Our program

NOTE: FishTracker is unfortunately on hiatus until new funding is found.

FishTracker is a student-oriented citizen science project based at Cornell University and funded by the USDA National Institute of Food and Agriculture. The program records and maps the presence of several species of fish, both endangered and invasive, in New York State.

Round goby
Ohio Sea Grant licensed under CC BY-NC 2.0

New York State teachers and students play a critical role in monitoring the range of fish species using materials and protocols supplied by this program. Students collect environmental DNA (eDNA) from water samples from nearby lakes, streams, or ponds, using GPS coordinates to identify each site surveyed.

eDNA samples are sent to Cornell University for analysis using a process known as quantitative PCR (qPCR). Although individual species are often difficult to detect, current qPCR technology shows great promise for determining the presence of even very low numbers of a wide range of species by monitoring for the presence of specific kinds of eDNA.

Bighead carp
USFWS Fish and Aquatic Conservation licensed under CC BY-NC-ND 2.0

We then incorporate the information from the qPCR analysis into a fish species database identifying the presence or absence of any of the species we monitor. We also send the results from the water samples submitted to the teachers and students for classroom analysis and discussion.

Monitoring invasive species

What are invasive species?

For centuries human activities have helped spread plants and animals around the world, intentionally or unintentionally expanding the range of many organisms beyond their original locations. Species (a group of similar animals, plants, or other living things that share common characteristics and can interbreed and produce young) living in an area where they are naturally and historically found are often called “native” species. Native species have adapted to their local habitats through a continuing interaction between their inherited characteristics and their environment. For thousands of years, natural barriers determined where organisms lived and helped defined their habitat, creating dynamic, natural ecosystems. Within their natural ecosystems, native organisms develop unique balanced relationships with both their physical environments and with the other organisms around them. As human activities have expanded, things have changed.

The ability to move people and products around the globe has been the basis of some of mankind’s greatest achievements, but increased mobility has also greatly increased the transfer of all types of organisms to new environments where they were not previously found. Species introduced into an area where they did not previously live are called “non-native” species, sometimes also known as exotic, nuisance, or non-indigenous species. Often, species introduced into a new wild environment will be unable to establish a viable population and will disappear with no ill effects. However, sometimes newly introduced species will thrive, outcompeting native species and destroying fragile ecosystems. Non-native species that damage the environment or disrupt existing ecosystems, or that result in economic loss or endanger human health, are generally referred to as “invasive” species. Many types of organisms, from plants to animals to microbes can be invasive. Invasive species can be introduced from other countries or from other parts of the same country.

Why are invasive fish species a problem?

Invasive fish species are a growing problem nationwide, especially in coastal regions and in the Great Lakes and surrounding areas. Invasive fish species can cause serious environmental problems and cause significant economic losses, often rapidly disrupting the fragile balance of natural ecosystems, and threatening the diversity and abundance of native aquatic species. The resulting loss of native fish can lead to important economic consequences, affecting a wide range of commercial, agricultural, aquacultural, and recreational activities. Globally, the introduction and spread of non-native species around the world has been described as a major threat to a stable natural environment and to global species biodiversity.

The introduction of invasive fish species is of particular concern because of the ease and frequency of waterway contamination by non-native fish. Aquatic species are often introduced into new areas as a result of the dumping of large amounts of ballast water (the water that is pumped into huge tanks to stabilize unloaded ships, and discharged at the next port of call, along with any surviving organisms) by large ships. Around the world, millions of tons of ballast water are exchanged daily, transporting within it aquatic species from microscopic plankton to fish. On a smaller scale, commercial activities such as aquaculture and the aquarium trade in exotic fish species can sometimes lead to the accidental or purposeful release of fish species into areas where they have never been found before. Even well-intentioned plans to introduce non-native species to control biological problems have backfired and resulted in serious damage by invasive species. For example, the introduction of grass carp to control the spread of unwanted aquatic plants has lead to the destruction of native plant species in inland lakes, resulting in tremendous damage to lake ecology and ecosystems at all levels. Recreational boaters and fishermen can also contribute to the problem by transporting fish (even baitfish) between rivers and lakes, resulting in cross-contamination of previously unaffected waters. Owners of household aquaria can potentially contaminate a waterway simply by dumping the contents of their home aquarium into a lake or stream. While nuisance species are most commonly first introduced into navigable waters, recreational users can easily spread them to pristine rivers, streams, lakes, ponds, and reservoirs.

Invasive species we’re tracking

Sea lamprey (Petromyzon marinus)

Sea lamprey. Petromyzon marinus.

Fish with two sea lampreys attached. USGS Great Lakes Science Center.

Boca de lamprea licensed under CC BY-SA 3.0 via Wikimedia Commons

Sea lamprey are native to the Atlantic Ocean but were introduced into the Great Lakes in the 1800s through a series of manmade locks and shipping canals. By the late 1940s all of the Great Lakes contained large populations of sea lamprey that caused serious damage to lake trout and other important fish species.

For part of its life cycle, the sea lamprey feeds on the blood of host fish. Sea lamprey have a large sucking disc for a mouth, filled with sharp teeth and a file like tongue. They use the sucking disc and teeth to attach to prey fish, and rasp through the scales and skin to feed on blood and other body fluids, often resulting in the death of the prey. The lamprey attack is so destructive that only about 1 out of 7 fish will survive an attack. During its life, which can last from an average of 6 to as long as 20 years, a single lamprey can kill large numbers of native lake and rainbow trout, whitefish, chubs, walleye, and catfish.

The economic effect of this invasive species has been enormous. For example, before the spread of the sea lamprey invasion, the United States and Canada harvested about 15 million pounds of lake trout from the upper Great Lakes each year. By the 1960s the total lake trout catch had dropped to only about 300,000 pounds. In Lake Michigan alone the catch dropped from 5.5 million pounds in 1946 to 402 pounds in 1953 (data from the Great Lakes Fishery Commission). Today there is an ongoing sea lamprey control program that is helping to reduce sea lamprey populations in many areas, but vigilant monitoring is still a key factor in controlling this highly destructive invasive species.

Asian carp (grass carp – Ctenopharyngodon idella; silver carp – Hypophthalmichthys molitrix; bighead carp – Hypophthalmichthys nobilis; black carp – Mylopharyngodon piceus)

Asian Carp Regional Coordinating Committee licensed under CC by 2.0

Asian carp were originally brought to the United States in the 1970s to help control algae growth on catfish farms and in wastewater treatment ponds. Two species of Asian carp were released from southern aquaculture facilities following flooding in the 1990s, and the invasion has been spreading north along the Mississippi ever since. In some areas of the Mississippi River,

Asian carp have become the most abundant fish species, having already out-competed native fish. Asian carp have been identified in the canals connecting the Mississippi River to the Great Lakes. Unfortunately, Asian carp, which can grow up to four feet long and weigh more than 100 pounds, have no natural predators in their new environment. A single carp can eat up to 5 -10% of their body weight in plankton each day. By consuming nearly all of the available plankton, the primary food source for most of the native fish, the Asian carp can rapidly wipe out entire populations of native fish.

In an effort to decrease the spread of Asian carp into new rivers and lakes, the U.S. Fish and Wildlife Service has placed several species of Asian carp to the federal list of injurious wildlife, making it illegal to transport live Asian carp, including viable eggs or hybrids of the species, across state lines except by special permit for zoological, education, medical, or scientific purposes.

Round goby (Neogobius melanostomus)

NOAA Great Lakes Environmental Research Laboratory licensed under CC BY 2.0

Round goby were introduced into the Great Lakes through the ballast water from large cargo ships and were first identified here in 1990. Since their introduction, round goby have caused significant ecological and economic problems. They have spread throughout the Mississippi River drainage area and into tributaries of the Great Lakes, including a sighting in one of the New York Finger Lakes (Cayuga Lake).

Round goby, which are bottom dwellers, compete very successfully with native bottom dwelling species like sculpins and darters for food, habitat, and spawning areas, and can cause substantial decreases in local populations of native fish. They also prey on small fish and eat the eggs and fry of larger native fish like lake trout.

The increased presence of round goby has been shown to potentially impact the food chain supplying recreationally important fish like walleye and smallmouth bass. It has been noted that round goby eat large amounts of zebra mussels, which in the short term may seem like an unexpected benefit. But, as with most environmental and ecological issues, it is important to look at the broad picture. Despite their large appetites, it is unlikely that round goby will have a significant impact on zebra mussel populations. Equally important, the zebra mussels eaten by round goby contain large amounts of various toxins that are found throughout the Great Lakes. Following intake of the zebra mussels, the toxins become concentrated in the goby, which are in turn eaten by a variety of sport fish, including smallmouth and yellow bass, walleyes, yellow perch, and brown trout. This food chain can lead to high concentrations of dangerous toxins in sport fish that are eaten by humans, increasing health concerns related to consuming sport fish.

Northern snakehead (Channa argus)

Brian Gratwicke, licensed under CC BY 2.0

Northern snakehead fish are native to parts of China, Russia, and the Korean peninsula, where they are considered a valuable food fish. Snakeheads are also popular exotic additions to home aquariums and have been introduced into United States waters primarily by aquarium owners discarding their unwanted pets into local waterways. The fish may also have been intentionally released to provide a local source for fishermen interested in catching snakehead for consumption. As a result, the northern snakehead has successfully established wild breeding populations in some parts of the United States and is gradually expanding its range.

Snakeheads can live in freshwater lakes, ponds, rivers, streams, and wetlands, including slow moving or even stagnant water. They can also survive cold winters. Northern snakehead fish can spread by swimming in water, but they can also breathe air. Therefore, they are capable of surviving on land for up to four days, as long as they are wet, and they can move up to ¼ mile on land by wriggling their bodies and using their fins.

Northern snakeheads are aggressive predators that grow up to 4 feet in length, with large mouths and sharp canine-like teeth. Invasive snakeheads thrive in the absence of their natural enemies, with a single female capable of laying up to 150,000 eggs in just 2 years. Adult snakeheads eat other native fish, small amphibians, reptiles, crustaceans, and even some birds and mammals, while juvenile snakeheads pose a significant threat to zooplankton, larvae, small fish, and crustaceans. Snakeheads also compete with native species for food and habitat.

Because snakeheads are considered injurious wildlife, it is illegal to import the fish or viable eggs from other countries, or to transport them across state borders. Efforts aimed at preventing further spread are important because of the potential ecological, environmental, and economic effects of this invasive species. Establishment of the northern snakehead in the United States could result in serious ecological and environmental damage, costing millions of dollars in management efforts and impacting aquaculture and the sport fishing industry.

White perch (Morone americana)

Ohio Sea Grant, licensed under CC BY-NC 2.0

White perch are native to the east coast of the United States and Canada and are often found in fresh, brackish and coastal waters. They have invaded other areas in the United States, primarily through bait fish release and movement through watersheds. Access to the Great Lakes probably occurred via the Welland Canal and the Erie Barge Canal starting in the 1930s.

White perch reproduce rapidly since they can spawn multiple times per year under optimal conditions, and can successfully breed in a variety of water conditions. There are several important negative impacts associated with the introduction of white perch, including predation, competition for food, resources, and habitat, and hybridization. Fish eggs are a substantial part of the white perch diet, and predation on the eggs of walleyes and white bass have caused a decline in some fisheries. White perch also eat small fish like minnows, and successfully compete for food with native species such as yellow perch, white bass, and black bullhead. As a result, a decrease in the abundance of native fishes often follows the introduction of white perch. White perch also consume large amounts of zooplankton, which may contribute to algal blooms in waters where they become heavily established.

White perch are closely related to white bass, but are normally not found in the same waters. When non-native white perch are introduced into an area where white bass are found, fertile hybrid offspring can be produced that are capable of reproducing with the parent species, potentially diluting the gene pool of both parent species. Because of the problems resulting from the introduction of non-native white perch, possession of live white perch is illegal in several states, and release of captured white perch back into the water is not recommended.

Asian swamp eel (Monopterus albus)

U.S. Geological Survey, licensed under CC public domain

Asian swamp eels are native to Asia and were first introduced into the continental United States from multiple geographic areas in the mid 1990s as a food source and also for use in home aquaria. Escape from fish farms and intentional release of pet fish have resulted in the establishment of wild populations in Florida and Georgia. Although not yet found in New York state, the presence of swamp eel was confirmed in New Jersey in 2008.

The swamp eel lives in fresh water, including stagnant waters, marshes, shallow wetlands, streams, rivers, lakes and ponds, but can also tolerate brackish and saline conditions. Swamp eels can survive cold temperatures and a wide range of oxygen levels since they can absorb up to 25 percent of the oxygen they need from the air. As a result, swamp eels can migrate short distances over land, increasing their ability to disperse to new habitats. They have a voracious appetite and eat a wide range of prey, competing with native species for food, and potentially disrupting fragile ecosystems.

Swamp eels are hermaphroditic, with all young initially being female. As they mature, some fish become male, but are capable of reverting to the female form when females become rare. Females can lay up to 1000 eggs each time they spawn, and spawning can occur throughout the year. This reproductive flexibility can provide a survival advantage over native fish. To help limit the spread of this invasive species, the United States Geological Survey discourages catching and transporting the eel for use as bait, food, or aquarium pets.

Tench (Tinca tinca)

Tench (Tinca tinca)
Christophe Quintin licensed under CC BY-NC 2.0

Tench, a member of the minnow/carp family, is a freshwater game fish native to Europe that has been introduced to many different countries around the world, including the United States. Tench are potamodromous, meaning they migrate and complete their life cycle in fresh water only. Tench average about 10 inches in length, but can live up to 20 years and grow to nearly 3 feet in length and weigh up to 16 pounds. Tench mature between 2 and 7 years of age and breed in the late spring or summer. Females lay a new clutch of eggs every 15 days for about 2 months. Tench prefer to live in shallow lakes and rivers in areas of heavy vegetation with a weedy, muddy bottom. Tench can survive in low-oxygen environments and in some areas spend the winter buried in mud. Tench are voracious eaters, consuming huge quantities of insect larvae, snails, mollusks, plants, algae, and organic debris that native species depend on. Tench also eat the eggs of other fish species, placing further stress on native fish like yellow perch and the copper redhorse that are already struggling with pollution and habitat loss. Tench are also a source of fish parasites that can spread to other species. In 2018 the Great Lakes St. Lawrence Governors & Premiers coalition added tench to the “least wanted” fish list and the St. Lawrence–Eastern Lake Ontario Partnership for Regional Invasive Species Management (SLELO-PRISM) in New York is trying to raise awareness of the impending problems that could result from invasive Tench.

Tench were first introduced into the Great Lakes basin in the 1980s, likely after escaping from aquaculture ponds in Quebec, and became established in Lake Champlain in 2000.Tench have expanded their range into Lake St. Francis in the St. Lawrence Seaway and are steadily pushing upstream into Lake Ontario. Unfortunately, habitat conditions that were expected to limit feeding and spawning have not halted their expansion. The spread of tench has also been facilitated by illegal fish transport, illegal pond stocking, and use of tench as baitfish. Currently tench are a potential problem, but not yet a direct threat to New York waterways. However, tench are already found in the Great Lakes, and given their ability to spread and thrive in a wide variety of conditions, tench are poised to become a major invasive problem in New York waters. Increasing community awareness, developing strategies to slow the invasion, and early monitoring are important factors in limiting the tench invasion while there is still time.

Tracking native species

Tracking native species

Since invasive species often contribute to the decline of important native fish species, our new grant expands our  monitoring  program to include threatened, endangered, and declining native fish species.

According to the Federal Endangered Species Act of 1973, two categories of declining species of plants and animals need protection: endangered species and threatened species. Endangered species are defined as “any species that is in danger of extinction throughout all or a significant portion of its range”, while a threatened species is defined as “any species that is likely to become an endangered species within the foreseeable future throughout all or a significant portion of its range”. Simply put, endangered species are at the edge of extinction now, and threatened species are likely to be at the edge of extinction in the near future. Declining species not yet characterized as threatened or endangered can show significant decreases in population, and will benefit from monitoring information to help understand population levels.

Species we’re tracking

Declining New York native species

Deep water cisco, also called Lake Herring (Coregonus artedii)

USFWS Fish and Aquatic Conservation, licensed under CC BY-NC-ND 2.0

Ciscoes are freshwater schooling fish that are predominantly found in waters below 18°C (~65°F). These cold-water fish breed once a year, spawning in shallow coastal waters in the winter and returning to deeper waters during the spring.  Cisco eggs develop slowly, hatching in the spring as the ice starts to thaw. Juveniles usually live in shallow bays for their first month, and mature within 1 to 4 years.

Ciscoes play an important role in the ecosystem. They feed predominantly on zooplankton and insect larvae and are a primary food for other economically important fish species like lake trout, yellow perch, walleye, and northern pike. In the 1940s, ciscoes were one of the most commercially important fish in the Great Lakes, where fisheries produced an average of 19 million pounds annually. However, the combined pressures of over-fishing, competition by invasive species like rainbow trout and alewives, and pollution have caused a significantly declining population.

Once abundant in all five Great Lakes, ciscoes are now common only in Lake Superior. Currently one of the greatest risks to ciscoes in the Great Lakes is the increasing level of nutrients being added to the lakes each year, which results in a decrease in the amount of oxygen in the water. Ciscoes are sensitive to changes in temperature and levels of dissolved oxygen.  Being forced to move into shallower, warmer parts of the water column where higher temperatures during the summer months can cause large die-offs in cisco populations.

In New York, ciscoes are native to ten watersheds in Great Lakes drainage, including the Finger Lakes, lower elevations of the Adirondacks, and Chautauqua Lake. However, populations have declined in the westernmost watersheds and in lower elevation lakes, including Lake Erie. Re-establishing Cisco in the lower Great Lakes would help improve connections in the food web. Additional information on location and abundance of native populations will aid efforts to protect and restore this important native species.

Map of cisco range in New York pre/post 1976-1977

American eel (Anguilla rostrate)

Chesapeake Bay Program, licensed under CC BY-NC 2.0

American eels are the only freshwater eel native to North America. American eels hatch in the Sargasso Sea in North Atlantic. Larvae drift with the Gulf Stream, reaching the US Atlantic coast about a year later. American eels undergo several distinct morphological stages as they mature. Depending on the environment, they can take up to 40 years to reach sexual maturity, at which time they return to the Sargasso Sea where each female lays 20 -30 million eggs.

Although the American eel remains widely distributed throughout much of its historical range, the population has decreased significantly over the last several decades, a result of the combined effects of habitat destruction, dam construction, water pollution, parasites, and overfishing, along with a huge increase in demand by Asian food markets following large decreases in the native Asian eel populations.  Although the U.S. Fish and Wildlife Service has not yet provided endangered species protection to the American eel, populations are declining, and according to the International Union for Conservation of Nature (IUCN), the American eel is at very high risk of extinction.

Conservation of the American eel is important for many reasons. American eels are an ecologically important species, playing various roles as prey, predator, and host species that help maintain ecosystem balance. In New York, the American eel is native to 17 of 18 watersheds. It was introduced to Lake Erie but the population was not sustained.  American eel  numbers have been greatly reduced throughout the watersheds of the Great Lakes. It has been completely eliminated from the Allegheny, and has declined to levels below detection in the Chemung and Susquehanna.

Although conservation efforts are now underway, much more will need to be done to restore this important species to healthy, sustainable levels. Efforts to protect and restore this important native species will benefit from additional information on current locations and abundance of native populations.

Map of American eel range in New York pre/post 1976

Brook trout (Salvelinus fontinalis)

Brook trout (Salvelinus fontinalis)
National Fish Habitat Partnership licensed under CC BY-NC-ND 2.0

Brook trout are popular small game fish generally weighing two pounds or less and seldom living more than five years. They require clean high-quality cold water (below 72 degrees Fahrenheit) to survive and depend on clean gravel areas for spawning. Once widely distributed, brook trout are now most commonly found in small streams and the headwaters of larger streams in mountainous areas. Brook trout are so sensitive to environmental conditions that they are considered an environmental indicator species. A large number of brook trout generally indicates a relatively healthy aquatic environment while a decline in the brook trout population often indicates a deteriorating habitat and decreased water quality. Brook trout are native to all 18 New York watersheds and have been introduced to additional areas throughout the state where they are not native. However, intact stream populations of brook trout now exist in only 5% of sub-watersheds, and the vast majority of large rivers that were historically home to thriving brook trout populations no longer support self-reproducing populations.

Although not listed under the Endangered Species Act, the brook trout have suffered decline due to a combination of factors.  Brook trout evolved in waters where there were few other fish species competing for resources. Brook trout do not compete well when non-native fish like yellow perch, bass, golden shiner, and various baitfish (small fish used as bait to attract larger fish, often game fish) are introduced into their waters. In the presence of non-native fish, brook trout populations generally experience a serious decline. As a result, the use of baitfish is prohibited in many brook trout ponds and it is illegal in New York to introduce any fish into waters they did not come from. Brook trout are also particularly sensitive to the effects of acid rain, especially in areas low in limestone that cannot naturally buffer increases in acidity. As a result of acid rain coupled with illegal fishing, in some areas of the Adirondacks, only ~3% of the waters that previously supported brook trout still maintain a viable population. To help counter this problem, New York State has stringent acid rain control requirements and is working to support reductions in power plant emissions outside the state.

An active brook trout restoration program has been established in the Adirondack Park. To secure the survival of the species in this area, ponds are selectively treated with lime each winter to decrease acidity levels, and competitive non-native fish populations are eliminated. When acidity levels suitable for fish survival are reached and competing fish species have been eradicated, ponds are restocked with brook trout.

Map of brook trout range in NY pre/post 1976

Threatened and endangered New York native species


Three types of sturgeon are found in New York waters, the Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus), the Lake Sturgeon (Acipenser fulvescens), and the Shortnose sturgeon (Acipenser brevirostrum). The FishTracker sturgeon primers detect all three species.

Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus)

Atlantic Sturgeon
Arthur Chapman licensed under CC BY-NC 2.0

The Atlantic sturgeon is the biggest and longest-living of the sturgeons found in New York, with adults often reaching 6 to 8 feet or more in length and weighing over 100 pounds. Atlantic sturgeon are anadromous fish, which means that they are born in fresh water, but spend most of their lives in the ocean. Adults migrate from the salty ocean into rivers to lay their eggs in fresh water, sometimes traveling hundreds of miles to spawn, and then returning to the ocean when spawning is complete.

After hatching, young Atlantic sturgeon remain in the fresh water environment for several years before migrating to the ocean, where they live for several more years before reaching sexual maturity. When ready to spawn, each generation of Atlantic sturgeon briefly returns to fresh water to lay their eggs. Female sturgeon can lay up to 2 million eggs during a single spawning season, but females do not spawn every year.

Atlantic sturgeon are toothless bottom feeders, using a tubular mouth to suck up food including plants, invertebrates such as mollusks, worms, and crustaceans, as well as small bottom-dwelling fish. Atlantic sturgeon were once an abundant, commercially important fish in the Hudson river, especially prized for their meat, tough skins that were made into leather, and eggs (caviar). However, over the span of 100 years the catch of Atlantic sturgeon dropped from nearly 7 million pounds in1887 to only 400 pounds in 1989. As a result of this dramatic decrease, Atlantic sturgeon are now considered an endangered species in New York and are protected from fishing. The New York Department of Environmental Conservation, NOAA (National Oceanic and Atmospheric Administration) Fisheries and other groups are attempting to conserve and rebuild Atlantic sturgeon populations along the East Coast. However, the species still faces a number of threats including entanglement in fishing gear, bycatch (the unintentional capture of non- target species), dams and other barriers that impede habitat access, and being hit by boats.

Lake sturgeon (Acipenser fulvescens)

Lake Sturgeon
NYS DEC licensed under CC BY-NC-ND 2.0

The lake sturgeon is New York’s largest fresh water fish, averaging between 3 to 5 feet in length and weighing up to 80 pounds. Lake sturgeon are bottom feeders, eating primarily insect larvae, worms, leeches, other invertebrates including snails and clams, and algae. Lake sturgeon can live up to 80 years or more, and take 4 to 23 years to reach sexual maturity. Once mature, a female can lay 200,000 to 800,000 eggs during a single season, but lake sturgeon only spawn every four to six years. Lake sturgeon lay their eggs from April to June in rapidly moving water, like rocky island shores and quickly moving gravel streams where, after being scattered by currents, the eggs stick to rocks and logs.

The lake sturgeon population underwent a precipitous decline in the 1900s. From 1879 – 1900 the commercial catch of lake sturgeon in the Great Lakes averaged over 4 million pounds. However, by 1929 the commercial harvest of lake sturgeon in Lake Michigan was only 2000 pounds, a result primarily of high demand for their eggs (caviar) and meat. More recently the lake sturgeon population has been further impacted by the construction of dams that cut off spawning and nursery areas; pollution and channelization (altering the course of a waterway to form straight channels) that caused degradation of habitat; and invasive aquatic species. Remnant populations of lake sturgeon are believed to currently exist in several waterways in New York, including the St. Lawrence River, Niagara River, Oswegatchie River, Grasse River, Lake Ontario, Lake Erie, Lake Champlain, Cayuga Lake, and in the Seneca and Cayuga canals. However, the lake sturgeon is currently listed as threatened by the American Fisheries Society since the population has not recovered from the losses that occurred in the 1900s.

To help protect and manage lake sturgeon populations, the New York State Department of Environmental Conservation (DEC) is researching lake sturgeon populations and attempting to reestablish lake sturgeon populations in some tributaries of Lake Ontario, the St. Lawrence River, the Oswegatchie River, Black Lake, the St. Regis River, Oneida Lake and Cayuga Lake.

Shortnose sturgeon (Acipenser brevirostrum)

Shortnose Sturgeon
Chesapeake Bay Program licensed under CC BY-NC 2.0

The shortnose sturgeon is the smallest sturgeon found in New York waterways, averaging under 4 feet long and less than 14 pounds. Shortnose sturgeon are bottom feeders, primarily eating mollusks, worms, insects and crustaceans. Like other sturgeon, the shortnose sturgeon is a long-lived, slow maturing fish. Females take 6 to 17 years to become sexually mature, and can live nearly 70 years. Adult females can lay up to 200,000 eggs in one season, but only breed every 3 to 5 years.

In New York, the shortnose sturgeon is found only in the lower part of the Hudson River, from the southern tip of Manhattan to the Federal Dam at Troy. Shortnose sturgeon overwinter in the Hudson River and spawn in fresh water areas north of Coxsackie. The shortnose sturgeon population in New York was decimated as a result of over-fishing due to demand for its meat and caviar. In addition, during the 1800s and early 1900s tidal rivers like the Hudson were used as dumping grounds for pollutants, causing severe decreases in water oxygen levels that resulted in high die-offs of the once common shortnose sturgeon, along with many other fish species. Damming of the Hudson River, which cut off upriver spawning grounds, also contributed to the shortnose sturgeon decline.

Currently the shortnose sturgeon is listed as endangered by the National Marine Fisheries Service and is therefore protected by the Endangered Species Act. State and national agencies are working to re-establish the shortnose sturgeon population through research and strict regulations prohibiting fishing of this endangered species.

Common native species

Rock Bass (Ambloplites rupestris)

Rock Bass
Chesapeake Bay Program licensed under CC BY-NC 2.0

Rock Bass are found in streams and lakes throughout New York, generally in areas of clear water, abundant vegetation, and rocky or sandy areas. Rock bass average 6 to 8 inches in length but can grow to 10 to 12 inches long and weigh over 1 pound, feeding mostly on aquatic insects, crayfish, and other small fishes. Rock bass take 2 – 3 years to become sexually mature. Adult females lay 2,000 to 11,000 eggs between April and early June, after which the male guards the eggs and the newly hatched young for a brief time.

Rock bass are found in all New York watersheds but are not native to the Adirondacks or to the Atlantic slope watersheds, where they were introduced between 1889 and 1936 by the United States Fish Commission.

Given their population stability, rock bass are listed as a species of “least concern” by the International Union for Conservation of Nature and currently do not require monitoring or conservation management plans, although due to their status as a sport fish, their population is managed in some areas. Because of their abundance and widespread distribution, rock bass can be used for comparative purposes when analyzing results for declining, threatened, and endangered fish species.

A bit of both

A bit of both

Some species are both native and invasive in New York State. They may be native to some watersheds but invasive in others.

Alewives (Alosa pseudoharengus)

Alewife (Alosa pseudoharengus)
Smithsonian Environmental Research Center licensed under CC BY-2.0

Alewives are small herring, usually less than 9 inches long, that live in both deep and shallow waters. Alewives are an anadromous species, which means that the young are born in fresh water but migrate to the sea during their first year and spend most of their adult lives in the ocean, only returning to fresh water coastal streams and rivers to spawn. Ocean migrating alewives are native to several coastal areas of New York, including coastal streams on Long Island, the Lower and Upper Hudson, and the Susquehanna, Chemung and Delaware watersheds.

Alewives also are found in landlocked lakes, where they have been purposely introduced at various times in history as a forage fish (small schooling fish that feed on microscopic plankton and are in turn eaten by seabirds, aquatic mammals, and larger fish, including economically important game fish). Alewives have also been illegally introduced into other waterways in New York. As a result, alewives now occur in all but 4 watersheds throughout the state.

Alewives play a major role in coastal and marine ecosystems. The impact of alewives varies depending on location.  Through much of their native range, Alewife populations have declined significantly, due in part to loss of habitat, decreased access to spawning areas as a result of dam construction and other impediments to migration, degradation of native habitats, fishing, and increased predation. As a result, several coastal states now prohibit catching or possessing alewives. The US National Marine Fisheries Service considers the marine alewife a “Species of Concern”, which means there are concerns about status ongoing threats to the species, but that there is not enough information available to support listing the species under the US Endangered Species Act.

In inland waterways alewives are often considered an invasive species. Alewife introduction has led to reduced zooplankton populations and significant alterations of local food webs. Alewives also prey on larvae of native fishes, depressing populations and contributing to the decline and loss of native fish species such as whitefish, lake herring, and chub in the Great Lakes. Native fish that feed primarily on introduced alewives can also experience a thiamine deficiency since alewives contain high concentrations of thiaminase, an enzyme that breaks down thiamine. Thiamine deficient eggs from females that feed heavily on alewives often show Early Mortality Syndrome (EMS), a condition characterized by abnormal behavior, physical abnormalities, and death. EMS has resulted in lowered reproductive success of ecologically and economically important species like landlocked Atlantic Salmon and native lake trout.

Monitoring alewife populations is important from two perspectives, depending on location. In coastal areas it is important to support efforts to restore and maintain dwindling alewife populations, while in landlocked locations inhabited by invasive alewives, to protect native species it is vital to understand the depth and spread of this often environmentally destructive fish.

How we monitor

How is the monitoring carried out?

A critical part of environmental monitoring is the widespread, accurate collection of water samples. The distribution of monitored species can change very rapidly, and the presence and abundance of species is often unknown in a particular area.

The collection of water samples is at the heart of this project. The engagement of citizen scientists has been important in monitoring both aquatic and terrestrial species. As part of this project, students and teachers help track the range of several invasive species throughout New York, which will greatly contribute to efforts to control the rapid spread of these destructive, costly pests. They also help track the locations of the endangered native species deepwater cisco and American eels, which maps habitat loss or gain.

There are a number of ways of monitoring a body of water for fish species, including visual sightings, catching or trapping, and, more recently, monitoring of species specific DNA from cells shed into the environment. We use a very sensitive technology that monitors DNA found in environmental samples (environmental DNA or eDNA). eDNA is genetic material that is found in environmental samples like water, soil, or air. eDNA can be either nuclear or mitochondrial DNA that is released into the environment as a result of the constant shedding of cells by all organisms into the environment. For example, fish cells can be shed into the water in multiple ways, including in mucous, feces, urine, or blood, or as flaked off skin cells. The cells shed into the environment all contain genetic material (DNA) that is unique to their species. When eDNA is collected, it is made up of DNA from all the different organisms present in the environment, including plants, animals, singled celled organism like protozoa, and bacteria.

Therefore, eDNA can be used to provide information about what organisms are or were recently present in a particular area.

When you isolate eDNA, you don’t know what DNA is in the sample until you conduct a genetic analysis. For example, if you collect a bucket of water from a lake and collect DNA from that water, you potentially have eDNA from all of the organisms living in that lake. If that lake has fish in it, that eDNA will contain some fish DNA, along with many other DNAs from unknown sources. eDNA monitoring has been used in both fresh water and marine environments and provides a highly efficient, sensitive, and cost-effective way to monitor for the presence of different species.

How is the eDNA collected?

We provide a kit containing all of the materials needed to collect and filter multiple water samples from each site to be tested. The water sample is pumped through porous filters that will retain any cells shed by fish in the collection area. Although there is free eDNA in the environment, for this test we will actually be looking at DNA contained in cells released into the environment. That’s because the filters we are using will generally not trap free DNA molecules, but will retain intact cells. Since the half life of DNA (the amount of time required for the amount of measurable DNA to fall to half its value as measured at the beginning of the time period) from fish cells shed into the fresh water is at least 4-6 hours following shedding, the presence of a fish can potentially be detected even if it swam by several hours earlier. The filter paper containing cells from the water sample is placed into a vial containing a solution that protects the DNA from further breakdown and is sent back to Cornell University for DNA extraction and qPCR analysis. A detailed description of the collection technique is available for download.

How is qPCR used to monitor for the presence of eDNA from different species?

To determine if the water collected contained DNA from any of the species being monitored, total eDNA is extracted from the collection filter. A variation of the polymerase chain reaction (PCR) technique is used to determine if the eDNA sample contains DNA from any of the fish species being tested for. The polymerase chain reaction (PCR) is a way to make thousands or even millions of copies of a small, highly specific region of DNA, starting with a very tiny amount of DNA. Generally the copies of DNA made are analyzed at the end of the reaction, usually by running them on an agarose gel. Using standard PCR methods, only the final product made during the PCR reaction can be analyzed. Quantiative PCR (qPCR) is a variation of the standard PCR technique that allows an analysis of the DNA copies being made in real time, as the reaction is actually going on. During the qPCR process, a fluorescent dye is incorporated into the newly made product. The DNA containing the dye can be measured on a special instrument that provides real time information about what DNA containing the dye is present in the reaction and how much.

One question commonly asked is “what does a qPCR test of eDNA actually tell us”. qPCR results are basically a single snapshot in time of the site sampled. The signal produced by the eDNA during the qPCR test relates to the presence or absence of a specific species, and the approximate density of that species at a the location tested at the time the sample was taken. The detection of eDNA from a fish species does not provide information about the age or sex of individuals present at the time of sampling, and does not indicate whether the DNA came from a live organism or a recently dead one (for example a bait fish). Detection sensitivity is limited by how far away from the original source of the DNA the water was collected. The dispersal of eDNA in the environment is affected by factors like rapid water flow or wind. In addition, the rate at which eDNA breaks down is affected by environmental conditions like temperature and the local bacterial community. If the qPCR test signal does not give a positive signal, that may mean that the species being tested for is not present, or is there in such low abundance that the signal cannot be detected. A weak eDNA signal could represent a few cells from a non-resident fish that was transiently at the site tested and left behind some shed cells, or a fish that has recently died, or a fish that has just entered the site and has not yet deposited many cells in the water. A strong signal suggests the presence of a larger population of fish. Secondary testing of the same site later in time can help establish patterns of fish populations. Overall, qPCR is a very sensitive test that can be used to identify specific fish species even when they are present at very low numbers. For example, qPCR analysis of grass carp eDNA in a single water sample has picked up the presence of one grass carp in a 50 acre pond 10 feet deep under good conditions, although a lower sensitivity of one grass carp in a 2 acre pond has been seen when environmental conditions favor the rapid breakdown of shed cells.

The qPCR instrument and representative data collected on Asian carp eDNA.

What happens to the data collected?

The information generated by the qPCR analysis is incorporated into a fish species database identifying all locations tested, and indicating those sites that produced a positive test for any of the species being monitored. This information can help provide a clearer overview of the extent of invasive species throughout New York and will be very useful in framing potential responses. A map depicting all monitoring locations and the results obtained is publicly available. In addition, the qPCR results are returned to the teachers and students for classroom analysis and discussion.