Wildlife forensics turns to eDNA

Genetic residues can show scientists which species live where — even when critters never come out of hiding
Nov 17, 2015 — 7:15 am EST
giant python

More than 4.5 meters (15 feet) long, this Burmese python was caught in the Florida Everglades. Despite their size, these scary predators can be very hard to find. So researchers are tracking them by their eDNA.

Mike Rochford

A Burmese python is scary enough to be featured in a horror flick. Adults can be more than 4.8 meters (16 feet) long. In the Florida Everglades, these snakes have swallowed mammals as large as deer and alligators. Yet spotting a python in the wild has been proving hard.

Scientists describe these snakes as cryptic, meaning they can hide in plain sight.

“It is very difficult to visually detect them,” says Margaret Hunter. She’s a geneticist with the U.S. Geological Survey (USGS) in Gainesville, Fla. The giant snake’s scales have a pattern that blends in with tall swamp grasses. The snakes also are sneaky. They often hide so they can ambush prey. That behavior is an advantage in the snake’s native habitat of Southeast Asia. But it causes havoc in the Florida Everglades. There, Burmese pythons have become an invasive species.

Most likely, people bought some snakes as pets and later released them into the Everglades. Or pet snakes might have escaped into the swamp. Whatever their source, these snakes found a great home there and soon multiplied. And then multiplied some more. A lot more. Today, an estimated 30,000 to 80,000 live in the wilds of Florida. Nobody knows precisely how many because they’re so hard to see.

But those reptiles have been doing plenty of damage. After preying on mammals and birds, numbers of both groups in the Everglades are way down. “Because [the snakes are] so harmful to the environment, we need to be able to manage them,” says Hunter. But, she adds, that’s hard to do without good information about where the snakes are.

With a new method called environmental DNA — or eDNA — scientists can learn where a species is without laying an eye on one. This method detects genetic material left behind by these snakes and every other species. This genetic debris can identify all of the species that call an area home without someone spying them.

Environmental DNA is letting scientists find species faster and more accurately than ever. And it might even point to species no one has yet recorded seeing.

DNA detectives

DNA is the genetic material found in the cells of all living organisms. It looks like a long, twisting ladder. Each rung on that ladder is a pair of chemicals called nucleotides. There are four of these chemicals: adenine, thymine, cytosine and guanine. Scientists refer to them as A, T, C and G for short. Each nucleotide on one long side of the ladder must pair with a specific one on the other side. A’s only pair with T’s. Any C’s must pair with G’s.

Humans have about 3 billion rungs, or base pairs, in their DNA. Other species have more or fewer. The order of base pairs in every individual’s DNA is unique, but their’s will be very similar to other members of its species. Scientists can use that code to identify a species.

Ryan Kelly is an ecologist with the University of Washington at Seattle. He also works at the Center for Ocean Solutions at Stanford University in Palo Alto, Calif. “Traces of DNA are left behind by every species everywhere,” he says. Scratch an itch, and you shed skin cells containing your DNA. Pets and other animals leave behind bits of dead skin known as dander. Reptiles shed skin as they grow. There’s even DNA in poop.

“Just like forensic scientists do at a crime scene every day, we are detecting that trail of DNA that’s left behind,” explains David Lodge. He’s a biologist at the University of Notre Dame in South Bend, Ind.

On the hunt

Scientists are prowling for eDNA throughout the environment — in water, soil, even ice cores. Lodge’s group starts with water. It may come from a lake, a river or some other wet area.

Researchers in the lab then pour that sample through a filter that catches cells and other particles. The filter then goes into a liquid with hard-working chemicals. One chemical in the mix breaks down cell walls to release the DNA. Another chemical grabs onto proteins and other materials that are not DNA. A machine then spins the mix at high speed. DNA-filled liquid floats to the top. Everything else sinks to the bottom. More steps get rid of extra liquid from that top layer.

Additional work might be needed along the way to “clean up” samples even more, Hunter says. For example, her lab had to remove certain compounds produced by trees in the area. Those compounds could have stopped reactions that take place in the next set of steps in her search for python eDNA.

In projects focused on a particular species, those next steps search through the sample for a particular span of rungs from the DNA’s ladder-like structure. This specific sequence of DNA is unique to its species. If it’s found, the method will then make many, many copies of that DNA fragment. This copying process is called the polymerase (puh-LIM-er-ase) chain reaction, or PCR. In effect, it works like a photocopier for DNA.

Using PCR boosts that DNA signal, explains Eva Egelyng Sigsgaard. She’s a biologist with the Natural History Museum of Denmark in Copenhagen. Think of turning up the volume on your cell phone. After you amplify the sound, you can hear the ring over any background noise in the room. “When we amplify the DNA, we make large amounts of the specific DNA that we’re looking for,” Sigsgaard says. Doing that makes that DNA stand out against the “noise” of other species’ genetic debris.

Hunter at USGS tailored her work to find and copy a part of the Burmese python’s DNA that is different from that in all other species. That let her team show for the first time that the big snakes could be detected through eDNA. They described their success in PLOS ONE on April 15, 2015. If eDNA sampling becomes more routine, it could help Florida researchers track the snakes quickly and at relatively low cost.

Fish finders

Fishing expeditions often try to catch whatever is near. But homing in on one particular type of fish isn’t always easy. That’s especially true when a lake or other water body is large, and the desired fish is not common. Again, here’s where eDNA can help.

In recent decades, bighead and other Asian carp species have been found in many American waters. They already have spread through much of the Mississippi River region. Scientists hope to keep them out of the Great Lakes. 

Like Burmese pythons, Asian carps are invasive species. Native to China, each bighead carp can weigh as much as 40 kilograms (88 pounds) and grow to 1.4 meters (4.6 feet). The fish eat huge amounts of not only algae, but also tiny animals and fish eggs. As a result, these invaders can quickly deprive other species of the food they need.

Scientists want to know as soon as signs emerge that the invasive carp is spreading further, says Lodge. In the past, researchers would have tried to catch fish with nets or using equipment that stuns them with an electric shock. But those methods didn’t always catch potentially harmful invaders such as the bighead carp. Also, nets and electric shocks could harm native fish. With eDNA, though, scientists can search for invasive carp without ever touching a fish. Indeed, eDNA has now become an important tool for water managers worried about the carp.

“Another advantage of the eDNA approach is because you’re not capturing the organism, there’s much less of a risk that you’re going to harm it,” Locke adds. “We may not care about harming Asian carp, but we do care about harming threatened and endangered organisms.” So, scientists can search for Asian carp with little risk of hurting native species.

Indeed, that advantage makes eDNA a great tool for hunting rare and endangered species. Sigsgaard used the process to find and copy a unique part of the DNA of the European weather loach. This freshwater fish got its name because it swims to the surface when the air pressure changes. (People who witness that behavior thus come to expect a change in the weather.)

Before Sigsgaard’s study, scientists thought the eel-like fish had vanished from all but one location in Denmark. But with eDNA, she found evidence of the rare fish in samples from two places. She and her colleagues reported the finding in the March 2015 issue of Biological Conservation.

Sigsgaard’s eDNA work took less time than earlier fishing surveys. Better still, she says, “We don’t disturb the animals at all or the ecosystem.” That’s important because she and other scientists want to protect the rare fish. And now her research shows just where that protection is needed.

What’s next?

Environmental DNA can detect more than one species at a time. In fact, it can also tell scientists about whole groups — or even all the species — in an area.

Before eDNA technology, surveys to find species often took months to years. Now eDNA can provide answers quickly. Search results scouting for just one species from a single sample may come back within a few days, reports Hunter. Results of surveys for multiple species take longer, but still might be back within weeks, says Kelly. In both cases, people can act sooner if results show that a species or habitat needs protecting.

“What you’re getting is pretty much a real-time sample of the environment,” at least in seawater, says Kelly. That’s because DNA does not stick around forever. It degrades, or breaks down — often within a few weeks or months. 

In one project, scientists sampled water off of the California coast. Sea otters depend on kelp forests, and their DNA was found there — but not elsewhere. Dolphin DNA was found offshore but not in kelp forests. If DNA lasted for years, water currents would have carried it much farther, Kelly says. The scientists would have found their DNA in places where the animals don’t live.

How fast eDNA breaks down can differ with the species. Some also shed DNA at different rates. And various features of the environment can affect the shedding rate. One project at Notre Dame is measuring DNA as it flows through an experimental ecosystem at a local county park. Researchers can change conditions in the system and see whether this affects the amount of eDNA.  

One other big challenge is that eDNA can’t yet say how many individuals are present. It can only tell if at least one member of its species is present. And the results don’t say if that DNA came from a few animals nearby or many animals inhabiting a large area. Scientists hope future improvements might resolve such details. Then they could see if the size of a population is growing or shrinking.

Even now, though, the technology is already “an amazingly powerful tool” for research, says Michael Pfrender. He’s a geneticist at Notre Dame. “I think we’re just starting to appreciate how powerful this really is.”

“Everything we know about the world depends on people going out and counting things or finding things,” adds Kelly. Environmental DNA “allows us to do that in a way that’s potentially much better and much faster and much cheaper.”

 

Word Find (click here to enlarge for printing)

Power Words

(for more about Power Words, click here)

algae    Single-celled organisms, once considered plants (they aren’t). As aquatic organisms, they grow in water. Like green plants, they depend on sunlight to make their food.

amplify     To increase in number, volume or other measure of responsiveness.

bacterium (plural bacteria) A single-celled organism. These dwell nearly everywhere on Earth, from the bottom of the sea to inside animals.

base pairs  (in genetics) Sets of nucleotides that match up with each other on DNA or RNA. For DNA, adenine (A) matches up with thymine (T), and cytosine (C) matches up with guanine (G).

biology  The study of living things. The scientists who study them are known as biologists.

carp    A type of catfish, usually referring the Asian freshwater varieties that can grow to enormous size and are often farmed as food.

cell   The smallest structural and functional unit of an organism. Typically too small to see with the naked eye, it consists of watery fluid surrounded by a membrane or wall. Animals are made of anywhere from thousands to trillions of cells, depending on their size.

chemical     A substance formed from two or more atoms that unite (become bonded together) in a fixed proportion and structure. For example, water is a chemical made of two hydrogen atoms bonded to one oxygen atom. Its chemical symbol is H2O.

chemical reaction  A process that involves the rearrangement of the molecules or structure of a substance, as opposed to a change in physical form (as from a solid to a gas).

core In geology, Earth’s innermost layer. Or, a long, tube-like sample drilled down into ice, soil or rock. Cores allow scientists to examine layers of sediment, dissolved chemicals, rock and fossils to see how the environment at one location changed through hundreds to thousands of years or more.

cryptic  Having abehavior that is mysterious or possessing the ability to hide by concealing itself within the surrounding environment.

dander Flakes of skin in an animal’s fur or hair.

database  An organized collection of information.

debris  Scattered fragments, typically of trash or of something that has been destroyed. Space debris, for instance, includes the wreckage of defunct satellites and spacecraft. 

degrade To break down into smaller, simpler materials — as when wood rots or as a flag that’s left outdoors in the weather will fray, fade and fall apart. (in chemistry) To break down a compound into smaller components.

DNA  (short for deoxyribonucleic acid) A long, double-stranded and spiral-shaped molecule inside most living cells that carries genetic instructions. In all living things, from plants and animals to microbes, these instructions tell cells which molecules to make.

DNA sequencing  The process of determining the exact order of the paired building blocks — called nucleotides — that form each rung of a ladder-like strand of DNA. There are only four nucleotides: adenine, cytosine, guanine and thymine (which are abbreviated A, C, G and T). And adenine always pairs up with thymine; cytosine pairs with guanine.

dolphins  A highly intelligent group of marine mammals that belong to the toothed-whale family. Members of this group include orcas (killer whales), pilot whales and bottlenose dolphins.

ecology  A branch of biology that deals with the relations of organisms to one another and to their physical surroundings. A scientist who works in this field is called an ecologist.

ecosystem  A group of interacting living organisms — including microorganisms, plants and animals — and their physical environment within a particular climate. Examples include tropical reefs, rainforests, alpine meadows and polar tundra.

eel    A fish with a snake-like body and no scales. Many migrate from freshwater to salt water when it’s time to spawn.

endangered  An adjective used to describe species at risk of going extinct.

environment    The sum of all of the things that exist around some organism or the process and the condition those things create for that organism or process. Environment may refer to the weather and ecosystem in which some animal lives, or, perhaps, the temperature, humidity and placement of components in some electronics system or product.

environmental DNA (eDNA)  A tool for detecting the presence of a species solely from the DNA it has left in the environment.

enzymes   Molecules made by living things to speed up chemical reactions.

forensics  The use of science and technology to investigate and solve crimes.

genetic Having to do with chromosomes, DNA and the genes contained within DNA. The field of science dealing with these biological instructions is known as genetics. People who work in this field are geneticists.

genetic sequence   A string of DNA bases, or nucleotides, that provide instructions for building molecules in a cell. They are represented by the letters A,C,T and G.

Great Lakes  A system of five interconnected lakes — Superior, Michigan, Huron, Erie and Ontario — the Great Lakes constitute the largest freshwater source in the world (based on surface area). They hold an estimated 6 quadrillion gallons of water, or about a fifth of the world's fresh surface water. To give some perspective on that amount, the lakes' water would, if spread evenly, cover the 48 touching U.S. states to a depth of about 2.9 meters (9.5 feet) deep.

habitat The area or natural environment in which an animal or plant normally lives, such as a desert, coral reef or freshwater lake. A habitat can be home to thousands of different species.

invasive species  (also known as aliens) A species that is found living, and often thriving, in an ecosystem other than the one in which it evolved. Some invasive species were deliberately introduced to an environment, such as a prized flower, tree or shrub. Some entered an environment unintentionally, such as a fungus whose spores traveled between continents on the winds. Still others may have escaped from a controlled environment, such as an aquarium or laboratory, and begun growing in the wild. What all of these so-called invasives have in common is that their populations are becoming established in a new environment, often in the absence of natural factors that would control their spread. Invasive species can be plants, animals or disease-causing pathogens. Many have the potential to cause harm to wildlife, people or to a region’s economy.

kelp    Large seaweeds that are usually a type of brown algae. They grow underwater and form large forests, providing habitat for many organisms. Some kelp forests are so large they can be seen from space.

mammal  A warm-blooded animal distinguished by the possession of hair or fur, the secretion of milk by females for feeding the young, and (typically) the bearing of live young.

molecule  An electrically neutral group of atoms that represents the smallest possible amount of a chemical compound. Molecules can be made of single types of atoms or of different types. For example, the oxygen in the air is made of two oxygen atoms (O2), but water is made of two hydrogen atoms and one oxygen atom (H2O).

native    Associated with a particular location; native plants and animals have been found in a particular location since recorded history began. These species also tend to have developed within a region, occurring there naturally (not because they were planted or moved there by people). Most are particularly well adapted to their environment.

nucleotides  The four chemicals that link up the two strands that make up DNA. They are: A (adenine), T (thymine), C (cytosine) and G (guanine). A links with T, and C links with G, to form DNA.

organism Any living thing, from elephants and plants to bacteria and other types of single-celled life.

particle  A minute amount of something.

polymerase chain reaction (PCR)  A biochemical process that repeatedly copies a particular sequence of DNA. A related, but somewhat different technique, copies genes expressed by the DNA in a cell. This technique is called reverse transcriptase PCR. Like regular PCR, it copies genetic material so that other techniques can identify aspects of the genes or match them to known genes.

proteins     Compounds made from one or more long chains of amino acids. Proteins are an essential part of all living organisms. They form the basis of living cells, muscle and tissues; they also do the work inside of cells. The hemoglobin in blood and the antibodies that attempt to fight infections are among the better-known, stand-alone proteins. Medicines frequently work by latching onto proteins.

reptile   Cold-blooded vertebrate animals, whose skin is covered with scales or horny plates. Snakes, turtles, lizards and alligators are all reptiles.

sea otter  A member of the weasel family, sea otters have the densest fur known among animals. That helps keep them warm in frigid waters, because these marine mammals don’t produce blubber — a thick layer of fat — as do seals and walruses.

sequencing Technologies that determine the order of nucleotides or letters in a DNA molecule that spell out an organism’s traits.

species A group of similar organisms capable of producing offspring that can survive and reproduce.

survey  (in statistics) A questionnaire that samples the opinions, practices (such as dining or sleeping habits), knowledge or skills of a broad range of people. Researchers select the number and types of people questioned in hopes that the answers these individuals give will be representative of others who are their age, belong to the same ethnic group or live in the same region.

technology The application of scientific knowledge for practical purposes, especially in industry — or the devices, processes and systems that result from those efforts.

NGSS: 

  • MS-LS2-1
  • MS-LS2-2
  • MS-LS2-5
  • MS-ESS3-3
  • MS-ETS1-4
  • HS-LS1-1
  • HS-LS2-1
  • HS-LS2-2
  • HS-LS2-7
  • HS-ESS3-3
  • HS-ESS3-4
  • HS-ESS3-6

M. Hunter et al. “Environmental DNA (eDNA) sampling improves occurrence and detection estimates of invasive Burmese Pythons.” PLOS ONE. Vol. 10, April 15, 2015. doi: 10.1371/journal.pone.0121655.

E Sigsgaard et al. “Monitoring the near-extinct European weather loach in Denmark based on environmental DNA from water samples.” Biological Conservation. Vol. 183, March 2015, p. 46. doi: 10.1016/j.biocon.2014.11.023.

P. Thomsen and E. Willerslev. “Environmental DNA — An emerging tool in conservation for monitoring past and present biodiversity.” Biological Conservation. Vol. 183, March 2015, p. 4. doi: 10.1016/j.biocon.2014.11.019.

Institute for Journalism & Natural Resources. “Talking Science, Telling Stories: A Science Communication Workshop at the University of Notre Dame.” March 2, 2015.

C. Turner et al. “Improved methods for capture, extraction, and quantitative assay of environmental DNA from Asian bigheaded carp (Hypophthalmichthys spp.).” PLOS ONE. Vol. 9, December 4, 2014. doi: 10.1371/journal.pone.0114329.

R. Kelly et al. “Harnessing DNA to improve environmental management.” Science. Vol 344, June 27, 2014, p. 1455. doi: 10.1126/science.1251156.

C. Jerde et al. “Detection of Asian carp DNA as part of a Great Lakes basin-wide surveillance program.” Canadian Journal of Fisheries and Aquatic Sciences. Vol. 70, April 2013, p. 522. doi: 10.1139/cjfas-2012-0478.

Further Reading

S. Perkins. “Cool jobs: Crime scene detectives.” Science News for Students. December 5, 2012.

J. Raloff. “Python-palooza.” Science News for Students. August 22, 2012.

Questions for Wildlife forensics turns to eDNA