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Fishing changes silverside genes

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.

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.

A History of the R/V Connecticut

Prior to the launch of the original R/V Connecticut in 1998, the University had operated a former U.S. Army-Transport boat (a T-441) acquired from Scripps Institution in 1969 and renamed the R/V UConn. Because it had a limited capacity for research instrumentation, it only spent about 20 days per year at sea. To develop modern marine research, the Department of Marine Sciences (DMS) and the former Marine Sciences and Technology Center eventually proposed a purpose-built coastal research vessel.

In 1996, Roger Long and the Elliott Bay Design Group designed the R/V Connecticut followed by construction in the fall of 1997. J. Turner Cabaniss, our current Marine Operations Manager, was hired in 1998 as captain and to provide onsite supervision of the construction. The boat’s design and construction were funded by state economic development funds through a state agency called Connecticut Innovations in addition to a loan from the University. The original R/V Connecticut was a 76’ research vessel with 12 bunks and a small lab space. It was equipped for heavy-duty oceanographic research with features like a stern A-frame for lifting buoys and a deck crane. It could house 7 scientists and 5 crew members and spent about 125 days at sea a year; being repeatedly chartered by other research institutions and federal agencies including NOAA, Woods Hole Oceanographic Institution, and the University of Maine.

The vessel operates as a university service center that is largely self-supporting through funding from federal agencies, making it realistic for UConn to house the boat, charter it to other researchers, and use for DMS research. The R/V Connecticut is well traveled along the east coast, particularly in Long Island Sound and Gulf of Maine waters. It has even spent some time in the great lakes, when Dr. Bob Ballard chartered the vessel for ROV work in the Thunder Bay NOAA Marine Sanctuary. To support Ballard’s work, NOAA provided funds to incorporate dynamic positioning into the R/V Connecticut’s existing propulsion. Dynamic positioning works through a computer integration of the bow and stern thrusters to maintain the boat’s position above ground. For a small research vessel, this is an extraordinary feature.

However, more recently the ship’s limited bunk and lab space proved to be an obstacle for larger collaborations and research expeditions. According to Dr. James O’Donnell, this was apparent during projects like the LISICOS program (Long Island Sound Integrated Coastal Observing System, 2004-2006), a large interdisciplinary estuarine project with more than a dozen researchers involved. People had to be shuttled on and off the ship throughout an expedition to meet project needs. With funding from the Provost and the College of Liberal Arts and Sciences, the R/V Connecticut was refitted in 2017, with the addition of a 14′ mid-body extension, making it a 90’ vessel. The ship now holds double the lab space and 18 bunks for 5 crew members, a technician, and 12 scientists. The refitted boat is already benefiting DMS’s education program in the form of a graduate level course for ocean expeditions and will allow for greater collaboration opportunities at UConn and other marine research programs.

Read more about the recommissioning here

The R/V Connecticut out on an expedition,  Photo Credit: James O’Donnell
The R/V Connecticut,  Photo Credit: Turner Cabaniss

Where Are They Now? One Year After Avery Point

In 2018, seven graduate students from the Department of Marine Sciences completed their degrees, five with master’s and two with doctorates. We checked in a year later to see what they’ve been up to.

Michelle Fogarty landed a postdoctoral researcher position in Marine Energy Resource Characterization at the National Renewable Energy Laboratory in Boulder, Colorado. On the other side of the country, Ellen Johnson is in San Diego, California working as a content writer and science communicator. Check out her blog, currentseablog.com, to read some of her articles about sustainability and the ocean. After completing his undergraduate and master’s studies at UConn, Matthew Lacerra began his doctorate at Princeton University where he is studying paleo-oceanography in Dr. Daniel Sigman’s group. Almariet Palm scored a position as a Project Geologist with HRP Associates Inc in Farmington, Connecticut. Gihong Park conferred his doctorate and continued at Avery Point as a postdoctoral research associate with his PhD advisor, Dr. Hans Dam. Julie Pringle moved back to Martha’s Vineyard, Massachusetts and began working as a Field Science Coordinator for a local non-profit called the Great Pond Foundation. She commented on being back in the field, “after spending the majority of my graduate research in the lab, I’m really enjoying all the field work!”  Last but not least, Heidi Yeh started her doctorate studying oyster aquaculture at Rutgers University in New Jersey. She is “employing genetic techniques to promote sustainable seafood production.”

Some recent alumnae/i entered the next step in academia, while others moved into the work force. This just goes to show that a graduate degree from the Department of Marine Sciences can prepare you for a variety of career paths. It will be interesting to see where they wind up next!

 

Molly James

Getting to know our staff: Bob Dziomba – Machine Shop

After a 13-year stint working on nuclear reactors for the US Navy, Bob has been our marine research technician in the machine shop for 26 years. After Gary Grenier’s retirement in 2017, he now has to manage the workload in the shop himself. Bob simply describes his day-to-day job as “fix and repair,” which is an understatement. Without his skills, the Department of Marine Sciences (DMS) would be at a loss.

As a trained machinist, Bob has contributed to a majority of DMS research projects by helping faculty design, build, and test prototype equipment, while also maintaining and repairing it when it breaks. Earlier during his tenure, Bob also enjoyed servicing the departments’ small submersibles and remotely operated vehicles (ROV), which required particular care due to the nature of high-pressure equipment. Over the years, he helped shape the machine shop into the highly functional facility that it is today.

Major experimental setups like the flow-through system in the Rankin Seawater Lab were constructed with Bob’s input and hard work. Bob also helped building the Larval Fish Rearing System that allows experimental manipulations of water temperature, CO2 and oxygen levels to study potential effects of marine climate change on marine organisms. In Bob’s spare time, he helps other technicians with repairs on our marine vessels and teaching laboratories. Outside the machine shop, Bob’s friends and family value his mechanical skills.

DMS research operations rely on Bob’s expertise to construct prototypes and conserve functional equipment. As a department we fortunate to have such a skilled and caring technician.

 

Bob Dziomba in the machine shop
The automated Larval Fish Rearing System in Rankin Lab. Photo credit: Hannes Baumann

The First Ocean Expedition Course

On October 17-19, 2018, six graduate students from Department of Marine Sciences participated in the first ocean expedition course ever offered by the university. Students have long lobbied for a course that teaches ship-based oceanographic methods, and after much logistical and scientific preparation by faculty, staff, and students, the team set sail aboard the R/V Connecticut. The objective of the cruise was to sample oceanographic data from Long Island Sound outwards to the continental shelf break. The team was led by Professors Jim O’Donnell, Frank Bohlen, Samantha Siedlecki, and Hannes Baumann, with research support from Kay Howard-Strobel and David Cohen. The student participants were Molly James, Jimmy deMayo, Alec Shub, Michael Mathuri, Amin Ilia, and Callie Concannon.

The course was designed to give students a chance to experience data collection aboard a research vessel from all oceanographic disciplines. Students oversaw around-the-clock deployment of CTD/rosette casts, sediment grabs/cores, Methot net trawls, and vertical plankton tows at a total of 7 stations. On board the ship, students analyzed pH and prepared samples for later analysis. Unfortunately, weather conditions limited the trip to just 36 hours instead of the intended 48 hours, but the team still managed to collect the data they intended to analyze. With the help of Dr. Claudia Koerting, students used analytical spectroscopy techniques to measure dissolved oxygen, nutrients, and chlorophyll concentration. After all the data was analyzed, the final cruise report was constructed, and the results were presented the following semester at the weekly Brown Bag seminar series hosted by the Marine Sciences Graduate Students. This course provided students with great hands-on experience and introduced the students to areas of oceanography previously beyond their knowledge levels.

To access all the data that was collected during the expedition, log on to ftp://nopp.dms.uconn.edu/ocean_course.

The graduate student class with faculty

Nighttime sampling station

 

Jimmy deMayo

Climate change is rapidly reshaping the Long Island Sound, as citizen science data shows

DMS scientists digitized old records from Project Oceanology and discovered a treasure chest of data on warming oceans and shifting marine populations

For more than 45 years, the non-profit Project Oceanology on UConn’s Avery Point Campus has inspired middle and high school students to care about the ocean. Students learn how measure water temperature, pH and oxygen and sift through trawl catches of fish and crabs that many have never seen for real before. Thereby, Project Oceanology did something else of enormous value: it routinely collected data for decades. Steel cabinets swallowed the student’s records and obliviously guarded this growing treasure.

In 2016, Master’s student Jacob Snyder and Professor Hannes Baumann decided to lift the treasure. They painstakingly entered every recording from every data sheet they found, anxious for the time, when the data would finally speak. The study, published in April 2019, shows how rapidly temperatures in eastern Long Island Sound have increased over the past four decades (+0.45C per decade), at a rate four times faster than in the global ocean (Levitus et al. 2000). This is also true for the larger Northwest Atlantic shelf, of which Long Island Sound is a part, where some areas have warmed faster than 99% of all ocean waters on earth (Pershing et al. 2015).

Another symptom of marine climate change is ocean acidification, measured as a pH slow decline in the ocean which swallows the increasing amounts of carbon dioxide emitted by humans (Doney et al. 2009). In coastal waters, nutrient pollution (e.g., nitrogen, phosphate) from sewers, waste water treatment plants and fertilizer runoff can intensify acidification. The Project Oceanology data revealed that pH declined much more rapidly in Long Island Sound than globally, which could imply worsening conditions for shellfish farmers.

Trawl records were particularly telling, showing that cold-water species such as American lobster, rock crab or winter flounder became less frequent over time. This is exactly what long-time instructors at Project Oceanology said they had noticed too. Lobsters once supported a proud fishery in Long Island Sound, but warmer, more acidic waters, shell disease, and overfishing have now decimated them to nearly complete absence.

However, a winner of dubious qualities emerged too. Over the past decades, spider crabs have moved into Long Island Sound from the south and are now the dominant crab species in the trawls. Spider crabs are no equivalent to lobsters, humans do not like to eat them and they can alter the ecosystem, as they eat much more plant-based food than lobsters.

Long Island Sound has been rapidly changing, and the data collected by generations of middle and high school students re-affirmed this. Other time-series from Norwalk Harbor and the Connecticut Department of Energy and Environmental Protection (CTDEEP) have shown similar trends. It is therefore undeniable that marine climate change is happening right now in Long Island Sound.

 

Snyder, J., Whitney, M., Dam, H., Jacobs, M., and Baumann, H. Citizen science observations reveal rapid, multi-decadal ecosystem changes in eastern Long Island Sound. Marine Environmental Research 146:80-88

Contacts/Links:

Hannes Baumann, Assistant Professor, Department of Marine Sciences, University of Connecticut, 1080 Shennecossett Road, 06340 Groton, CT, hannes.baumann@uconn.edu, Twitter: @Baumannlab1, 860-405-9297

Project Oceanology: 1084 Shennecossett Road, 06340 Groton, CT www.oceanology.org, Twitter: @Proj_Oceanology

 

Department Award and Publication Highlights

Graduate Student Publications:

 

Ilia, A., & O’Donnell, J. (2018). An Assessment of Two Models of Wave Propagation in an Estuary Protected by Breakwaters. Journal of Marine Science and Engineering, 6(4), 145. doi:10.3390/jmse6040145

 

Hedley, J.D.; Mirhakak, M.; Wentworth, A.; Dierssen, H.M. Influence of Three-Dimensional Coral Structures on Hyperspectral Benthic Reflectance and Water-Leaving Reflectance. Appl. Sci. 2018, 8, 2688.

 

Sasaki, M., Hedberg, S., Richardson, K., & Dam, H.G. (2019). Complex interactions between local adaptation, phenotypic plasticity and sex affect vulnerability to warming in a widespread marine copepod. R. Soc. open sci., 6(3). https://doi.org/10.1098/rsos.182115

 

Faculty Awards:

 

Sandra Shumway was awarded the FUCOBI Foundation Award for Outstanding Contributions by Women in Aquaculture, the APEX Award for Publishing Excellence (Journal of Shellfish Research) and the Association Trends Gold Award (Journal of Shellfish Research).

 

Senjie Lin (PI) and Huan Zhang (Co-PI) received a two-year grant from the Gordon and Betty Moore Foundation to develop a CRISPR/Cas9 genome editing technique for studying dinoflagellate gene functions. Titled “Moving from transformation to CRISPR/Cas9 gene knockout for dinoflagellates.”

 

Michael Whitney, has been awarded a Fulbright fellowship at the University of Iceland, set to start in 2020.

Highlights:  https://clas.uconn.edu/2019/03/18/marine-sciences-professor-awarded-fulbright-fellowship/

 

Samantha Siedlecki was awarded a NCAR (National Center for Atmospheric Research) fellowship.

Highlights: https://today.uconn.edu/school-stories/marine-knowledge-is-power/#

 

 

Student Awards:

 

Jo-Marie Kasinak was awarded the Torrey Botanical Society’s Greller Graduate Student Research Award for the Conservation of Local Flora and Ecosystems.

 

Incoming graduate student, Monica Garity was awarded a Harriott Fellowship through the UConn Graduate School.

 

Amin Ilia, Matt Sasaki, and Brittany Sprecher received awards from the William A. Lund, Jr. Fellowship in Marine Sciences and the Andrew J. Nalwalk Memorial Award.

 

Tyler Griffin, Yipeng He, Amin Ilia, Molly James, Ewaldo Leitao, Michael Mathuri, Patricia Myer, Sean Ryan, Matt Sasaki, Emma Shipley, Sue Smith, and Mengyang Zhou received UConn Graduate School predoctoral fellowship awards through the department of Marine Sciences.

 

Graduate students Halle Berger, Sean Ryan, and Lingjie Zhou received awards from the John Rankin Scholarship Fund, Department of Ecology and Evolutionary Biology.

 

Marine Knowledge is Power

Marine Knowledge is Power: Predicting Ocean Resources for Coastal Communities

Big ocean changes are happening, but global trends may not accurately represent what happens in coastal regions. With support from the National Center for Atmospheric Research (NCAR), UConn marine scientist Samantha Siedlecki’s research aims to help address this gap in knowledge.

Through a new NCAR program launching this summer, Siedlecki will couple global models with regionally refined systems so that coastal communities can better predict what biogeochemical changes their waters might face in the future. Her NCAR project focuses specifically on coastal biogeochemistry and health metrics relevant to marine resource management on the Northeast Atlantic shelf.

UConn Today: https://today.uconn.edu/school-stories/marine-knowledge-is-power/Twitter: https://twitter.com/UConnResearch/status/1131164302327595009LinkedIn: https://www.linkedin.com/feed/update/urn:li:activity:6536935526912573441

Jim O’Donnell sits down with Face the Facts

Jim O’Donnell is a professor of marine sciences at UConn and leader of the Connecticut Institute for Resilience and Climate Change. He sat down with Face the Facts With Max Reiss to talk about our changing climate and what impacts Connecticut residents could see in the future, especially along the shoreline Face the Facts With Max Reiss airs Sundays at 10 a.m.

Congratulations 2019 Graduates!

Yan Jia, Qiang Sun, Michael Whitney, Steven Deignan-Schmidt

Yan Jia, Qiang Sun, Prof. Michael Whitney, and Steven Deignan-Schmidt at the doctoral commencement ceremony. Steven Deignan-Schmidt was profiled for the CLAS Class of 2019: https://clas.uconn.edu/class-of-2019/#deignan-schmidt.

 

Gihong Park, Youngmi Shin, James O'Donnell

Gihong Park, Youngmi Shin, and Prof. James O’Donnell at the doctoral commencement ceremony.

 

Chris Murray

Christopher Murray after the doctoral commencement ceremony.

 

Penny Vlahos and Allison Byrd

Prof. Penny Vlahos and Allison Byrd after the master’s commencement ceremony.

 

2019 Senior Recognition Avery Point

Marine Sciences graduates and faculty at the Senior Recognition Ceremony at Avery Point on May 10, 2019.