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SESYNC
The National Socio-Environmental Synthesis Center (SESYNC) is dedicated to accelerating scientific discovery at the interface of human and ecological systems. We support new interdisciplinary collaborations that pursue data-driven solutions to pressing socio-environmental problems. SESYNC features a range of services from project inception through results dissemination, including supporting the team science process, meeting planning and facilitation, travel and logistical support, and cyberinfrastructure resources. SESYNC is funded by an award to the University of Maryland from the National Science Foundation. Learn more about SESYNC.

ESA Sustainability Science Award

SESYNC Director, Dr. Margaret Palmer, and Vanderbilt University Law School's Dr. J. B. Ruhl receive the Ecological Society of America's 2016 Sustainability Science Award.

Computational Summer Institute

SESYNC invites applications from small teams of researchers for the third annual Computational Summer Institute, July 26-29.

SESYNC Releases R Package for Working with PostGIS

May 4, 2016

by PHILIPPE MARCHAND

Data Scientist

From geotagged social media posts to satellite-based remote sensors, the variety and volume of geodatasets – data items associated with specific spatial coordinates or areas – are rapidly growing, as is their use in socio-environmental systems research. Today, free and open source spatial analysis software offer a level of functionality and efficiency matching that of proprietary Geographical Information Systems (GIS). At SESYNC, we provide tools for and training on how to use the R programming language for spatial data analysis and visualization, and also host a PostGIS server to store larger geodatabases. PostGIS is the spatial extension to the popular open source database system, PostgreSQL. A typical workflow integrating both resources might involve importing a subset of the geodata from PostGIS into R, performing some analysis, and possibly re-exporting the output to the database.

A data table containing both geometries (spatial points, lines or polygons) and hstores (sets of key-value pairs) – Diagram made by Kelly Hondula, SESYNC

Above graphic: A data table containing both geometries (spatial points, lines or polygons) and hstores (sets of key-value pairs) – Diagram courtesy of Kelly Hondula, SESYNC

To simplify data transfer between PostGIS and R, we developed a set of functions that was recently released as a R package on CRAN. These functions automate the conversion between the PostGIS “geometry” data type and the standard spatial data types in R; they can also read and write data in the PostgreSQL “hstore” format, a flexible data type where each table cell can contain multiple named attributes. Example use cases can be found in the accompanying vignette/tutorial.

We plan to update these tools based on user needs, and thus welcome any feedback on current features or potential new features that would be of interest. For more details or to open an issue concerning the software package, please visit our Github site.

The National Socio-Environmental Synthesis Center, funded through an award to the University of Maryland from the National Science Foundation, is a research center dedicated to accelerating data-driven scientific discovery at the interface of human and ecological systems. Visit us online at www.sesync.org and follow us on Twitter @SESYNC.

Associated SESYNC Researcher(s): 

Emerging Force on Building Resources for Complex, Action-Oriented Team Science: Gabriele Bammer’s Mission to Join Scholarly Knowledge

April 1, 2016

Gabriele Bammer, Leader of the Building Resources for Complex Action-Oriented Team Science Theme and professor in the Research School of Population Health at The Australian National University (ANU).

Gabriele Bammer, Leader of SESYNC's "Building Resources for Complex, Action-Oriented Team Science" Theme and Professor in the Research School of Population Health at The Australian National University (ANU).

by LISA PALMER
Fellow for Socio-Environmental Understanding

A scholar in the 1990s played a hunch and is now giving rise to a new field of study focusing on enhancing complex team science--including socio-environmental research and education--through the synthesis of practices and theories.

No academic discipline in multidisciplinary studies existed when Gabriele Bammer received her joint BS in biology and BA in psychology/geography at Flinders University in Australia in the 1970s. But she was excited when her professors announced, “Multidisciplinarity is the way of the future!” She remembers, “At the time, no one was talking about multiple disciplinary studies.” 

After receiving her Ph.D. in behavioral pharmacology, Bammer spent the next 20 years trying to find where, exactly, these shared scholarly approaches lived at universities. She found that they were fragmented across many areas of study. Because scholars and decision-makers would ultimately benefit from a unified repository of knowledge, she developed a formal name for it: Integration and Implementation Sciences, which seeks to improve research impact on complex real-world problems. She and 26 other scholars are currently writing a paper advocating for the development of this joint knowledge bank.

Bammer is leading a new theme at SESYNC that uses Integration and Implementation Sciences to build resources for studying complex, real-world problems. The theme focuses on effective team science and addresses problems that may arise from complex, action-oriented research. For example, researchers may encounter trouble communicating both qualitative and quantitative data across academic disciplines because of differences in language or specified concept. The aim is to build a repository of knowledge so that new collaborations can accelerate discovery. “Researchers won’t need to reinvent the wheel each time,” Bammer says.

Bammer’s insights have emerged over time. She has integrated ideas, data, and methods across diverse disciplines while researching and teaching. She researched and taught in the neurosciences, where she focused on behavioral pharmacology; human sciences, where she helped students integrate the theories of Darwin, Marx and Freud in a course; and occupational health, where she investigated an upsurge in repetition strain injuries—better known in the U.S. as carpal tunnel syndrome—associated with the introduction of computers into offices. It may be no surprise to learn she moved from department to department—six different times—at The Australian National University (ANU) until she finally landed an appointment in 1989 to ANU’s National Center for Epidemiology and Population Health, where she remains today. 

The research process Bammer advocates gained prominence in the 1990s when she directed a study that spanned multiple fields while investigating the feasibility of prescribing pharmaceutical heroin to dependent heroin users as a new treatment option in Canberra, the capital of Australia. The work engaged a wide range of disciplines, including epidemiology, economics, anthropology, pharmacology, criminology, philosophy, political science, demography, and clinical science. It also engaged with stakeholders, including illicit drug users and ex-users, their families, police, drug treatment and other service providers, and policy makers. After five years of investigating every conceivable aspect, and two additional years of political debate, a limited trial was approved only to be overturned 18 days later. But all was not lost. The research informed successful trials in Switzerland and the Netherlands. 

The field of Integration and Implementation Sciences is poised to gain further traction with socio-environmental synthesis. Bammer is convening a meeting this month with one of the three Pursuits SESYNC supports under this research theme. SESYNC is also inviting proposals for synthesis projects focused on tools, methods, and other practices applicable to actionable team science. Multiple teams will be supported, and together their syntheses will contribute towards the development of new toolkits, roadmaps, curricula, and other practical advice. Applications are due May 16

The National Socio-Environmental Synthesis Center, funded through an award to the University of Maryland from the National Science Foundation, is a research center dedicated to accelerating data-driven scientific discovery at the interface of human and ecological systems. Visit us online at www.sesync.org and follow us on Twitter @SESYNC.

Associated SESYNC Researcher(s): 

Teaching Socio-Environmental Synthesis with Case Studies: Moving Toward Best Practices

SESYNC invites past participants of the Teaching about Socio-envrionmental Synthesis with Case Studies short course to apply for a 3.5 day workshop to be held June 21-24, 2016 at SESYNC in Annapolis, MD. Approximately 12-15 participants will be selected to attend, and priority will be given to those who have tested their cases in the classroom, and who have, or plan to, revise their case studies to reflect these teaching experiences.

Teaching Socio-Environmental Synthesis with Case Studies: July 2016

   
Background

Preparing students to tackle urgent and complex environmental problems is a critical challenge. Problems such as global climate change, water resource management, and sustainable development are dynamic, multi-faceted issues that require interdisciplinary and collaborative approaches to solve.

Conservation by the Numbers: Mathematical Models Link Illegal Wildlife Trade & Disease Risk

February 16, 2016

Above image: Wall of cages: wild and domestic birds for sale at a Peruvian animal market, courtesy of Elizabeth Daut.

by MELISSA ANDREYCHEK
Communications Coordinator

A new paper recently published in the peer-reviewed journal PLOS ONE by conservation medic Elizabeth Daut and coauthors is among the first to investigate the influence of illegal wildlife trade on the introduction and spread of infectious diseases.

The researchers developed two mathematical models to evaluate the hypothetical transmission of the highly infectious and fatal Newcastle disease among white-winged parakeets, Peru’s most trafficked parrot. Their results suggest that an outbreak of the disease, combined with a conservative illegal harvest rate, would lead to a nearly 25 percent population decline in two years, and up to 44 percent with higher—albeit still realistic—poaching rates.

“Introducing just one infected individual could provoke an outbreak of Newcastle disease in susceptible populations of white-winged parakeets. The conservation concern is that Newcastle-related deaths, combined with illegal harvest for the wildlife pet trade for domestic consumers, could result in overwhelming losses of these birds,” said Daut, a postdoctoral fellow at the National Socio-Environmental Synthesis Center (SESYNC).

The illegal wildlife pet trade is thriving in Peru—and it is also often a gateway for disease outbreaks. Newcastle disease is fairly common in Peru among birds that aren’t vaccinated, such as with backyard poultry flocks and fighting cocks. In animal markets, where chickens are housed in wire cages alongside illegally caught parrots, pathogens can easily spread from infectious to healthy birds.

After being exposed to sick birds at markets or along the transport chain, infected white-winged parakeets often make their way back to the wild, either by escape or deliberate release. In many cases, the birds are released—without any health surveillance—after being confiscated by authorities. Lacking funds to maintain the animals in captivity or to pay for diagnostic testing to rule out any worrisome infectious diseases, the authorities frequently release animals back to the wild shortly after confiscation.

When infected parakeets are released, wild populations are put at risk. The paper’s authors point out that introduced infectious diseases have previously been linked to major declines of wildlife populations (as in the case of white-nose syndrome and little brown bats), and even species extinctions (as in the case of the parasite Trypanosoma lewisi and Christmas Island rats).

But disease outbreaks in wildlife populations can be difficult to identify, especially in the dense Amazon jungle of Peru, where live animals are often difficult to observe and carcasses disappear quickly.

“That’s why mathematical models are such a valuable tool for the conservation community: they help us evaluate the interaction between illegal wildlife trade and risk of diseases that might otherwise go unseen—until it’s too late,” Daut said.

The paper, “Interacting Effects of Newcastle Disease Transmission and Illegal Trade on a Wild Population of White-Winged Parakeets in Peru: A Modeling Approach,” Elizabeth F. Daut, Glenn Lahodny Jr., Markus J. Peterson, and Renata Ivanek, was published online January 27, 2016, in the journal PLOS ONE.

Mathematical codes for the epidemic model of Newcastle disease transmission are accessible here.

The National Socio-Environmental Synthesis Center, funded through an award to the University of Maryland from the National Science Foundation, is a research center dedicated to accelerating data-driven scientific discovery at the interface of human and ecological systems. Visit us online at www.sesync.org and follow us on Twitter @SESYNC.

Associated SESYNC Researcher(s): 

Salamanders at Risk: New Listing Protects from Deadly Pathogen

February 1, 2016

Above: The California newt is a salamander species endemic to California, in the Western United States. Photo courtesy John Clare via Flickr/Creative Commons.

by ELIZABETH DAUT
Postdoctoral Fellow

Last week, the U.S. Fish and Wildlife Service (USFWS) acted to protect native amphibians from a newly-described and potentially lethal fungus. The culprit—called Batrachochytrium salamandrivorans, or Bsal—has all but wiped out some salamander populations in Europe. And researchers are worried the U.S. could be next.

The movement of Bsal from overseas to the U.S. may likely be hastened by international trade, which is a well-known factor contributing to the spread of infectious diseases (Fèvre et al. 2006). For example, outbreaks of foot and mouth disease, which devastated the livestock industry in Europe, were spread by the international transport of live farm animals. In the case of Bsal, research has confirmed that Asian salamanders, which are imported primarily for the exotic pet industry, are carriers of the fungus. As carriers, these species are resistant to the disease but are able to transmit the fungus to susceptible wild salamanders.

The USFWS has good reason to worry. From 2004 to 2014, nearly 2.5 million live salamanders comprising roughly 60 species were imported into the U.S. Wild salamander populations are at high risk of being exposed to Bsal through the release of imported, infected salamanders (Yap et al. 2015). Although to date, Bsal has not been identified in the U.S. (Berger et al. 2016), a similar fungus—Batrachochytrium dendrobatidis, or Bd—has devastated many amphibian species in the U.S. and worldwide, some to the point of extinction (Woodhams et al. 2011).

That’s a concern that cannot be overstated. The U.S. is a global hotspot for salamander diversity, with roughly 40 percent of the more than 650 living species. Many native salamanders are endemic to the U.S.—i.e., not found anywhere else in the world—and are already threatened (USFWS 2016). Despite being rarely seen, salamanders are considered keystone species. They are highly abundant in many terrestrial and aquatic systems and important contributors to nutrient cycling as predators of arthropods and prey for other vertebrates.

Disease surveillance and regulation in the U.S. are stringent and effective when pathogens harmful for agriculture or humans are involved. However, less attention is spent on regulating animal imports for potential pathogens harmful for native wildlife. But things are now changing.

In a bold new step to halt the spread of Bsal to the U.S., the USFWS adopted an interim rule to ban commercial importation from overseas and interstate transportation across state lines of 201 salamander species.

Under the Lacey Act, the USFWS has the authority to regulate trade in wild animals they determine as injurious to humans, agriculture, or native wildlife. Typically, the Lacey Act has been used to prevent the introduction or spread of invasive vertebrate species, such as pythons in the Everglades (USFWS 2012). This is only the second time that the USFWS has amended the Lacey Act to prevent introduction of a potential pathogen (Bsal) by regulating import and trade of its host species (salamanders). The 201 species listed as injurious under the new USFWS ruling include species from 20 genera known to be susceptible to or carriers of Bsal.

With the looming fungal threat, the USFWS opted for an interim rule that took effect on 28 January 2016, instead of a typical proposed rule, which would have allowed salamander imports to continue while providing an opportunity for public comment. Interested persons are still encouraged to submit written comments on the interim rule before mid-March. Visit the Federal eRulemaking Portal here, search for Docket No. FWS–HQ–FAC–2015–0005, and follow the instructions for submitting comments (USFWS 2016).

The interim rule is an important step toward protecting native salamander populations, but there’s still much work to be done to shield U.S. wildlife from introduced diseases spread through commercial trade. At the National Socio-Environmental Synthesis Center (SESYNC), I’m working with researchers at the University of Maryland to investigate the disease risks associated with importation of exotic animals and—now that the USFWS has taken action on Bsal—to identify the next big potential threats facing native wildlife. Our hope is that this research will provide the scientific, evidence-based knowledge necessary to inform policies that best prioritize disease threat and ensure social and economic benefits from trade.

Further Reading

Berger, L., Roberts, A.A., Voyles, J., Longcore, J.E., Murray, K.A., Skerratt, L.F., 2016. History and recent progress on chytridiomycosis in amphibians. Fungal Ecology 19, 89–99.

Fèvre, E.M., Bronsvoort, B.M.d.C., Hamilton, K.A., Cleaveland, S., 2006. Animal movements and the spread of infectious diseases. Trends in Microbiology 14, 125–131.

USFWS. 2012. Salazar announces ban on importation and interstate transportation of four giant snakes that threaten everglades. U.S. Fish and Wildlife Service. <http://www.fws.gov/southeast/news/2012/003.html> (22 December 2015).

USFWS, 2016. Injurious wildlife species: listing salamanders due to risk of salamander chytrid fungus. Federal Register, Vol. 81, No. 8  Rules and Regulations.

Woodhams, D., Bosch, J., Briggs, C., Cashins, S., Davis, L., Lauer, A., Muths, E., Puschendorf, R., Schmidt, B., Sheafor, B., Voyles, J., 2011. Mitigating amphibian disease: strategies to maintain wild populations and control chytridiomycosis. Frontiers in Zoology 8, 8.

Yap, T.A., Koo, M.S., Ambrose, R.F., Wake, D.B., Vredenburg, V.T., 2015. Averting a North American biodiversity crisis. Science 349, 481–482.

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