of researchers including Hannes Baumann, UConn assistant professor of Marine Sciences, who collaborated with researchers at Cornell University, the University of Oregon, the National Marine Fisheries Service, and Stanford University.

In unprecedented detail, the study shows sweeping genetic changes and how quickly those changes occur in fish populations extensively harvested by humans, says Baumann.

“Most people think of evolution as a very slow process that unfolds over millennial time scales, but evolution can, in fact, happen very quickly,” said lead author Nina Overgaard Therkildsen, Cornell assistant professor of conservation genomics in the Department of Natural Resources.

Observed shifts in adult size. Trends across generations in mean length at harvest (standardized as the difference from the mean of the control populations in each generation) ± the standard deviations in up-selected (blue shades), down-selected (yellow and orange shades), and control populations (green shades).

The all-pervasive human meddling in our planet’s affairs undeniably reached the genetic make-up of its organisms.
— Hannes Baumann, UConn.

In heavily exploited fish stocks, fishing almost always targets the largest individuals. “Slower-growing fish will be smaller and escape the nets better, thereby having a higher chance of passing their genes on to the next generations. This way, fishing can cause rapid evolutionary change in growth rates and other traits,” said Therkildsen. “We see many indications of this effect in wild fish stocks, but no one has known what the underlying genetic changes were.”

Therkildsen and her colleagues took advantage of an influential experiment published back in 2002. Six populations of Atlantic silversides, a fish that grows no bigger than 6 inches in length, had been subjected to intense harvesting in the lab. In two populations, the largest individuals were removed; in another two populations, the smallest individuals were removed; and in the final two populations, the fishing was random with respect to size.

After only four generations, these different harvest regimes had led to evolution of an almost two-fold difference in adult size between the groups. Therkildsen and her team sequenced the full genome of almost 900 of these fish to examine the DNA-level changes responsible for these striking shifts.

The team identified hundreds of different genes across the genome that changed consistently between populations selected for fast and slow growth. They also observed large linked-blocks of genes that changed in concert, dramatically shifting the frequencies of hundreds of genes all at the same time.

Surprisingly, these large shifts only happened in some of the populations, according to the new paper. This means that there were multiple genomic solutions for the fish in this experiment to get either larger or smaller.

“Some of these changes are easier to reverse than others, so to predict the impacts of fisheries-induced evolution, it is not enough to track growth rates alone, we need to monitor changes at the genomic level,” said Therkildsen.

When the experiment was originally conducted nearly two decades ago by co-authors David Conover, professor of biology at the University of Oregon, and Stephan Munch of the National Marine Fisheries Service, the tools to study the genomic basis of the rapid fisheries-induced evolution they observed were not available. Fortunately, Conover and Munch had the foresight to store the samples in a freezer, making it possible to now return – armed with modern DNA sequencing tools – and reveal the underlying genomic shifts.

Research like this can assess human impacts, and improve humanity’s understanding of “the speed, consequences and reversibility of complex adaptations as we continue to sculpt the evolutionary trajectories of the species around us,” Therkildsen said.

“What’s most fascinating about this is that life can find different genetic ways to achieve the same result. In this study, two experimental populations evolved smaller body size in response to the selective removal of the largest fish, which is what most trawl fisheries do. However, only by looking at the genetic level we demonstrated that these two experimental populations evolved via two completely different genetic paths,” says Baumann.

The good news for the Atlantic silversides is that the fisheries selection was able to tap into the large reservoir of genetic variation that exists across the natural range of this species from Florida into Canada, said Therkildsen: “That genetic bank fueled rapid adaptation in the face of strong fishing pressure. Similar responses may occur in response to climate-induced shifts in other species with large genetic variability.”

“Scientists have coined the term Anthropocene in recognition of the all-pervasive human alteration of the earth’s climate, oceans, and land. No matter how ‘pristine’ a piece of nature may look to us at first glance, examine it thoroughly enough and you will find a trace of human in it. Take a cup of water from the middle of Pacific Ocean and a handful of sand from a ‘pristine’ beach – and you will find little plastic particles under the microscope,” says Baumann. “The parallel to this study is that the all-pervasive human meddling in our planet’s affairs now undeniably reached the genetic make-up of its organisms. Today’s fishes may superficially look the same as always, but their genes are not. They bear witness to human alteration.”

In addition to Baumann, Therkildsen, Conover, and Munch, co-authors included former Cornell postdoctoral researcher Aryn P. Wilder, now a researcher at San Diego Zoo Institute for Conservation Research; and Stephen R. Palumbi, Stanford University.

This work was funded by the National Science Foundation.

[Lab news] Hannes, Chris and Emma at the 43rd Larval Fish Conference!


Chris, Hannes, and Emma

Beautiful view from Mallorca’s most northern point, Cap Formentor

Peter Gronkjaer, Dominique Robert, Arild Folkvord, Hannes during the conference tour
25 May 2019. Hannes, Chris and Emma attended this years 43rd Annual Larval Fish Conference in Palma de Mallorca, Spain. The event was hosted by IMEDEA’s Ignacio Catalan and colleagues and was attended by more than 140 participants. As usual, the small but international make-up of the meeting and made it into a memorable event of science, networking and seed for potential future collaborations. While Chris reported on our past experiments on factorial CO2 by O2 effects on Atlantic silverside early life stages, Emma presented the latest findings on our silverside experiments using computer-controlled CO2 and O2 co-fluctuations.

Before and after the conference, there was also some time to explore the beautiful island of Mallorca with its breathtaking mountain scenery and turquoise coves.

Chris and Emma’s presented:

  • Murray, C.S., Cross, E.L., and Baumann H. A factorial evaluation of the combined effects of acidification and hypoxia in Atlantic silverside offspring. Talk.
  • Cross, E.L., Murray, C.S. and Baumann H.Diel and tidal cycles of CO2 and dissolved oxygen conditions provide physiological refuge to a coastal forage fish, Menidia menidia under acidification and hypoxia. Talk.

A special thanks to Lucas and Callie for holding the fort at home!

Cala des Moro

Martha Moyano and Hannes

Cap Formentor