DNA Reveals Genetic Bottleneck in Chesapeake Sturgeon

At The Conversation, Atlantic sturgeon were fished almost to extinction − ancient DNA reveals how Chesapeake Bay population changed over centuries

In North America, sturgeon have played important subsistence and cultural roles in Native communities, which marked the seasons by the fishes’ behavioral patterns. Large summertime aggregations of lake sturgeon (Acipenser fulvescens) in the Great Lakes area inspired one folk name for the August full moon – the sturgeon moon. Woodland Era pottery remnants at archaeological sites from as long as 2,000 years ago show that the fall and springtime runs of Atlantic sturgeon (Acipenser oxyrinchus) upstream were celebrated with feasting. Archaeologists uncover bony scutes – modified scales that resemble armor for the living fish – in places where people relied on sturgeon for subsistence. Logan Kistler and Natalia Przelomska

Archaeological finds of sturgeon remains support that early colonial settlers in North America, notably those who established Jamestown in the Chesapeake Bay area in 1607, also prized these fish. When Captain John Smith was leading Jamestown, he wrote “there was more sturgeon here than could be devoured by dog or man.” The fish may have helped the survival of this fortress-colony that was both stricken with drought and fostering turbulent relationships with the Native inhabitants.

Capt. John Smith was wrong. While the dogs didn't get much but the scraps, men did catch and ear virtually all the sturgeon out of the Chesapeake. 

This abundance is in stark contrast to today, when sightings of migrating fish are sparse. Exploitation during the past 300 years was the key driver of Atlantic sturgeon decline. Demand for caviar drove the relentless fishing pressure throughout the 19th century. The Chesapeake was the second-most exploited sturgeon fishery on the Eastern Seaboard up until the early 20th century, when the fish became scarce.
Conservation biologists capture the massive fish for monitoring purposes, which includes clipping a tiny part of the fin for DNA analysis. Matt Balazik

At that point, local protection regulations were established, but only in 1998 was a moratorium on harvesting these fish declared. Meanwhile, abundance of Atlantic sturgeon remained very low, which can be explained in part by their lifespan. Short-lived fish such as herring and shad can recover population numbers much faster than Atlantic sturgeon, which live for up to 60 years and take a long time to reach reproductive age – up to around 12 years for males and as many as 28 years for females.

To help manage and restore an endangered species, conservation biologists tend to split the population into groups based on ranges. The Chesapeake Bay is one of five “distinct population segments” the U.S. Endangered Species Act listing in 2012 created for Atlantic sturgeon.

Since then, conservationists have pioneered genetic studies on Atlantic sturgeon, demonstrating through the power of DNA that natal river – where an individual fish is born – and season of spawning are both important for distinguishing subpopulations within each regional group. Scientists have also described genetic diversity in Atlantic sturgeon; more genetic variety suggests they have more capacity to adapt when facing new, potentially challenging conditions.

Archaeological remains are a direct source of data on genetic diversity in the past. We can analyze the genetic makeup of sturgeons that lived hundreds of years ago, before intense overfishing depleted their numbers. Then we can compare that baseline with today’s genetic diversity.

The James River was a great case study for testing out this approach, which we call an archaeogenomics time series. Having obtained information on the archaeology of the Chesapeake region from our collaborator Leslie Reeder-Myers, we sampled remains of sturgeon – their scutes and spines – at a precolonial-era site where people lived from about 200 C.E. to about 900 C.E. We also sampled from important colonial sites Jamestown (1607-1610) and Williamsburg (1720-1775). And we complemented that data from the past with tiny clips from the fins of present-day, live fish that Balazik and his team sampled during monitoring surveys.

DNA tends to get physically broken up and biochemically damaged with age. So we relied on special protocols in a lab dedicated to studying ancient DNA to minimize the risk of contamination and enhance our chances of successfully collecting genetic material from these sturgeon.

Atlantic sturgeon have 122 chromosomes of nuclear DNA – over five times as many as people do. We focused on a few genetic regions, just enough to get an idea of the James River population groupings and how genetically distinct they are from one another.

We were not surprised to see that fall-spawning and spring-spawning groups were genetically distinct. What stood out, though, was how starkly different they were, which is something that can happen when a population’s numbers drop to near-extinction levels. 

We also looked at the fishes’ mitochondrial DNA, a compact molecule that is easier to obtain ancient DNA from compared with the nuclear chromosomes. With our collaborator Audrey Lin, we used the mitochondrial DNA to confirm our hypothesis that the fish from archaeological sites were more genetically diverse than present-day Atlantic sturgeon.

Strikingly, we discovered that mitochondrial DNA did not always group the fish by season or even by their natal river. This was unexpected, because Atlantic sturgeon tend to return to their natal rivers for breeding. Our interpretation of this genetic finding is that over very long timescales – many thousands of years – changes in the global climate and in local ecosystems would have driven a given sturgeon population to migrate into a new river system, and possibly at a later stage back to its original one. This notion is supported by other recent documentation of fish occasionally migrating over long distances and mixing with new groups.

They've seen much the same with salmon. Occasional "infidelity" to the natal river tends to keep the populations of salmon from forming a separate species of salmon for each river. In one notable example, after the eruption of Mt. St. Helens on May 18, 1980, the Toutle and Cowlitz Rivers were deluged with warm volcanic ash. Salmon migrating up the Columbia headed for those rivers bypassed them, and settled for a non-natal stream.  

The Wombat has Rule 5 Sunday: Babe in Boots up and garnering clicks at the Other McCain.

Ships Killing Bay Sturgeon

This sturgeon’s tail was cut off in a likely vessel strike. 

Bay Bulletin, Endangered Atlantic Sturgeon Threatened By Ship Strikes In Busy James River

Early 2024 will mark 20 years since the first evidence came to light that Endangered Atlantic sturgeon, believed to be wiped out in the James River, were still spawning there.

The Rice Rivers Center at Virginia Commonwealth University (VCU)has been keeping a close eye on the river’s stock of these “living fossils”, which haven’t changed much since they swam around in the time of the dinosaurs.

As the 2023 fall spawning run wraps up, Chesapeake Bay Magazine talked with the
Center’s sturgeon expert Dr. Matt Balazik about a concerning trend that parallels a larger issue with endangered whales along the Atlantic coast: vessel strikes. In Balazik’s latest update from Nov. 4, he notes, “Lots of ship strikes are being reported.”

Researchers count on citizen scientists to gather information about possible vessel strike victims they find and even salvage the fish carcass for study. Balazik says, “Data suggest that relatively there are a lot of carcasses floating around right now so please keep a lookout and report your discoveries.”

The ship strikes on adult (spawning age) sturgeon have been concerns for years. The James has considerable traffic, from U.S. Navy vessels around Hampton Roads to bulk carriers visiting Hopewell and multiple tugs pushing barges as far up as the Richmond Intermediate Terminal. While sturgeon hug the bottom when at rest and feeding, they swim 4-5 meters (13-16’) deep, just about the depth of many vessels’ large, powerful, slow-turning propellers.

Odd as it may seem, the VCU team has been placing ultrasonic tags in carcasses to see how they drift, in order to begin assessing how many sturgeon get hit each year. It’s a difficult research problem, but it’s important to gain mortality insight about a fish that can spawn for decades—unless its life is cut short.

VCU has implanted more than 200 ultrasonic tags on sturgeon during a catch and release process. The ultrasonic markers “talk” for up to ten years each to several coordinated arrays of receivers up and down the Atlantic coast. Researchers caught a sturgeon this fall that was tagged on Oct. 11, 2013. They say the battery in his tag should die any day now.

So, why didn't they swap out the battery, or at least retag the fish. 

The Wombat has Rule 5 Sunday: One Last Glimpse Of Bikini up at The Other McCain.

Eastern Shore Salmon Farm Cancelled

Not a farmed salmon

Bay Journal, Salmon farm developer withdraws discharge permit request amid sturgeon concerns

Facing growing public pushback, a Norwegian company hoping to build a large indoor salmon farm on Maryland’s Eastern Shore has — at least for now — dropped its bid for a permit to discharge wastewater into the only waterway in the state where endangered Atlantic sturgeon are known to spawn.

AquaCon Maryland LLC notified the Maryland Department of the Environment on Oct. 14 that it was withdrawing its application to discharge up to 2.3 million gallons a day of treated “purge” water into Marshyhope Creek, a tributary of the Nanticoke River.

The company said in a press release that the public comments on the application “drew attention to Atlantic sturgeons’ use of Marshyhope Creek, which warrants further consideration and evaluation.”

Not an Atlantic Sturgeon

 

Ryan Showalter, the company’s Easton-based lawyer, said in an email that AquaCon has not given up on developing an 18-acre salmon production facility in Federalsburg. Expecting that MDE would require additional information to address “uncertainties” about the facility’s impacts on the sturgeon, Showalter said, company officials decided to withdraw the application and investigate alternatives to year-round discharge into the Marshyhope.

MDE gave preliminary approval to the company’s permit in June, but since then the project has drawn pushback from scientists, environmentalists and local residents concerned about the plant’s potential impact on the creek and its fish, particularly sturgeon. An August hearing drew more than 100 people, with nearly all who spoke opposing it.

I didn't necessarily oppose the salmon farm, but I did wonder if it made a whole lot of economic sense to have an all indoors salmon farm on Maryland's Eastern Shore. But they could use the jobs. 

Chesapeake Sturgeon on the Road to Recovery

A pretty interesting article by David Secor in the Bay Journal, one of the better known fisheries scientists in the Bay region. Atlantic sturgeon: Not the ‘ghosts’ I once thought they were

In 1993, I began working at the Chesapeake Biological Laboratory, eager to make my mark. The attention-getting, prehistoric-looking Atlantic sturgeon looked like low-hanging fruit. They are living fossils from the time of dinosaurs, a grab bag of evolutionary pieces and parts: a vacuum cleaner mouth, a fused head shield, electric sensors, barbels, sharklike sand-paper skin and lobed tail, plus conspicuous boney plates of armor.

Also, they are giants: Atlantic sturgeon have been known to reach 12 feet and 500 pounds. They were prominent in the records of colonial Jamestown and in the late 1800s supported a lucrative caviar fishery. Yet by 1993, they were a distant memory in the Bay. A charismatic fish, a mysterious disappearance, a stressed estuary: The science and PR prospects looked good! So, as chronicled by Karl Blankenship in the Bay Journal, I embarked on a 25-year record of media statements — and sometimes misstatements.

 

I assembled a workshop of seasoned Chesapeake scientists and most of us agreed that sturgeon were gone from the Bay. We had striped bass in mind — sturgeon are also fish of oceans and big rivers, returning to spawn in spring. Yet in decades of surveys and catches for striped bass, never a bycatch of spawning sturgeon. In the 1990s, when confronted with the pound-net capture of a single large Atlantic sturgeon, I dismissed it. My quote in the November 1997 Bay Journal: “What it represents, if it is a Chesapeake Bay fish, is kind of a ghost. It’s a representative of something that once was — and probably no longer is — here.”

I scienced the heck out of their disappearance from the Bay. We filled the CBL’s three stories of seawater labs with young Atlantic sturgeon from elsewhere, enrolling them in Chesapeake water quality boot camp. The young fish fared poorly when exposed to low oxygen, and I helped to establish Chesapeake Bay Program water quality standards protective of sturgeon. Still, I was pessimistic: “Sturgeon may be a symbol of what we’ve lost in the Chesapeake Bay. If we could bring back sturgeon, it would signify a huge change in the Chesapeake,” I told Karl for a Bay Journal article in March 2003.

 

That day came sooner than I could have imagined. Juvenile sturgeon started appearing in surveys, large dead sturgeon washed up, and finally directed studies discovered spawning sturgeon in the James River, then in the Pamunkey River (a York River tributary), and then in the Marshyhope Creek (off the Nanticoke River). Now I really changed my tune: “I’m kind of optimistic,” I said in a November 2010 Bay Journal article. “I’m just pleased that we have sturgeon to talk about in the Chesapeake.”

Although a bit embarrassed by being wrong, I am also delighted. Duped by sturgeon, I became their student rather than their authority. I often reflect on how fortunate I am to be a part of this digital age, a truly unprecedented period of discovery about the hidden lives of fishes.

Throughout much of the Chesapeake Bay, hundreds of hydrophones are deployed at intervals spanning miles to tens of miles, awaiting signals from transmitters that have been implanted in sturgeon — the work of scientists up and down the Atlantic Coast. These “dial-up” signals track sturgeon migrations and have transformed our understanding of the fish. Historically known to be springtime big-river spawners, fall spawning now seems to be the dominant behavior. Further, large adults are pushing all the way up to head of tide. Imagine, a hulking 7-foot, 200 pounder pushing through a wading-depth channel that’s narrow enough to skip a rock bank to bank.

I appreciate his humility, in admitting his error in writing of the Atlantic Sturgeon as last.

Now I spend my days doing something I would not have considered remotely possible just 15 years ago: I am researching America’s smallest free-flowing sturgeon river, the Marshyhope Creek on Maryland’s Eastern Shore. Those familiar with Marshyhope Creek, mostly paddlers and anglers, know that the water is quite shallow in this scenic creek. Still, our team of scientists has discovered that sturgeon use all of the creek, as well as wandering downstream into the upper Nanticoke River.

We’ve discovered a persistence of clean scoured riverbed cobble (the necessary spawning substrate for these fish), and we are seeing small juveniles through sonar surveys and direct observation. Oh, yes, I forgot, direct observation. Sturgeon jump. And not just a little. They fling themselves entirely out of the water. Knowledgeable shoreline residents set out beach chairs to watch the evening show. Indeed, on a single outing recently, I saw four large sturgeon launch themselves out of the water — so energetically that for a moment I could see their entire impressive profile, snout to tail.

 

Let me leave you with this gift: Enjoy sturgeon. They are a present to ourselves as citizens of the Chesapeake Bay region. Without the Clean Water Act, without Bay Program water quality standards, and without Maryland’s Chesapeake Bay Critical Area Act, it is very likely that sturgeon would no longer be with us. Certainly, threats remain. In Marshyhope Creek, these include a critically small number of spawners, invasive blue catfish, and a proposed salmon factory (Aquacon) — a behemoth of a plant, six times the size of a Walmart — that could detrimentally alter riverbed and water conditions in the skinny waters where sturgeon spawn.

But please — enjoy. Visit the Marshyhope, particularly during September when sturgeon spawn. Take a paddle, wet a line, or stroll Federalsburg’s peaceful River Walk. If you miss them jumping — well, apologies, but I promise you they are lurking somewhere below the surface. Not a ghost, but a living breathing dinosaur-fish in our own backyard.

The Wombat is back from the hospital and cleaning up old business with Rule 5 Sunday: Clearing Out The Bodacious Babe Backlog.

Maryland Gets $300k to Save the Sturgeon

Or maybe just try to count them; $300,000 doesn't go as far as it used to. Feds grant nearly $300k to sturgeon research

Nanticoke River Atlantic sturgeon, once thought to have vanished from Maryland waters, are making a comeback — and U.S. Sens. Ben Cardin and Chris Van Hollen, both D-Md., are here for it.

The senators on Tuesday, Aug. 20, announced $296,071 in federal funding to the Maryland Department of Natural Resources to aid in research on the species.

Until Maryland and Delaware biologists’ recent discovery of adult sturgeon in the Nanticoke River and its streams, biologists reported not having seen the region’s sturgeon in 40 years.

 But what did the watermen not tell them?

The Atlantic sturgeon’s significant population decline has been attributed to overfishing and habitat loss. In the late 1800s, the fish were prized for their eggs, which were considered high-quality caviar.

Now, with the species’ reemergence, scientists are dedicated to tracking the fish, as well as helping to replenish and maintain its population.

Funding for the Maryland DNR’s efforts, awarded through the National Ocean and Atmospheric Agency Fisheries’ Species Recovery Grant Program, will help scientists develop new ways to estimate the species’ spawning run size.

NOAA, which is headquartered in Silver Spring, is a scientific agency within the U.S. Department of Commerce that focuses on the conditions of the oceans, major waterways and the atmosphere.

Its Species Recovery Grants Program is a longstanding, successful grant program that supports high-priority recovery actions for listed species. . . 

The rest of the article is mostly a campaign ad for Sens. Cardin and Van Hollen.

I suppose, it can't hurt to try to figure out how many there are, but it might not help either. The population began its recovery without anyone being aware of them.

The Wombat has Rule 5 Sunday: Labor Day With Jayne Mansfieldup on time and within budget at The Other McCain.

James River Sturgeon Surge

Skyrocketing Sturgeon - Once sparse, the population of the prehistoric species is surging back

In 2005, while in graduate school at Virginia Commonwealth University, Matt Balazik initiated a project on Atlantic sturgeon in the James. Now he works for the U.S. Army Corps of Engineers as chief researcher on sturgeon in the river, primarily tagging and tracking adults of the species, but also surveying hatchlings.

“We’ve been looking for young-of-year sturgeon for about a decade,” Balazik says. “We’ve been doing in-depth surveys since 2012, and we never caught one until last fall. Then we caught 272.”

It will be interesting to see if this is a continuing improvement, or a spike in a relatively low baseline number. We often see that in fisheries, and the reasons are not particularly well understood.

The floodgates, one might say, were opened.

The Atlantic sturgeon is an ancient ocean-dwelling fish that makes spawning runs into freshwater rivers every year. It was once a dominant force in the James, until overfishing and habitat loss dealt a severe blow to its status in the postbellum era, nearly exiling it from the river completely. But in the late 1990s, the U.S. Fish and Wildlife Service began to hear reports from commercial watermen that the sturgeon was still around.

A friend of mine once caught one in the Patuxent River in the course of a scientific survey.

Today, the sturgeon population in the James is relatively healthy, Balazik says, though it is impossible to know what the population was like before human impact.

There are four age classifications for a sturgeon: young-of-year, juvenile, sub-adult and adult. Young-of-year sturgeon are born within the last year. Juvenile sturgeon are at least a year old, but have yet to leave their natal river. Once the fish has taken its first journey to the ocean — in the James, that’s around year three — it is called a sub-adult. The sturgeon is not a full adult until it reaches sexual maturity, which is around 10 years for males and 16 for females. A sturgeon can live for 60 years, and, fully grown, typically weighs 90 to 160 pounds and measures 5 to 6 feet in length, according to the Chesapeake Bay Program. The largest sturgeon on record was 14 feet long and weighed more than 800 pounds.

I look forward to a viable population for fishing, like they have in the Columbia River. But not in this lifetime.

Once the sturgeon reaches adulthood, it returns to freshwater — usually its place of birth — to spawn.

“The young-of-year sturgeon are the barometer of progress,” Balazik says. “Those are the future generations.”

A variety of factors could have led to the sudden deluge of baby fish. The first is a moratorium on fishing ordered in 1998 by the Atlantic States Marine Fisheries Commission, which banned fishing and poaching of the Atlantic sturgeon from Maine to Florida. Because it takes females 16 years to reach sexual maturity, many of the fish saved by the moratorium are only recently able to reproduce.

Damn, that's slower than some people.

Wombat-socho has a double stuffed Rule 5 Sunday: Morena Baccarin.

Baby Sturgeon Caught In the James River

Sturgeon Making a Comeback in James River

A discovery no bigger than the palm of your hand has riverkeepers on the James River very excited.

Five juvenile sturgeon were found in the James, a positive sign for both the federally-protected species and the health of the waterway.

The tiny young fish are quite a contrast from adult Atlantic sturgeon, which can grow to be 14 feet long and live for 60 years.

White Sturgeon (West Coast)

 That's a big fish.

Baby sturgeon have just recently turned up in the river, after no sightings in more than 10 years. It’s a big deal because it shows sturgeon are spawning in the James. The species was harvested almost to extinction in the 1800s, and has only made a comeback in the last few years.

Jamie Brunkow, Riverkeeper with the James River Association (JRA), reports that JRA staff found the weeks-old sturgeon during an educational outing and released them back into the river.

“Juvenile sturgeon have been very scarce in the James River, but new and encouraging discoveries are continuing to happen,” he says. “Last fall, (Virginia Commonwealth University) VCU researchers documented the first two juvenile sturgeon discovered in the James River in more than a decade.”

That's a good sign!