Month: June 2016

Postcards from the field: Brandon Semel in Madagascar

Post author By jcoker
Post date June 22, 2016

POSTCARD from:

Brandon Semel, Ph.D. student in the Department of Fish and Wildlife Conservation

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The range of the Golden Crowned Sifaka on the island of Madagascar

“I’m currently writing this at 2:30 am, Madagascar time, as I wait for the local taxi brousse (or bush taxi) to take me from the small town of Daraina to the coastal cities of Vohemar and Sambava where I can finalize my research permits. Let’s just say that things here don’t always go according to a western schedule, as my ride is already half an hour late and there’s no sign of car, driver, or even other passengers! Fortunately, music from the town’s only discothèque is loud enough to keep even the drowsiest of travelers wide awake.

For the past two months, I’ve been in and out of Daraina and its surrounding forest fragments conducting surveys to estimate population sizes of several lemur species. The focus of my study is on the critically endangered golden crowned sifaka, which is found only within about a 40 mile radius of town. But, as lemurs are earth’s most threatened group of mammals and are endemic to (or found only on) the island of Madagascar, we’re keeping records of the six other lemur species also found in the area.

Golden-crowned sifakas are definitely among the most charismatic of the lemurs, with their long legs and tail that help them to leap 20-30 feet between tree trunks, bright white bodies accented by a crown of golden hair (thus the name!), and mellow disposition expressed by bright, orange eyes. Unlike other lemurs in the region, they’re protected from hunters by local taboos. However, as people from other regions come here to try their luck at finding gold, and law enforcement is still recovering from a recent coup d’état, this protection may be short-lived. Perhaps an even greater threat is the continued loss of habitat due to slash-and-burn agriculture, logging, and ever-expanding cattle pasture that are a direct result of Madagascar’s rapidly growing human population.

Thanks to conservation efforts by the Malagasy NGO, Fanamby, I have some hope for the region’s incredible biodiversity. But long-term protection can only be guaranteed if local people embrace the importance of conserving their few remaining natural resources. As one of the poorest countries in the world, Madagascar’s rich biodiversity has significant potential to bring in much needed international tourist and research dollars. Hopefully the continued presence of researchers, such as myself, not only will improve our understanding of how species are responding to ongoing global change, but also will impress upon the locals the international significance of their natural heritage.

Well, finally! It’s 4 am and we’re about to see just how many people, mattresses, sacs of rice, and live chickens can be squeezed into what should be a 12 passenger van (right now I count at least 20, 1, 10, 9, plus luggage). It’s going to be a long, bumpy ride!”

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Photo credit (Range map): IUCN Red List of Threatened Species, species assessors and the authors of the spatial data. [CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons

Photo credit (Sifaka): By Jeff Gibbs (email & Flickr) [CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons

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Evolution News

Joel McGlothlin’s research on snake resistance to tetrodotoxin featured in the Atlantic Magazine

Post author By jcoker
Post date June 10, 2016

From VT News

A select group of garter snakes can thank their ancestors for the ability to chow down on a poisonous newt and live to tell the tale.

Common garter snakes, along with four other snake species, have evolved the ability to eat extremely toxic species such as the rough-skinned newt — amphibians that would kill a human predator — thanks to at least 100 million years of evolution, according to Joel McGlothlin, an assistant professor of biological sciences in the Virginia Tech College of Science and a Fralin Life Science Institute affiliate.

The nature of that evolution was recently established by McGlothlin’s team and will be published June 20 in the journal Current Biology.

The international team of researchers discovered that the ability to withstand the toxin that the newt produces evolved following a “building blocks” pattern, where an evolutionary change in one gene can lead to changes in another.

In this case, over time, amino acids in three different sodium channels found in nerves and muscle changed, allowing select snakes to resist the numbness and paralysis typically brought on by the toxin.

Resistant muscle gives snakes the best protection against the newt’s toxin, but there’s a catch: Resistant muscle can evolve only in species that already have resistant nerves. McGlothlin’s team found that the ancestors of garter snakes gained toxin-resistant nerves almost 40 million years ago.

“Garter snakes and newts are locked in a coevolutionary arms race where as the newts become more toxic, the snakes become more resistant,” said McGlothlin, who is also affiliated with the Global Change Center at Virginia Tech. “However, without the leg-up provided by those resistant nerves, snakes wouldn’t have been able to withstand enough toxin to get this whole process started.”

This arms race is most intense in pocketed regions along the West Coast, where rough-skinned newts and garter snakes co-exist.

McGlothlin and his team sequenced three sodium channel genes found in 82 species (78 snakes, two lizards, one bird, and one turtle) and mapped the changes they found to evolutionary trees to date when toxic resistance emerged in each. They found that, as time went on, some groups of snakes built up more and more resistance to the toxin. These changes always happened in the same order, with resistant nerves evolving before resistant muscle.

The next step is to see if this pattern is a general phenomenon in other species. A few bird species can also eat the newt and survive. McGlothlin and his team recently received a grant from the National Science Foundation to test whether birds have built up resistance in the same way as snakes.

This work is not just relevant to understanding what snakes have for dinner. “We think that the garter snake’s evolved resistance to the newt’s toxin can be used as a model for understanding complex adaptations that involve more than one gene,” McGlothlin said.

“This study provides insight into the stepwise evolution of an ecologically important trait (resistance to prey toxins), and revealed that the adaptive benefit of changes to individual components of the trait were contingent on antecedent changes in other components,” said Jay Storz, the Susan J. Rosowski Professor of Biology at the University of Nebraska, who was not involved in the research. “This discovery has general significance for understanding the evolution of complex traits.”

Story by Lindsay Key

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This news was also highlighted in the Washington Post and the Atlantic magazine:

The Very Long War Between Snakes and Newts

From The Atlantic

In the mountains of Oregon, there are newts with so much poison in their skin that each could kill a roomful of people. There are also snakes that eat those newts; they’re completely resistant to the toxins. The two are locked in an evolutionary arms race. As the newts become more toxic, the snakes become more resistant. One team of scientists has been studying this evolutionary conflict for five decades, and they’ve now shown that its seeds were planted 170 million years ago—before either snakes or newts even existed.

We know about this ancient conflict because of a young undergraduate student named Edmund “Butch” Brodie Jr. In the early 1960s, he heard a local legend about three hunters who were found dead at their campsite, with no sign of theft, struggle, or foul play. The only thing amiss at the scene was a dead roughskin newt, which the hunters had accidentally boiled in their coffee pot. These dark-backed amphibians have vibrant yellow-orange bellies, which they display to predators by arching their heads and tails over their backs—a clear sign that they’re poisonous. Perhaps those poisons killed the hunters.

Butch tested this idea by collecting newts, grinding up tiny amounts of their skin, and feeding the extracts to other animals. Everything died. The newts proved to be absurdly lethal. Another team of chemists showed that they carry tetrodotoxin (TTX)— the same poison found in the skins and livers of pufferfish. It’s ten thousand times more toxic than cyanide, and among the deadliest substances in nature. Each newt seemed to carry enough to kill any predator hundreds of times over. Why would they be so ludicrously toxic?

Butch found a clue when he checked one of his traps and found a common garter snake devouring a newt. Overcoming his mild phobia of snakes, he collected some and found that they resisted amounts of tetrodotoxin that would kill far larger animals.

While Butch focused on the newts, his son, Edmund Brodie III, became fascinated by the snakes. Together, they showed that throughout western America, places with mildly toxic newts also had mildly resistant snakes. Meanwhile, hotspots with unusually lethal newts also had snakes that withstood staggering levels of tetrodotoxin. The two species were locked in a beautifully coordinated arms race of toxicity and resistance.

READ THE FULL STORY AT THE ATLANTIC

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News

Peer J offers free open access publishing for scientists

Post author By jcoker
Post date June 10, 2016

From VT News

When Professor Ignacio Moore, of biological sciences, and his research team heard about PeerJ through social media, they connected with the open access publishing philosophy. Even better, their research about a low-cost, automated playback recording system for use in behavioral ecology was accepted for publication in the journal.

PeerJ is an award-winning, leading peer-reviewed open access scholarly journal for biological and medical sciences — a perfect fit for Moore’s research.

“This paper is essentially a methodological publication, and with minimal tinkering it could be used in many applications, even in fields that are very different from ours, so a wide and unrestricted readership from a diverse research background seemed to be the perfect potential audience,” Moore said of his team’s decision to seek publication in the journal.

PeerJ is a great option for other Virginia Tech researchers, too, especially considering all university faculty, staff, and students can now publish at no cost if their submission passes peer review. Free open access publishing is also available to Virginia Tech researchers in PeerJ’s counterparts, PeerJ Computer Science and PeerJ Preprints.

The University Libraries will cover the article fee or an author’s Basic Publication Plan when his or her paper is accepted for publication in PeerJ, making it completely free for the researcher. As an added bonus, the free publishing continues even if an author leaves Virginia Tech — it’s a lifetime membership.

The partnership with PeerJ is one of the many ways University Libraries supports open access, the movement toward making online information freely accessible to everyone. Among other initiatives, University Libraries also offers discounted publication rates in other journals and celebrates open access annually with a week of events.

“We support open access because it is the most-efficient, equitable way to share and promote scholarship,” said Philip Young, a scholarly communication librarian in the University Libraries.

Young explained that most people do not have access to research, particularly in developing countries. Even most taxpayers here don’t have access, despite the fact that a lot of research is publicly funded. And though students at Virginia Tech are taught to use and cite peer-reviewed research, they lose access to all but a few databases after graduation.

Keeping research open and accessible helps combat those problems, and aligns with both University Libraries and Virginia Tech missions to engage citizens of the world and advance land-grant values of discovery, learning, and outreach.

“By supporting open access for Virginia Tech researchers, we are providing superior dissemination as well as facilitating reuse in teaching and research, including new methods, such as text and data mining,” Young said.

Because it is an open access journal, anyone, anywhere can access the research the journal has to offer, completely for free. PeerJ is indexed in PubMed, Web of Science, and Google Scholar, ensuring published research is discoverable where people are looking.

Launched in December 2012, the journal has quickly gained traction in academic circles, having even won, among other recognitions, a top 10 innovation award from The Chronicle of Higher Education in April 2013 — just four months after its launch. Since then, PeerJ has only grown, raking in almost 4 million views for its 1,841 published peer-reviewed articles and 2,323 preprints.

The journal uses a system of more than 1,000 editors and advisors (plus an editorial board of more than 300 for PeerJ Computer Science) to keep the peer review process quick — at around 26 days to first decision.

Edward Fox, a professor of computer science in the College of Engineering, was invited to be one of the editors on the board of PeerJ Computer Science. When research in his area of expertise is awaiting review, he receives a notification. He says the process is quick, and PeerJ is transparent about who is editing the work.

Studies show there are very few observable differences between research publications that have appeared in an open access journals versus comparable works that appear in subscription journals. And several studies indicate a citation advantage for open access articles.

“This suggests that there’s actually not a whole lot of difference between things that appear in a journal that has charges and considerable expense associated versus things that appear in an open literature repository,” Fox said. “One would expect that PeerJ, with even more editorial involvement than if something was just in a repository, would release quite comparable works to what appear in very expensive journals.”

Virginia Tech researchers only have to sign in with their vt.edu email address when submitting their work to a PeerJ publication, and if accepted, the cost will be covered automatically. Authors may choose between a one-time fee or a lifetime membership. This process is simple, and one Moore recommends.

“It seems like a good way to get work published and available to the scientific and general public,” he said. To date, Moore’s article has more than 1,200 views and 376 downloads since it was published in April 2015.

For more information or help with open access publishing, please contact Gail McMillan or Philip Young.

Written by Erica Corder.

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Image By PeerJ (PeerJ website (WebCite archive)) [CC BY 3.0 (http://creativecommons.org/licenses/by/3.0)], via Wikimedia Commons

News

Ed Fox and team receive grant for big data research

Post author By jcoker
Post date June 6, 2016

From VT News:

Every moment data is created.

When a member of the Flint Water Study team tests and records results from a drop of water. When a student steps into Goodwin Hall, activating sensors to track usability and traffic patterns.

But data, especially big data that has to be analyzed computationally, sometimes creates as many questions as it answers. Where does it all go? How do we store it? Who pays to store it? What kind of computer do we need to process the data? And how can we make sure that people years from now will still be able to access and reuse it?

University Libraries, in partnership with Virginia Tech researchers working with big data, is exploring these questions and more with the support of a $308,175 National Leadership Grant for Libraries from the Institute of Museum and Library Services.

The project team includes: Zhiwu Xie, technology development librarian in the University Libraries; Tyler Walters, dean and professor, University Libraries; Edward Fox, professor of computer science in the College of Engineering; and Pablo Tarazaga, assistant professor of mechanical engineering in the College of Engineering. Jiangping Chen, associate professor in the Department of Library and Information Sciences at the University of North Texas, will also help evaluate and review the project.

Libraries have recently supported research and data by hosting data sets, providing repositories for research, helping researchers manage their data, and even building custom infrastructures for storing and reusing big data.

“But libraries are starting to go beyond their capacity,” Xie said. “The big data projects we’re seeing at Virginia Tech and other institutions can hardly be handled using local infrastructures.”

Researchers need libraries to support data projects that require considerable processing power and quicker transfer rates when moving data from storage to processors.

“Much of the research landscape today is computational, and this is an awesome challenge for universities, government agencies, and other types of research institutes,” said Walters. “Researchers need partners like libraries to co-create new strategies and cyberinfrastructures, to advance their research, and sustain its products and findings.”

Read the full story at VT News

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