Author: dls00012

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.

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.

16th Annual Marine Sciences Day: May 9th, 2019

In collaboration with Project Oceanology, the graduate students from Department of Marine Sciences hosted workshops for middle schoolers to teach them about marine sciences and research being done in the department. Students extracted DNA from strawberries and put it in necklaces for all to see. Another workshop had students identify plankton under microscopes.

Thanks to students from the McManus, Lin, and Dam Labs for organizing and running these activities, and inspiring the next generation of scientists.

DMS graduate students present at UConn’s 2nd Climate Research Symposium

On April 30th, four graduate students from the Marine Sciences Department traveled to UConn, Storrs to present their research at UConn’s 2nd Climate Research Symposium cohosted by the Geology and Marine Sciences departments. The students were Kelly McGarry (Ph.D student; top left), Halle Berger (Master’s student; top right), Sarah McCart (Master’s student; bottom left) and Alec Shub (Master’s student; bottom right). Everyone’s presentations were well received, and Sarah McCart even won the graduate student poster competition!

The event featured two keynote speakers; Professor Margaret Rubega of UConn, and Professor Tim Cronin of MIT. Professor Rubega talked about science communication and how the scientific community could better communicate their climate change research to non-scientists without using overbearing jargon and too many words. Professor Cronin gave a speech on his past research on the suppression of Arctic air formation with climate warming.

By Callie Concannon

2nd Climate Research Symposium

Long Island Sound Habitat Mapping website now available

A new website highlighting the Long Island Sound Habitat Mapping Initiative went live on Earth Day. The website provides information on the background and motivation for the mapping initiative, summaries of the field work conducted, interpretive story maps describing some of the results, links to data products and publications generated and multimedia links to images and video of at-sea operations that illustrate the beauty and complexity of the underwater habitats of the Sound.

https://lismap.uconn.edu/

Grad students Sean Ryan and Halle Berger win awards at 2019 Benthic Ecology Meeting

Graduate students Sean Ryan and Halle Berger received Honourable Mention awards (top 10 graduate student presentations) for their presentations at the 2019 Benthic Ecology Meeting in St. John’s Newfoundland. Halle Berger, co-advised by Profs. Samantha Siedlecki and Catherine Matassa, was awarded for her interdisciplinary talk “Using regional oceanographic forecasts to assess the vulnerability of the Dungeness crab to climate change stressors.” Sean Ryan (advisor Catherine Matassa) was awarded for his poster “Induced herbivore resistance varies with latitude in the rockweed Fucus vesiculosus.” Sean and Halle were among ~180 student presenters at the meeting. Congratulations on your accomplishments, Halle and Sean!

New hydrothermal scavenging paper published in EPSL

The Lund lab recently published a paper in Earth and Planetary Science Letters on hydrothermal scavenging of trace metals at the East Pacific Rise. The results suggest that 230Th, a radionuclide commonly used to constrain sediment accumulation rates on the seafloor, is highly sensitive to changes in hydrothermal output, with important implications for the use of 230Th in paleoclimate and geochemical studies (https://davidlund.wixsite.com/averypointpaleo/page4).

Citizen science shows that climate change is rapidly reshaping Long Island Sound

21 March 2019. Marine Environmental Research just published a study about long-term ecological change in eastern Long Island Sound based on data collected by Project Oceanology! This non-profit ocean literacy organization has educated middle and high school students on boat trips to nearby estuarine sites for decades. For the first time, the digitization of these data allowed their quantitative evaluation, offering insights into the abiotic and biotic changes in nearshore waters of Eastern Long Island Sound.

Highlights

    • Citizen-science observations revealed rapid warming, acidification, and dissolved oxygen loss over the past 40 years in eastern Long Island Sound
    • Otter trawl catches showed significant decreases in overall species diversity and richness
    • Cold-water adapted species (American lobster, winter flounder) decreased, but warm-water adapted species (spider crabs) increased since 1997

News3-400x428Fig_6-CPUEs_4-species

Undergraduate Students Unravel Challenges to Predicting Zooplankton Vulnerability to Warming

Mentored by Professor Hans Dam and Ph.D. student Matthew Sasaki, Undergraduate students Sydney Hedberg and Kailin Richardson (participants in the UConn-Mystic Aquarium Research-Experience-for-Undergraduates Program, http://www.mysticaquarium.org/reu/) carried out experiments that yield important insights into how zooplankton respond to warming. The results of the work are now published in the journal Royal Society Open Science (https://royalsocietypublishing.org/doi/10.1098/rsos.182115). The research shows that predicting the vulnerability of populations to global warming involves complex interactions between evolutionary adaptation, phenotypic plasticity, and sex (females rule !). The paper has two important implications. Surprisingly, tropical populations are more at risk because animals are already living near their thermal limits. In addition, because of the low survival of males, populations facing warming may be limited by the ability of males to fertilize females.

Sydney-and-Kailin

Photos by Hans Dam

ASLO 2019 Aquatic Sciences Meeting well attended by UConn Department of Marine Sciences

More than 15 faculty members, graduate students, and undergraduates from the Department of Marine Sciences presented their research at last week’s ASLO (Association for the Sciences of Limnology and Oceanography) 2019 Aquatic Sciences Meeting in San Juan Puerto Rico.  DMS presentations reflected the diversity of our faculty’s research disciplines and approaches, including coral reefs, plankton ecology and physiology, nitrogen cycling, microplastics, salt marshes, and ecosystem impacts of storm events.

 

ASLO 2019 group picture ASLO 2019 booth