Pygmy Elephants Get Protection Boost from Genetics

To help protect a diminutive elephant researchers are taking an innovative look at the pachyderm's genome.

The goal is to understand the genetic diversity of pygmy elephants on the island of Borneo. Numbering about 2,000, these babyish-looking elephants are the most endangered subspecies of Asian elephant. They live primarily in the Malaysian state of Sabah on Borneo, where they are threatened by the loss and fragmentation of their forest, often by development associated with palm oil, widely used, edible plant oil.

"We are interested in looking at the diversity of elephants around the whole distribution range in Sabah," said study researcher Reeta Sharma, a postdoctoral fellow at the Instituto Gulbenkian de Ciência (IGC) in Portugal.

Sharma and colleagues want to see how genetic diversity is distributed within the Borneo elephant population and how the fragmentation — or breaking up — of their forest habitat is affecting it by, for example, isolating groups of elephants. Increased isolation can be problematic because it means inbreeding, which can lead to more sickly and vulnerable animals. Their results suggest low genetic diversity in the pygmy elephants. [Amazing Photos of Pygmy Elephants]

Not easy to find

From the outset, the researchers knew they would need a close look to find markers within the elephant's genetic code that they could use to assess diversity. Markers are spots in the sequence that should vary between individual animals.

Only one previous study, published in 2003, conducted a genetic analysis of Borneo elephants. Using information developed from other Asian elephants, this study found low levels of diversity among Borneo elephants, meaning researchers were on the hunt for needles in a haystack.

"There is diversity there but you need genomes to look at it," said study researcher Lounès Chikhi, a researcher at the Centre National de la Recherche Scientifiquein France and a principal investigator at the IGC.

A genome is an organism's DNA (deoxyribonucleic acid) sequence. Sharma and Chikhi hoped to harness rapidly evolving technology for reading large amounts of this sequence to identify markers they could use to assess diversity.

Before the arrival of genome-sequencing technology, identifying markers was a cumbersome and tedious process. Often, researchers had to rely on markers developed for relatives of the animal in question, the researchers said.

The Borneo elephant presented a particular challenge, because until this current study no sequencing work had been done on it.

The techniques

Sharma and Chikhi tried two genomic techniques to find genetic markers that differed from elephant to elephant. The first technique is known as shotgun sequencing; it breaks the genome into small pieces before sequencing them. Researchers at the University of Connecticut, led by Rachel O'Neill, performed this sequencing and identified the markers.

The second technique, known as RAD-seq, examined small subsets of the genome defined by sites at which an enzyme had cut the DNA sequence. A biotech company in Oregon, Floragenex, performed this work on blood samples from eight elephants.

Blood from Borneo elephants is hard to come by, but company vice president, Jason Boone, located one of the study elephants, a female named Chendra, at the Oregon Zoo, and arranged to have a sample taken from her. The other samples were collected from elephants in Sabah.

Each technique generated a unique set of thousands of markers.

"What we show is the two methods are good, but they have differences," Chikhi said.

He and Sharma are currently applying both sets of markers to DNA found in elephant fecal samples in Sabah.

Helping others

The genomic approach may make it possible to relatively quickly identify markers and assess them in samples from other rare and endangered species in which little to no prior genomic work has been done, according to Chikhi and Sharma, whose research was published in November in the journal PLoS ONE.

Others are beginning to apply genomics to endangered species.

For instance, in June 2011, researchers reported sequencing the whole genomes of two Tasmanian devils in the hopes of providing information that might help conservationists protect the animals from a devastating facial cancer.

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NASA's Mars Rover Curiosity Had Planetary Protection Slip-Up (SPACE.com)

All NASA spacecraft sent to other planets must undergo meticulous procedures to make sure they don't carry biological contamination from Earth to their destinations.

However, a step in these planetary protection measures wasn't adhered to for NASA's Mars Science Laboratory rover Curiosity, now en route to the Red Planet, SPACE.com has learned.

The incident has become a lessons-learned example of miscommunication in assuring that planetary protection procedures are strictly adhered to.

The issue involves a set of drill bits carried by the Curiosity rover, which launched Nov. 26 to Mars. When project developers made an internal decision not to send the equipment through a final ultra-cleanliness step, it marked a deviation from the planetary protection plans scripted for the Mars Science Laboratory mission. [Photos: Watching the Mars Rover Curiosity Blast Off ]

That judgment, however, didn't reach NASA's chief protector of the planets until "very late in the game," said Catharine "Cassie" Conley, NASA's planetary protection officer. "They didn't submit the request for the deviation not to comply with their planetary protection plan until several months ago," she emphasized.

Conley told SPACE.com that the initial plan called for placing all three of the drill bits inside a sterile box. Then, after Curiosity landed, the box would be opened for access to the sterilized bits via the rover's robot arm, extracted one by one and fit onto a drill head as the mission progressed.

But in readying the rover for departure to Mars, the box was opened, with one drill bit affixed to the drill head, Conley said. Also, all of the bits were tested pre-launch to assess their level of organic contamination. While done within a very clean environment, that work strayed from earlier agreed-to protocols, she said.

"That's where the miscommunication happened," Conley said. "I will certainly expect to have a lessons-learned report that will indicate how future projects will not have this same process issue. I'm sure that the Mars exploration program doesn't want to have a similar process issue in the future. We need to make sure we do it right."

Equatorial target

Conley said the deviation from protocol was reinforced by science and project officials concluding that Curiosity's target landing spot, Gale Crater, is free of potentially life-harboring ice — at least at depths that the drill bits would penetrate.

"That reinforced the reasonableness of not having the drill bits sterilized, because there's unlikely to be 'special regions' in the Gale Crater landing site," Conley said.

The $2.5 billion Mars Science Laboratory mission was designed to comply with a requirement to avoid going to any site on the Red Planet known to have water or water-ice within 3.3 feet (1 meter) of the surface.

Adhering to cleanliness standards is a way to make sure the mission does not transport Earth life to Mars. Doing so preserves the ability to study that world in its natural state and also avoids contamination that would obscure an ability to find native life on that planet, if it exists.

Conley emphasized that the Curiosity assembly team and technicians did an excellent job of keeping Curiosity cleaner than any robot that NASA' s sent to Mars since the Viking lander in the 1970s.

Still, the decision to not keep the drill bits ultra-clean shows the process needs to be fixed, Conley said.

"It would have been better for them to check with me before they opened the box of bits to confirm that it was okay … rather than trying to ask for it afterwards," she said. "In this case it was fine. But for future missions we want to make sure that they ask beforehand."

Habitable environments

The Mars Science Laboratory is not a life-detection mission. Rather, it will study whether the Gale Crater area of Mars has evidence of past and present habitable environments.

"Direct life detection is inherently difficult, some would argue currently impossible, because there is no uniform agreement on life," said Scott Hubbard, the former "Mars Czar" for NASA Headquarters in Washington.

Hubbard is now a professor in the Department of Aeronautics and Astronautics at Stanford University, Stanford, Calif., and author of the new book "Exploring Mars — Chronicles from a Decade of Discovery," published by the University of Arizona Press.

"There is no mathematical expression for life as there is gravity … only a series of attributes such as complexity, reproduction, metabolism, responsiveness and so on," Hubbard told SPACE.com. "We don't have a 'Star Trek' tricorder that says 'It's alive, Jim'."

Mars sample return

On-the-spot detection of life is difficult, underscoring the need to return to Earth well-selected samples from the Red Planet for analysis in a lab, Hubbard noted.

There are three reasons for pushing forward on a Mars return sample effort, he said: The best laboratory equipment can be employed, much of which cannot be reduced to spacecraft size; many labs and many scientists can be utilized to cross-check each other with alternate techniques; and discoveries can be followed and rechecked years later with new tools and techniques and hypotheses.

"The treaty-type agreements on planetary protection specify very rigorous levels of cleanliness to prevent forward and backward contamination," Hubbard said. "Spacecraft going to potential habitable zones on Mars must be cleaned to an amazing degree, even sterilized. Samples returned to Earth will be treated as if they were highly infectious until demonstrated otherwise."

Price tag estimates for a "Sample Receiving Facility" here on Earth have ranged as high as $300 million, Hubbard said. "Nevertheless, I think it is all worth it to find out 'Are we alone?'… 'Did life ever arise on Mars?'" he said.

Leonard David has been reporting on the space industry for more than five decades. He is a winner of this year's National Space Club Press Award and a past editor-in-chief of the National Space Society's Ad Astra and Space World magazines. He has written for SPACE.com since 1999.

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