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September/October 2009 cover
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The Tales Genes Tell

Genetics experts at the Smithsonian’s National Zoo crack codes to solve animal mysteries

by Susan Lumpkin

If there are mysteries to be solved at the National Zoo, genetics expert Robert Fleischer and his team in the Zoo’s Genetics Lab are often called to action. After a prehensile- tailed porcupine was born last summer, there was no easy way to determine its sex. All it took was one quill from the porcupine kit, and the lab scientists were able to conduct a DNA analysis to determine that the fluffy youngster was a female. The same process answered Zoo keepers’ questions about a newly hatched kiwi—just one feather was enough to say, “It’s a boy!” The Genetics Lab also conducts paternity analyses to verify “who’s the father” of some Zoo babies. Other times, the scientists help the Zoo’s pathologists by checking for deadly chytrid fungus in frogs and for other parasites in birds and mammals.

coendou
Prickly situation? Zoo scientists learned this prehensile-tailed porcupine’s gender by analyzing its quill. (Jessie Cohen/NZP)

When a Zoo crane died in 2008, a bite wound suggested it was killed by a carnivore that sneaked into its enclosure, a highly unusual event, even given that the Zoo is set within a natural area full of wild predatory animals. But which of the potential suspects that roam Rock Creek Park was it? A feral dog or cat, a coyote, or one of two kinds of fox that inhabit the park? To solve the mystery, Fleischer went into “CSI mode,” referring to the popular crime-solving television drama. He and his colleagues managed to collect saliva from the bite and use sophisticated equipment to analyze the DNA in the saliva. They were then able to match the DNA code in the saliva to the known DNA of a particular species. The genetic clues left no doubt: It was a gray fox that did the deed. This knowledge enabled keepers to appropriately bolster the defenses of bird enclosures, successfully preventing any further such incident.

“DNA is DNA,” says Fleischer. That’s why his lab can handle samples from such a diverse array of species to answer a questions about mammals that range from bats to elephants, birds from sparrows to ostriches, and a wide range of other organisms including fish, mosquitoes, protozoan parasites, and bacteria. Some of the studies conducted in the lab are part of long-term research projects by lab scientists and their close colleagues in the Zoo’s other science centers and at the Smithsonian’s National Museum of Natural History (NMNH). Others are carried out by graduate and postdoctoral students who come to the lab as one of the few place to do the DNA analyses required to answer their research questions.

Bigger, Faster, Drier

maned wolf
A feather from a newly-hatched kiwi
chick contained information about its gender and more. (Jessie Cohen/NZP)

All of this state-of-the-art sleuthing has been done inside an unassuming old stone building right on the Zoo’s grounds. The Genetics Lab, founded by Fleischer in 1991, is a section of the Zoo’s Center for Conservation and Evolutionary Genetics, which Fleischer now heads. The lab has an unusual Smithsonian history. It was first part of the Zoo, then became part of NMNH, and is now a joint program of both—all without ever moving an inch from its original quarters in the old Propagation Building behind the Small Mammal House. The Prop Building is not only old and cramped, it’s prone to flooding whenever Rock Creek’s waters spill over.

Soon the lab can weather rainstorms with no problem. In October, the 15 or so scientists and students currently working at the Genetics Lab will move their base of operations from the Prop Building to a sparkling new lab space set on higher ground at the Zoo. The new Genetics Lab will offer bench space for 15 people to work without doubling up and a more efficient layout. Better yet, the new lab’s location—near the vet hospital, the Conservation and Science building, and the pathology department—will facilitate the staff’s collaboration with those units. And for Fleischer and his colleague Jesus Maldonado, collaboration is the name of the game in applying genetic analysis to solve new problems, whether it is within the Zoo, with their Smithsonian colleagues, or with scientists around the world.

Secrets From the Past

They say dead men tell no tales, but today even extinct species can talk to us. They speak in the language of their DNA, translated by scientists through sophisticated processes that make their stories intelligible. Fleischer, Maldonado, and other scientists who work in the Genetics Lab are among the world’s best translators. They are detectives who decipher the language of genes to solve a host of biological mysteries about extinct species and living ones, too. They investigate cold cases, such as tracing the evolutionary history of an extinct, mostly stripeless zebra known as a quagga. They pursue hot cases, such as predicting the global spread of bird flu.

A specialty of the Genetics Lab is studying ancient DNA, and the lab is one of only a handful in North America with recognized excellence in the tricky procedures necessary to get reliable results. Ancient DNA is extracted from a no-longer-living source, such as hair, tissue, or teeth from museum specimens or bones preserved naturally in permafrost. Sometimes the sample is recent, and other times it dates to hundreds of thousands of years ago.

Hidden Meaning

Beyond solving mysteries of the past, genetic studies have very real applications to our world today. Very often research using ancient, modern, or both types of DNA can help scientists better conserve living species.

Working with colleagues from the Wildlife Institute of India, and using both modern and ancient DNA, Maldonado and Fleischer discovered that the Indian subcontinent was home to two distinct ancient lineages of wolf: an Indian wolf and a Himalayan wolf. These wolves were previously lumped with the wide-ranging gray wolf species that we know in North America and Eurasia. Finding out that they are probably two different species is extremely important from the conservation planning point of view. The Indian wolf population consists of only 2,000 to 3,000 animals, while the Himalayan wolf in India may number as few as 350 individuals. Little is known about either of these wolves, but both are persecuted by people and are not legally protected. Knowing that the Indian and Himalayan wolves are in greater danger of extinction than the better-known gray wolves helps conservationists target their efforts.

Another leadership area of the Genetics Lab is using non-invasive methods to collect DNA from living animals—many of which are hard to find or observe, much less catch. What clues can scientists use that animals leave behind? Answers can often be found in their poop. Maldonado and others have been perfecting methods to extract and study DNA from feces. This yields valuable information about an animal’s ecology, behavior, and genetics—and the more you know, the easier it is to help it.

In a research project on endangered San Joaquin kit foxes in California, Maldonado, Katherine Ralls, a research scientist in the Center for Conservation and Evolutionary Genetics, and others systematically collected the foxes’ scat with the help of specially trained dogs. Once they extracted DNA from the kit fox scat, they were able to identify individuals and their sex, to track the foxes’ movements through the study site, and even to understand social relationships by counting the number of individual foxes that contributed their scat to shared latrines and measuring their kinship.

maned wolf
Maned wolves offer valuable clues to geneticists.(Mehgan Murphy/NZP)

Similarly, Maldonado is working with Louise Emmons of NMNH to apply scat DNA analysis in her study of maned wolves in Argentina. Looking at samples from Argentinean maned wolves as well as those from wolves in the Zoo’s breeding colony at the Front Royal, Virginia, campus—which originated from Brazil—they learned that maned wolves as a species have low genetic diversity. Fortunately for their conservation in Argentina, the animals in Emmons’ study site exhibit a good amount of the genetic variability that exists in the species. The scientists are also using scat DNA to determine kinship among individuals in her study area to determine, for instance, whether neighbors are closely related in order to better understand the population’s social structure.

In a new collaboration with the Zoo’s Conservation Ecology Center, analysis of DNA extracted from tiger scats will be used to determine how much, if any, genetic interchange exists between tiger populations living in different Indian tiger reserves. Maldonado is also working with Penny Spiering of the Zoo’s Center for Species Survival on a study of inbreeding in African wild dogs.

DNA and Disease

One of Fleischer’s major long-term research programs focuses on avian malaria: the parasite that causes the disease, the mosquitoes that transmit it, and the birds that suffer from it. Avian malaria is similar to human malaria but only some birds are susceptible; species that evolved with the parasite have resistance to its ill-effects. But neither the parasites nor the mosquitoes that transmit them were found in Hawaii until after the mosquitoes were accidently introduced in the 1800s and the malaria in the 1900s. For many of the islands’ native birds, avian malaria was lethal, and the disease contributed to the extinction or near-extinction of a host of birds. Hawaii’s 57 species of honeycreepers were particularly hard hit, with avian malaria dealing a death blow to many of the more than 30 species that went extinct in the last few hundred years. And avian malaria continues to limit the distributions of the remaining species to high-elevation forests where colder temperatures don’t favor the mosquitoes.

Using his DNA detective’s tool kit, Fleischer and his colleagues have determined that some honeycreepers are evolving resistance to avian malaria and thus are recovering in low-elevation forests. This is the good news. The bad news is that a different genetic type of the parasite-transmitting southern house mosquito, more recently arrived in Hawaii, may be capable of thriving at high elevations.

In a study that looked at the DNA of more than 700 southern house mosquitoes from around the world, the researchers found that there are several distinct genetic strains of the species. The first strain to reach Hawaii was from a New World source—perhaps Mexico. Since then, however, at least one other strain has been introduced, this time from the southern Pacific, and these mosquitoes are adapted to cold environments like those of New Zealand in summer—and high-elevation habitats in Hawaii.

The long-term impacts of this genetic discovery about mosquito adaptability are still to be determined, but you can be sure that Genetics Lab scientists will be on case. As long as they keep translating the stories told by genes, we can better understand changes in the natural world.

—Freelance writer Susan Lumpkin has written several articles on the fascinating work of the Zoo’s Genetics Lab.

 

More: "A Simple Sequence"

More: "Looks Can Be Deceiving"

 

 

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Smithsonian Zoogoer 38(5) 2009. Copyright 2009 Friends of the National Zoo. All rights reserved.