Low coverage whole genome sequencing

NSF awards our collaborative sand lance grant!


24 June 2023. We are overjoyed to be able to announce today that NSF's Division of Integrative Organismal Systems has awarded our proposed research to better understand sand lance CO2 sensitivity!

With a sense of pride and humility we will take on this intriguing case, follow it down some rabbit holes, while keeping in mind the big picture. This fall, our collaborative team will begin its renewed work, now on both congeneric sandlance species (Ammodytes dubius, A. americanus).

We already have two talented PhD students recruited to the task, Lucas Jones and Emma Siegfried. With curiosity and anticipation, we look forward to the next years of eco-evolutionary research on some of the most important forage fish species on the Northwest Atlantic Shelf.

Earlier work showed that sand lance embryos are unusually sensitive to high CO2

NSF-ORCC (Organismal Response to Climate Change): Collaborative Research: Mechanisms underpinning the unusual, high CO2 sensitivity of sand lances, key forage fishes on the Northwest Atlantic Shelf (#2307813, 2023-2026, $1,050,000)

The research team: Hannes Baumann (lead-PI, UConn), Zofia Baumann (UConn), David Wiley (NOAA), Nina Therkildsen (Cornell), Chris Murray (WHOI), Neel Aluru (WHOI)

*** Why are sand lance so sensitive to future high CO2 conditions in the ocean? ***

Public Award Abstract
Ocean warming and acidification are direct, predictable consequences of man-made climate change with likely vast but still insufficiently understood consequences for marine life.

So far, most tested fish species appear only mildly sensitive to ocean acidification, but sand lances are an exception. Sand lances are small, eel-like, schooling fishes of enormous importance as food for marine fish, seabirds and mammals in temperate to polar ecosystems, and recent research conclusively demonstrated that many sand lance embryos have trouble developing and hatching under predicted future ocean conditions.

This project uses modern experimental and molecular tools to understand exactly WHY sand lance embryos are so unusually sensitive and which genes and enzymes are responsible for this. Genes will also reveal whether some specific genotypes are less sensitive to warming and acidification, which can then be used to predict whether the species could evolve to be more tolerant over time.

Another important objective is to test a closely related sand lance species to find out, whether the high climate sensitivity might be of general concern in this important group of forage fishes. This project combines innovative ecological, evolutionary, and genomic research to help society anticipate looming marine ecosystem changes in the 21st century, while equipping the next generation of scientists with the needed tools and expertise to succeed in the challenges ahead.

The project also creates opportunities for high school students from underprivileged Connecticut schools to accompany the team on sand lance sampling trips to Stellwagen Bank National Marine Sanctuary.

American sand lance (Ammodytes americanus) swimming in surface waters of Wells Harbor, ME in November 2021

Technical Award Abstract
Two recent studies on Northern sand lance (Ammodytes dubius), a key forage fish on offshore sand banks across the Northwest Atlantic shelf (NWA), have robustly demonstrated that predicted future CO2 conditions induce some of the most severe reductions in embryo survival and hatching success seen yet among tested fish species. This project has four objectives for revealing the mechanisms underpinning this unusual, high CO2-sensitivity as well as the ubiquity and genetic basis of this phenomenon.

[1] For the first time, we will rear A. dubius offspring produced from wild spawners to late larval stages at factorial CO2 × temperature conditions to test whether sand lance larvae are as CO2-sensitive as embryos.

[2] For the first time, we will use transcriptomic tools (RNAseq, RT-qPCR) to elucidate mechanisms causing ‘CO2-impaired hatching’, focusing specifically on hatching enzymes, to better understand a newly discovered mortality mechanism due to high CO2 in fishes.

[3] Modern genomic approaches (low-coverage whole genome sequencing; allele frequency shifts, relatedness analyses) will reveal whether high CO2-sensitivity has a genetic basis in sand lance and could therefore evolve.

[4] And for the first time, we will extend CO2 × temperature experiments to a congener, the American sand lance (A. americanus), which provides an important scientific contrast between nearshore vs. offshore species CO2-sensitivities and will yield critical insights whether high CO2-sensitivity is a wider concern within the sand lance family.

ICES JMS publishes sand lance population structure paper!

5 December 2022. We are proud to announce that the ICES Journal of Marine Science just published our latest sand lance study! The work spearheaded by Lucas Jones and subject of his Masters thesis research has brought together a large, international group of collaborators to better understand the genetic relationships between disparate sand lance populations across their large geographical range. This is an Open Access publication that will hopefully be of use to researchers studying sand lance everywhere.

Ammodytes dubius
Sand lance, a vital forage fish, may be facing new challenges as the oceans warm. Researchers have found two genetically distinct populations of Northern sand lance which may help inform conservation and management decisions. These sand lance were caught off the coast of Greenland (Photo courtesy of Thomas Pederson)

Press release. By Elaina Hancock

Genetic Barriers, a Warming Ocean, and the Uncertain Future for an Important Forage Fish

In the vast oceans, one would assume their inhabitants can travel far and wide and, as a result, populations of a species would mix freely. But this doesn’t appear to be the case for a vital forage fish called the sand lance.

Sand lance are small schooling fish impressively rich in lipids, which makes them a fantastic and significant food source for at least 70 different species ranging from whales and sharks to seabirds, says UConn Associate Professor of Marine Sciences Hannes Baumann.

The Northern sand lance can be found from the waters off New Jersey all the way north to Greenland. Researchers, including Baumann and Ph.D. student Lucas Jones, were interested to see if sand lance constitute a massive, homogenous population, or whether there are genetically distinct groups. Their findings are published in the ICES Journal of Marine Science.

Baumann explains these are important questions to answer when considering conservation and sustainable management of the species, especially since the regions where sand lance live are warming faster than many areas of the planet due to climate change.

Sampling fish from such a broad range is no small task, but two years ago, Baumann and Jones began reaching out to other researchers to see if they had tissue samples to spare. Baumann credits the work to the international group of colleagues who contributed samples including co-authors from Canada and Greenland, and who helped sequence and analyze the data including co-authors from Cornell University.

In all, Baumann, Jones, and the team were able to sequence and analyze nearly 300 samples from a variety of locations across the sand lance’s range using a technique called low-coverage whole genome sequencing. They also sequenced the first reference genome for sand lance.

In a nutshell, Baumann says they found an area on the Scotian Shelf, off the coast of Nova Scotia, where a genetic break occurs. The researchers distinguished two distinct groups, one north and one south of the divide, with parts of the genome differing quite dramatically – namely on chromosomes 21 and 24. Without obvious physical barriers like a mountain range separating the groups, Baumann says it’s logical to ask how these differences are possible.

“That is the scientific conundrum,” says Baumann, and the answer, it appears, lies in the currents.

“When fish from the north reproduce and drift south, they are genetically less adapted to warmer southern waters, even if it’s five or six degrees warmer in the winter, they are just not surviving,” Baumann says. “These populations may be linked by the ocean currents, but the realized connectivity is basically zero.”

Separation of 3 sand lance species based nuclear and mitochondrial DNA (Jones et al. ICES JMS 2022)

(A) Principal component analysis of SNP-based, individual-level covariance matrices with superimposed FST values for each interspecies comparison. The asterisk denotes 5 likely misidentified A. americanus specimens from the Northern GSL (B) Mitochondrial haplotype network of all analyzed specimens, with the number mutations separating congeners.

This finding is a first for the sand lance, but it has been shown in other species such as lobsters, cod, and scallops, and this research adds further evidence to an apparent temperature divide at the Scotian Shelf, and helps demonstrate that temperature is an important factor in survival.

“Example after example shows that the ocean is not as homogeneous a place as expected, and there are all kinds of things that prevent that constant mixing,”Baumann says. “We found another striking example of that.”

When researchers find adaptation in an environment where mixing is continuous, like in the ocean, Baumann says, the question is how it is possible that groups stay different, even though they are constantly encountering other genotypes. That is where powerful genomic methods, like the ones used in this paper, come in handy.

“Parts of the genome in many species have what we call a ‘genetic inversion,’ which means that the genes on the chromosome from one parent have a certain order and the genes on the same chromosome that come from the other parent that code for the same thing, and they’re the same area, but they’re flipped,” Baumann says.

These inversions mean recombination cannot occur; therefore, the genes are passed down through the generations and play an important role in adaptation.

“We discovered on chromosomes 21 and 24 there are whole regions that are completely different and that is like the trademark signature of what we call an inversion because there’s no recombination going on.”

Baumann says that knowing there are genetic and ecological barriers on the Scotian Shelf is important, because with climate change, this barrier may move north and while that may be good news for southern fish, it’s bad news for the fish currently there.

The researchers were also a little relieved in finding two clusters, because had there been many smaller clusters, it could make management and conservation more challenging, especially considering scenarios like the construction of offshore wind parks. Areas potentially well situated for wind turbines can also be habitats for sand lance, and construction disrupts habitats. If there were many, smaller population clusters, a single construction project could pose the risk of completely wiping out a cluster, whereas with more widely dispersed populations, though the local population may be temporarily disturbed, it will not be long before they are able to re-establish after construction is completed.

Baumann plans to focus further research on studying the genetic basis of the thermal divide.

“We want to make sure that this fish is productive and resilient, despite climate change, so we should make sure these areas where they are occurring are protected,” Bauman says. “These decisions should include experts to ensure if there’s an area that is very critical to sand lance, that any disturbance is temporary.”

It isn’t an unsolvable conflict, but it is something that we need to do, says Baumann, who also notes that it is possible that sand lance north of the thermal divide are already suffering more from warming because the region is warming faster.

“It could be that these two clusters have different vulnerabilities to climate change,” he says. “We don’t know that yet but that’s something that should be pursued.”