Lucas and Hannes celebrating the successful thesis presentation
Monday, November 22nd 2021. Big and heartfelt congratulations to Lucas Jones, who presented his Master thesis to his peers at the institute and colleagues national and international. Well done, Lucas!
A link to his recorded presentation will be posted here soon.
The UConn Department of Marine Sciences
Presents a Master’s Thesis Presentation by
Lucas Jones
B.A., University of Connecticut, 2018
4:00 p.m., Monday, November 22, 2021
Marine Sciences Building, Seminar Room 103
Using Low-Coverage, Whole Genome Sequencing to Study Northern Sand Lance (Ammodytes dubius) Population Connectivity in the Northwest Atlantic
Northern sand lance (Ammodytes dubius) are key forage fish in Northwest Atlantic (NWA) shelf ecosystems, where they exclusively occur on coarse-grain, offshore sand banks. This patchy occurrence may result in genetically more fragmented, less connected populations, but traditional morphological or genomic approaches have so far been unsuccessful in fully resolving the species’ population structure and connectivity. My study pursued an alternative genomic approach, using low-coverage, whole genome sequencing (LcWGS) to address these important questions. I extracted DNA from 273 A.dubius specimens collected by collaborators from sevenregions across the species geographical range, from Greenland to New Jersey, USA. From LcWGS data, I identified 11,558,126 single nucleotide polymorphisms (SNPs) that allowed quantifying genetic differentiation between populations (FST), thereby revealing the genetic structuring of populations throughout the NWA. Despite the potentially homogenizing influence of the general north to south ocean circulation, I found a clear genetic break around Nova Scotia that delineated a northern from a southern A. dubius supergroup. Only within the southern supergroup, genetic distances increased with the geographic distance between sample sites. At the focal site of Stellwagen Bank (southern Gulf of Maine), A. dubius samples collected over several years (2014 – 2019) revealed small but significant temporal genetic differences that imply varying occupation of this offshore habitat by genetically different sand lance contingents. Inclusion of samples from the inshore congener A. americanus confirmed the clear genetic separation between both species and further determined that all sand lance caught on Stellwagen Bank are exclusively A. dubius. Overall, my work suggests the existence of two spatially distinct A. dubius populations with little ‘realized’ connectivity, which is critical knowledge to aid protection and management of offshore marine resources.
2 November 2021. We are happy report that the ICES Journal of Marine Science just published the last major experimental paper on Atlantic silverside CO2-sensitivity from our lab. Callie Concannon and co-authors report on two complementary, long-term rearing trials in 2015/16 and 2018/19, where silverside juveniles or newly fertilized embryos were reared under contrasting temperature and CO2 conditions to maturity. This revealed negative effects of high CO2 conditions on female fecundity, but only at the warm, not the cold temperature treatments (Fig. below). Our study and its data are novel, because they were generated by the first whole-life CO2 rearing experiment of a fish and are the first empirical fecundity effects shown for a broadcast-spawning fish species.
The paper is also special to us, because its publication marks the erstwhile conclusion of our yearlong, NSF-funded efforts (OCE#1536165) to understand the CO2 sensitivity and its mechanisms in this important forage fish and long-standing model in fish ecology and evolution. The project ran from 2015 - 2020, produced 15 publications, 2 book chapters, and over 40 presentations, while furthering the careers of a post-doc, a PhD student, 5 Master students and over 10 undergraduates.
Reposted from UConn Today | August 26, 2021 | By Elaina Hancock
The world’s oceans are becoming increasingly stressful places for marine life, and experts are working to understand what this means for the future. From rising temperatures; to acidification as more carbon enters the waters; to changes in the currents; the challenges are multifaceted, making experiments and projections difficult.
Copepods are small marine animals that are abundant, widely dispersed, and serve as major structural components of the ocean’s food web. A team of scientists from the University of Connecticut, Jinan University in China, and the University of Vermont have found that a species of copepod called Acartia tonsa can cope with climate change, but at a price. Their research was just published in Nature Climate Change.
“We have this problem of climate change and in the ocean, it is a multi-dimensional problem because it’s not just the warming, the ocean is becoming more acidic where pH is going down as we pump more CO2, into the atmosphere. Organisms need to cope, they are under more stress, and things are happening very fast,” says Hans Dam, UConn professor of Marine Sciences.
Dam explains that previous studies suggest some animals will be more sensitive than others to changes like shifts in pH. Prior studies with copepods showed they are not particularly sensitive to pH changes, but Dam points out those studies were only done with a single generation, or few generations, to a single stressor and shows the ability to acclimate rather than adapt. This new study not only looks at adaptation across 25 generations, it also considered both ocean warming and acidification (OWA), something that few studies have done until now.
“If you want to study the long-term effects, you must consider the fact that animals will adapt to changes or stress in the environment, but to do that you have to do the right experiments. Most people do not do those experiments with animals because it takes a long time to study in multiple generations.”
The researchers looked at fitness, or the ability of a population to reproduce itself in one generation, and how fitness would change through generations in increased OWA conditions. The first generation exposed to new OWA conditions suffered extreme reductions of over 50% of population, says Dam. It was as if OWA was a big hammer that greatly reduced the population fitness. By the third generation, the population seemed to have mostly recovered. However, by the 12th generation, the researchers began to see declines once again.
Though the copepods were able to adapt, the adaptation was limited because fitness was never fully recovered, and the researchers suspect there are some antagonistic interactions at play, leading to a tug of war situation between adaptation to warming and to acidification. These antagonistic interactions complicate predicting what responses can be expected.
James deMayo, co-author and UConn Ph.D. student adds, “Perhaps what’s important to emphasize with this project is that the effects of warming combined with acidification are not the same for every generation or organism that is adapting to that environment. That’s suggested by the data and why the adaptation is limited. While within intermediate generations, organisms might be very well adapted, in later generations, the effects of warming and acidification start to behave differently on the population. That’s one of the exciting parts about the research. It’s not a static, expected result for how organisms or their populations are going to continue to grow or decay.”
For example, deMayo explains, if you took individuals in later generations that had adapted to the experimental OWA conditions and placed them into the conditions of today’s ocean, they would not fare as well.
“That’s one negative consequence, that ability to not tolerate environmental shifts is a cost and an unpredicted consequence for evolutionary adaptation in a lot of systems, not just in copepods,” says deMayo.
Changes in egg production rate (EPR) and hatching success (HS) during the transgenerational experiment
The researchers point out that studies looking at single stressors run the risk of making overly simplified inferences about an organism’s ability to adapt, an especially risky proposition when making conclusions about such an integral component of the food web as copepods.
“Particularly when you involve living organisms, there are complexities that you can’t predict,” says Dam. “A priori, you might make the predictions, but you have no certainty that they’re going to unfold that way. In biology these are referred to as ‘emergent properties’ or things that you cannot predict from what you know in advance and this research is a good example.”
In thinking back to the hammer comparison, Dam says impacts in the copepod population have ripple effects through the whole food web and beyond.
“If fitness decreases by say, 10%, down the road we will have a 10% decrease in population size and since these animals are the main food source for fish, a 10% decrease in the world fishery is pretty significant,” says Dam. “And this is really the best-case scenario since in the lab, they’re essentially living in hotel-like conditions so that 10% isn’t taking into consideration other factors like predation or disease. In the real world we could see fitness recovery is actually much worse.”
Additionally, Dam points out another implication is that copepods sequester CO2 and reductions in their numbers reduce the ocean’s carbon sequestration capabilities, bad news at a time when more carbon sequestration is needed.
While the research offers promise for rapid adaptation, it is a reminder that as with many things in nature there’s a catch.
“There is some welcoming news, that yes, there is a recovery of fitness but there is also sobering news that the evolutionary rescue is not complete. There’s no such thing as a free lunch,” says Dam.
Groton, CT 24-26 June 2021. The long awaited and anxiously prepared virtual 44th Larval Fish Conference was held, featuring more than 240 participants from 28 countries. 58 scientific talks, including 3 keynote lectures were given via Cisco’s WebEx platform, whereas networking activities such as poster presentations, ‘Meet the Speaker’ events, and Mentor hours used the innovative Gatherly platform. The technology was working out well, the preparation paid off, and delegates were overall enthusiastic about this virtual alternative, which was forced on us by Covid-19, but may have shown us new ways and concepts to broaden the societies reach and equality.
Special thanks go to the scientific steering committee Eric Schultz, Jacqueline Webb, and Paul Anderson. Lauren Schaller, Anne Hill, Harley Erickson, and Kate Copeland from UConn’s conference services did a great job as well preparing and running parts of the events. Support came from NOAA’s Northeast Fisheries Science Center.
27 July 2020. Big and proud congratulations to Chris Murray, who published his last big chunk of data from his PhD research on the effects of marine climate change on coastal marine fish. The publication in PLOS One synthesized 3 years of multiple, long-term experiments on Atlantic silversides (Menidia menidia) demonstrating consistent negative growth effects on high CO2 conditions. However, sometimes it takes more than just looking at means and standard deviations to elucidate these effects. Hence, in this paper, shift functions analyzing the different percentiles of distributions are employed.
As humans continue to send large quantities of carbon into the atmosphere, much of that carbon is absorbed by the ocean, and UConn researchers have found high CO2 concentrations in water can make fish grow smaller.
Researchers Christopher Murray PhD ’19, now at the University of Washington, and UConn Associate Professor of Marine Sciences Hannes Baumann have published their findings in the Public Library of Science (PLoS One).
“The ocean takes up quite a bit of CO2. Estimates are that it takes up about one-third to one-half of all CO2 emissions to date,” says Murray. “It does a fantastic job of buffering the atmosphere but the consequence is ocean acidification.”
Life relies on chemical reactions and even a slight change in pH can impede the normal physiological functions of some marine organisms; therefore, the ocean’s buffering effect may be good for land-dwellers, but not so good for ocean inhabitants.
Baumann explains that in the study of ocean acidification (or OA), researchers have tended to assume fish are too mobile and tolerant of heightened CO2 levels to be adversely impacted.
“Fish are really active, robust animals with fantastic acid/base regulatory capacity,” says Murray. “So when OA was emerging as a major ocean stressor, the assumption was that fish are going to be OK, [since] they are not like bivalves or sea urchins or some of the other animals showing early sensitivities.”
The research needed for drawing such conclusions requires long-term studies that measure potential differences between test conditions. With fish, this is no easy task, says Baumann, largely due to logistical difficulties in rearing fish in laboratory settings.
“For instance, many previous experiments may not have seen the adverse effects on fish growth, because they incidentally have given fish larvae too much food. This is often done to keep these fragile little larvae alive, but the problem is that fish may eat their way out of trouble — they overcompensate – so you come away from your experiment thinking that fish growth is no different under future ocean conditions,” says Baumann.
In other words, if fish are consuming more calories because their bodies are working harder to cope with stressors like high CO2 levels, a large food ration would mask any growth deficits.
Additionally, previous studies that concluded fish are not impacted by high CO2 levels involved long-lived species of commercial interest. Baumann and Murray overcame this hurdle by using a small, shorter-lived fish called the Atlantic silverside so they could study the fish across its life cycle. They conducted several independent experiments over the course of three years. The fish were reared under controlled conditions from the moment the eggs were fertilized until they were about 4 months old to see if there were cumulative effects of living in higher CO2 conditions.
Murray explains, “We tested two CO2 levels, present-day levels and the maximum level of CO2 we would see in the ocean in 300 years under a worst-case emissions scenario. The caveat to that is that silversides spawn and develop as larvae and early juveniles in coastal systems that are prone to biochemical swings in CO2 and therefore the fish are well-adapted to these swings.”
The maximum CO2 level applied in the experiments is one aspect that makes this research novel, says Murray,
“That is another important difference between our study and other studies that focus on long-term effects; almost all studies to date have used a lower CO2 level that corresponds with predictions for the global ocean at the end of this century, while we applied this maximum level. So it is not surprising that other studies that used longer-lived animals during relatively short durations have not really found any effects. We used levels that are relevant for the environment where our experimental species actually occurs.”
Baumann and Murray hypothesized that there would be small, yet cumulative, effects to measure. They also expected fish living in sub-ideal temperatures would experience more stress related to the high CO2 concentrations and that female fish would experience the greatest growth deficits.
The researchers also used the opportunity to study if there were sex-determination impacts on the population in the varying CO2 conditions. Sex-determination in Atlantic silversides depends on temperature, but the influence of seawater pH is unknown. In some freshwater fish, low pH conditions produce more males in the population. However, they did not find any evidence of the high CO2 levels impacting sex differentiation in the population. And the growth males and females appeared to be equally affected by high CO2.
“What we found is a pretty consistent response in that if you rear these fish under ideal conditions and feed them pretty controlled amounts of food, not over-feeding them, high CO2 conditions do reduce their growth in measurable amounts,” says Murray.
They found a growth deficit of between five and ten percent, which Murray says amounts to only a few millimeters overall, but the results are consistent. The fish living at less ideal temperatures and more CO2 experienced greater reductions in growth.
Murray concludes that by addressing potential shortcomings of previous studies, the data are clear: “Previous studies have probably underestimated the effects on fish growth. What our paper is demonstrating is that indeed if you expose these fish to high CO2 for a significant part of their life cycle, there is a measurable reduction in their growth. This is the most important finding of the paper.”
This work was funded by the National Science Foundation grant number OCE #1536165. You can follow the researchers on Twitter @baumannlab1 and @CMurray187.
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.
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 lfc44.uconn.edu
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.
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.
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.
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!
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.”
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.
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!
“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!
