PLOS’ New Data Policy: Public Access to Data

UPDATE 7 MARCH: Please see new blog post

UPDATE 26 FEBRUARY : A flurry of interest has arisen around the revised PLOS data policy that we announced in December and which will come into effect for research papers submitted next month. We are gratified to see a huge swell of support for the ideas behind the policy, but we note some concerns about how it will be implemented and how it will affect those preparing articles for publication in PLOS journals. We’d therefore like to clarify a few points that have arisen and once again encourage those with concerns to check the details of the policy or our FAQs, and to contact us with concerns if we have not covered them.

Is the policy about what to share, or about how and where to share it?

There is nothing new in the policy about what types and forms of data should be shared. As we said in December, “PLOS journals have requested data be available since their inception, but we believe that providing more specific instructions for authors regarding appropriate data deposition options, and providing more information in the published article as to how to access data, is important for readers and users of the research we publish.” As we have further clarified, “the Data Policy states the ‘minimal dataset’ consists “of the dataset used to reach the conclusions drawn in the manuscript with related metadata and methods, and any additional data required to replicate the reported study findings in their entirety. This does not mean that authors must submit all data collected as part of the research, but that they must provide the data that are relevant to the specific analysis presented in the paper.” The ‘minimal dataset’ does not mean, for example, all data collected in the course of research, or all raw image files, or early iterations of a simulation or model before the final model was developed. We continue to request that the authors provide the “data underlying the findings described in their manuscript”. Precisely what form those data take will depend on the norms of the field and the requests of reviewers and editors, but the type and format of data being requested will continue to be the type and format PLOS has always required.

What is changing is that authors need to indicate where the data are housed, at the time of submission. We want reviewers, editors and readers to have that information transparently available when they read the article. We strongly encourage deposition in subject area repositories (such as GenBank for sequences, clinicaltrials.gov for clinical trials data, and PDB for structures) where those exist, and in unstructured repositories such as Dryad or FigShare where there is no appropriate subject-domain repository. Some institutions provide appropriate centralized repositories for their researchers’ data; We recognize that for those with small amounts of data, they may be wholly included within the article itself as they are now, and that for some other smaller data types it might be most appropriate to include Supplementary Files with the article – although we would also like to ensure these files are used optimally.

What if my dataset is too large for any of these solutions?

We appreciate that some people now work with datasets that are too large for any of these solutions, and would like to work with them to develop methods of sharing that work in these instances. Authors should submit their manuscripts, noting the details of their situation, and we will work with you to arrive at a solution.

What about human patient data?

Like some other types of data, it is often not ethical or legal to share patient data universally, so we provide guidance on the routes available to authors of such data, and we encourage anyone with concerns of this type to contact the journal they would like to submit to, or the data team at data@plos.org.

Concerns about someone else benefiting from the data

Some raise the concern that, having collected data, they want to be the ones to analyze it and benefit from it. In our view, this sentiment applies to the period before publication. But after publication (in particular, after publication in an Open Access journal) the data should be available for re-use by others. This is not just our view: many institutions and funding agencies (e.g. NIH) now make data sharing a requirement. We understand that some authors will not want to share data, just as some choose not to make their articles available Open Access, but trust that most authors publish their work precisely in order to allow others to benefit from it.

Liz Silva, PLOS ONE
Theo Bloom, PLOS Biology
Emma Ganley, PLOS Biology
Maggie Winker, PLOS Medicine


ORIGINAL POST: Access to research results, immediately and800px-Open_Data_stickers without restriction, has always been at the heart of PLOS’ mission and the wider Open Access movement. However, without similar access to the data underlying the findings, the article can be of limited use. For this reason, PLOS has always required that authors make their data available to other academic researchers who wish to replicate, reanalyze, or build upon the findings published in our journals.

In an effort to increase access to this data, we are now revising our data-sharing policy for all PLOS journals: authors must make all data publicly available, without restriction, immediately upon publication of the article. Beginning March 3rd, 2014, all authors who submit to a PLOS journal will be asked to provide a Data Availability Statement, describing where and how others can access each dataset that underlies the findings. This Data Availability Statement will be published on the first page of each article.

What do we mean by data?

“Data are any and all of the digital materials that are collected and analyzed in the pursuit of scientific advances.” Examples could include spreadsheets of original measurements (of cells, of fluorescent intensity, of respiratory volume), large datasets such as

next-generation sequence reads, verbatim responses from qualitative studies, software code, or even image files used to create figures. Data should be in the form in which it was originally collected, before summarizing, analyzing or reporting.

What do we mean by publicly available?

All data must be in one of three places:

  • the body of the manuscript; this may be appropriate for studies where the dataset is small enough to be presented in a table
  • in the supporting information; this may be appropriate for moderately-sized datasets that can be reported in large tables or as compressed files, which can then be downloaded
  • in a stable, public repository that provides an accession number or digital object identifier (DOI) for each dataset; there are many repositories that specialize in specific data types, and these are particularly suitable for very large datasets

Do we allow any exceptions?

Yes, but only in specific cases. We are aware that it is not ethical to make all datasets fully public, including private patient data, or specific information relating to endangered species. Some authors also obtain data from third parties and therefore do not have the right to make that dataset publicly available. In such cases, authors must state that “Data is available upon request”, and identify the person, group or committee to whom requests should be submitted. The authors themselves should not be the only point of contact for requesting data.

Where can I go for more information?

The revised data sharing policy, along with more information about the issues associated with public availability of data, can be reviewed in full at:

http://www.plos.org/data-access-for-the-open-access-literature-ploss-data-policy/

http://www.plos.org/update-on-plos-data-policy/

Image: Open Data stickers by Jonathan Gray

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It’s a Mad, Mad, Mad, Mad, but Predictable World: Scaling the Patterns of Ancient Urban Growth

cities from sapce

With more than 7.1 billion people living across the globe, cities house more than 50% of the world’s population. The United Nations Population Fund projects that by 2030 more than 5 billion people will live in cities across the world. The Global Heath Observatory, a program run by the World Health Organization, predicts that by 2050, 7 out of 10 people will live in cities, compared to 2 of 10 just 100 years ago.

Recently, researchers developed what is called “urban scaling theory” to mathematically explain how modern cities behave in predictable ways, despite their unprecedented growth. Recent work in urban scaling research considers cities “social reactors”. In other words, the bigger the city, the more people and more opportunity for social interaction.  Think for a moment about the social interactions that occur just on the block outside of your local coffee shop; now multiply those interactions by millions. Cities magnify the number of interactions, increasing both social and economic productivity and, ultimately, encouraging their own growth.

The authors of a recent PLOS ONE paper sought to determine whether ancient cities “behaved” in predictable patterns similar to their modern counterparts. To do so, they developed mathematical models and tested them on archaeological settlements across the Pre-Hispanic Basin of Mexico (BOM, approximated by the red square in the figure below). Based on their findings, they suggest that the principles of settlement organization, which dictate city growth, were very much the same then as they are now, and may be consistent over time.

To test their predictions, the researchers analyzed archaeological data from over 1,500 sites in the BOM, previously surveyed in the 60s and 70s by researchers from the University of Michigan and Penn State.

BOM Location

Using low-altitude aerial photographs and primary survey reports from the original surveyors, the researchers organized the following data from approximately 4,000 sites: the settled area, the average density of potsherds—broken pieces of ceramic material—within it, the count and total surface area of domestic architectural mounds, the settlement type, the estimated population, and the time period.

The researchers were interested in examining areas of the BOM that enabled social interaction between residents, so they excluded site types that did not allow social interaction, for example, isolated ceremonial centers, quarries, and salt mounds. They then grouped the remaining 1,500 sites into both chronological groups and size groups. For chronological grouping, each site was assigned to one of four time periods: the Formative period (1150 B.C.E.–150 B.C.E.), the Classic period (150 B.C.E.–650 C.E.), the Toltec period (650–1200 C.E.), and the Aztec period (1200-1519 C.E.). By the Aztec period, the area had developed from amorphous rural settlements to booming metropolises comprising over 200,000 people.

BOM Population

For site grouping, settlements greater than 5,000 people were categorized differently than smaller settlements. In the figure above, panel B denotes settlements dating to the Formative period (1150 B.C.E.–150 B.C.E.), and panel C, settlements dating to the Aztec period (1200-1519 C.E.).

After separating the data into both chronological groups and size groups, the researchers applied their mathematical models and tested their predictions about urban growth in the settlements of the BOM. One aspect of city development assessed by the researchers was the evolution of defined networks of roads and canals in growing cities. Because roads act as conduits, directly influencing social interaction—much like the roads leading to the aforementioned coffee shop—growing cities develop increasingly defined networks to connect social hubs to one another.

Take, for example, the figure below, which displays both a city in an early stage (panel A) and later (panel B) of growth:

Settlements

Panel A shows the early, or Amorphous Settlement Model, displaying a small settlement easily accessible to the individual via walking, and thus negating the necessity for clearly defined networks of roads. Panel B, on the other hand, shows the Networked Settlement Model, an infrastructure-dense area where networks are clearly defined to accommodate the increased size of the city and density of the residents. Larger cities analyzed by the authors, like Teotihuacan of the Classic period and Tenochtitlán of the Aztec period, epitomize the Networked Settlement Model with its organized network of roads and canals. The findings from the BOM echo the earlier-stated notion that, like their modern counterparts, ancient cities may have acted as “social reactors”, in part by facilitating an increasingly defined network of roads, themselves directly influencing the ability of residents to socially interact.

Scientists use urban scaling theory to show that population and social phenomena follow distinct, mathematical patterns over time. By developing mathematical models to predict measurable changes in city growth, these researchers applied the same patterns to ancient cities and concluded that the development of settlements over time in the BOM seem analogous to those observed in modern cities. Researchers predict that the same mathematical models could be reformatted to estimate population size of ancient cities, as well as to develop measures for calculating socio-economic output like the production of art and public monuments based on the relationship between settlement size and division of labor. Although there is still much to be solved through the equations of urban scaling theory, the consistency of city growth over time has implications for both the past and the present.

Citation: Ortman SG, Cabaniss AHF, Sturm JO, Bettencourt LMA (2014) The Pre-History of Urban Scaling. PLoS ONE 9(2): e87902. doi:10.1371/journal.pone.0087902

Image 1: Auroras Over North America as Seen From Space by the NASA Goddard Space Flight Center

Image 2: doi:10.1371/journal.pone.0087902

Image 3: doi:10.1371/journal.pone.0087902

Image 4: doi:10.1371/journal.pone.0087902

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Ask EveryONE: Corrections

My paper was recently published in PLOS ONE, but I’ve noticed an error. Can it be corrected?

PLOS ONE corrects major errors found in published articles via the addition of a Formal Correction to the paper. Formal Corrections are reserved for errors that significantly affect the understanding or utility of the paper.  In addition to being published on the PLOS ONE website, corrections are also indexed in PubMed Central and PubMed.

When a paper has been corrected, a correction notice will appear in a gray box at the top of the article page.  A CrossMark logo now appears on every PLOS article page and in the downloadable PDF; clicking the logo on a corrected article’s page will bring up a status box showing that the paper has been corrected.

To see the full correction, click the “View correction” link in the gray box.  This will direct you to a page with the full correction details, including any updated figures, tables, or supporting information, along with a PDF version of the correction notice available for download.  An example of a correction notice on the original article is shown below.

corrections image 1

Example of a Formal Correction notice (click to enlarge)

If you notice an error in your published paper, you should contact our corrections team at corrections@plos.org.  Please include the title and DOI of your paper; a description of the problem; and any corrected figures, tables, or supporting information files. PLOS staff will decide whether a Formal Correction is appropriate and will work with you to publish a correction as quickly as possible.

If there is an error in one of your figures, tables, or supporting information files, the corrected items will be included in the Formal Correction. An example of a Formal Correction is shown below.

corrections image2Example of a Formal Correction (click to enlarge)

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Ask EveryONE: Why does my corrected article show up twice in PubMed?

After my paper was published, I discovered an error and contacted PLOS ONE to have it fixed. Now my paper shows up twice in PubMed. Is this a mistake?

If your paper had a formal correction, this is not a mistake; your paper will be listed in PubMed twice.

If a published paper contains a significant error, we publish a Formal Correction to fix that error; the Formal Correction is its own publication and therefore has its own DOI.  The Formal Correction then receives its own, separate entry in PubMed in order to link to the original correction on the PLOS ONE website. The correction’s title will include the word “Correction” followed by the original paper’s title. PubMed mandates that the original and the correction both be entered in its database, as you can see here.

Please note that your corrected paper will show up only once in PMC (PubMed Central), because the correction will be embedded in the PMC entry for the original paper itself.

 

 

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Buzz Me Baby: Unusual Courtship Songs for Valentine’s Day

 We heart the Ostrinia nubilalis

When most people think of Valentine’s Day, images of love, candy, and flowers pop to mind.  However, this Valentine’s Day, we thought we’d share two animals with you that use scales, wings, and other things to create songs that attract that special someone.

Moth Melodies

Male moths use a combination of pheromones and ultrasound—sound with frequencies above the range of human hearing—to woo females. To better understand moth sounds during courtship, researchers in this PLOS ONE study recorded and examined the ultrasounds emitted by three types of grass moths. They found that two of the three moth species had sex-specific wing and thoracic scales that played a role in ultrasound production, and that using these scales increased mating success. This audio clip is the recorded ultrasound of Ostrinia nubilalis (pictured above), aka the European corn borer, slowed down 10 times so that human ears can hear it.

CotesiaWasp Chorus

Cotesia Wasp

Rapid wing fanning is the attraction tool of choice for male wasps when courting females. According to this PLOS ONE study, parasitic wasp wing fanning has been studied before, but the mechanism for how the sound is generated has not.  The researchers characterized the wasp songs and found that they contain a two-part signal with sequences of buzzes and boing sounds. While scientists could characterize  the male courtship songs, how they produce the sound remains a mystery. This audio clip starts with wing fanning, which produces a buzz sound, and is followed by a series of boing sounds.

 


Whether you choose to scale, buzz, or boing to impress your mate with beautiful music, we wish you a Happy Valentine’s Day from PLOS ONE!

 

Citations: 

Takanashi T, Nakano R, Surlykke A, Tatsuta H, Tabata J, et al. (2010) Variation in Courtship Ultrasounds of Three Ostrinia Moths with Different Sex Pheromones. PLoS ONE 5(10): e13144. doi:10.1371/journal.pone.0013144

Bredlau JP, Mohajer YJ, Cameron TM, Kester KM, Fine ML (2013) Characterization and Generation of Male Courtship Song in Cotesia congregata(Hymenoptera: Braconidae). PLoS ONE 8(4): e62051. doi:10.1371/journal.pone.0062051

Image Credits:

Photo a Ostrinia nubilalis by dhobern. Heart added by us.

Dorsal view of one pair of wings of a male Cotesia congregata. Figure 8. doi:10.1371/journal.pone.0062051.g008

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It’s Not Easy Being Green: Assessing the Challenges of Urban Community Gardening

urbangardenSF

From vertical gardens to succulent gardens to community veggie gardens like the San Francisco garden pictured above, city dwellers all around us have started embracing their (hopefully) green thumbs.  For urbanites in particular, community gardening provides us with much needed “outside time” with likeminded individuals, with the added gift of hyper-local produce available throughout the growing season. These benefits have led to increases in residential and community garden participation in major cities across the US.

While many people are jumping on the garden-fresh bandwagon to reap the obvious, verdant benefits, it is important to consider the potential side effects that come alongside urban farming. Urban soil is not only closer to possible sources of pollution, like traffic and industrial areas, but could also contain residual chemicals from past land use. Residential land previously occupied by industrial buildings has been found to contain dangerous levels of toxins like lead, which can poison residents and contaminate food grown on-site. But it doesn’t take a former factory to contaminate your backyard. Soil can absorb and hold toxins left over from something as small as a previous homeowners dumping of cleaning water down the drain or off the back porch.

Researchers from Baltimore published an article in PLOS ONE earlier this month assessing Baltimore community gardeners’ knowledge of soil contamination risks and explored what steps can be taken to mitigate the dangers of urban pollution in urban gardens.

The authors, hailing from Johns Hopkins, University of Maryland, and the Community Greening Resource Network, conducted interviews with Baltimore’s community garden members, and found that unfortunately, the gardeners generally seem to have low levels of concern about potential contaminants in their soil. Those working in established community gardens were least concerned as they often assumed that any issues with soil contamination had been addressed in the early days of the garden’s use.

When participants were asked what soil contaminants they are aware of, lead was the most common response—likely due to city interventions concerning lead poisoning—with 66% of surveyed gardeners mentioning it in their interviews. The study results also indicate that gardeners are more worried about the presence of pesticides and other added chemicals than most other residual chemicals in the soil. Soil quality and fertility even took greater precedence for some gardeners than the presence of contaminants.

By interviewing Baltimore officials knowledgeable about community gardening practices and soil contamination issues, the researchers determined key steps in assuring the safety of gardening sites. Above all, officials suggested the creation of a central source of information related to soil contamination concerns. Similar projects relating to regulation and urban agriculture are already underway in places like Los Angeles, though these resources aim to help residents navigate the maze of confusing legislation related to urban agriculture, and focus less on providing information on how to evaluate the safety of specific plots of land.

The authors suggest other important ways to determine the safety of a garden site, including learning about the site’s past uses and testing the soil for lingering chemicals, both of which might not seem necessary to those untrained in urban planning or chemical analysis. They also recommend that officials in urban areas provide services that will encourage use of these tools and help gardeners find and interpret the results of soil testing or historical research.

In the meantime, the authors suggest limiting exposure to potentially contaminated land. For instance, we should minimize contact with dirt from garden sites by washing our hands and taking off shoes before entering any indoor spaces. Many interviewed gardeners have tried to mitigate this problem by using raised beds, which they believe eliminates concern about contaminants in homegrown vegetables. However, researchers have found limitations with this method, and it should not be seen as a fix-all. Raised beds do not prevent contamination from soil around the beds, which can still be ingested or tracked into the home, and surrounding pollutants have been known to blow into beds or seep into the soil from treated wood used to build the structures.

Urban community gardening is a trend that is here to stay, and we have it to thank for fresher local produce, greener surroundings, a greater sense of community, and for the physical, and sometimes therapeutic, activity it provides. The potential dangers associated with gardening in urban areas probably do not outweigh the benefits, as long as gardeners remain diligent and become better informed. Though their study focused on a limited group, this paper’s findings draw attention to the fact that they’re not. So, next time you’re digging into a grassy patch in your backyard with visions of veggies or working in your local community garden, take a minute to think about what you know about your area, discuss past developments with longtime residents, and above all, clean up afterward.

More information on soil testing and good gardening practices can be found on this site from the EPA.

UPDATE: This post has been updated to clarify that the statistics on gardener awareness of soil contaminants measured only awareness, and not concern for the soil they work with. It was also changed to clarify that raised beds do provide some protection against soil contamination from the surrounding area, though they have limitations.

Citation: Kim BF, Poulsen MN, Margulies JD, Dix KL, Palmer AM, et al. (2014) Urban Community Gardeners’ Knowledge and Perceptions of Soil Contaminant Risks. PLoS ONE 9(2): e87913. doi:10.1371/journal.pone.0087913

Image: Tenderloin People’s Garden by SPUR

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Two Shark Studies Reveal the Old and Slow

Sharks live in the vast, deep, and dark ocean, and studying these large fish in this environment can be difficult. We may have sharks ‘tweeting’ their location, but we still know relatively little about them. Sharks have been on the planet for over 400 million years and today, there are over 400 species of sharks, but how long do they live, and how do they move? Two recent studies published in in PLOS ONE have addressed some of these basic questions for two very different species of sharks:  great whites and megamouths.

The authors of the first study looked at the lifespan of the great white shark. Normally, a shark’s age is estimated by counting growth bands in their vertebrae (image 1), not unlike counting rings inside a tree trunk. But unfortunately, these bands can be difficult to Great white vertdifferentiate in great whites, so the researchers dated the radiocarbon that they found in them. You might wonder where this carbon-14 (14C) came from, but believe it or not, radiocarbon was deposited in their vertebrae when thermonuclear bombs were detonated in the northwestern Atlantic Ocean during the ‘50s and ’60s. These bands therefore provide age information. Based on the ages of the sharks in the study, the researchers suggest that great whites may live much longer than previously thought. Some male great whites may even live to be over 70 years old, and this may qualify them as one of the longest-living shark species. While these new estimates are impressive, they may also help scientists understand how threats to these long-living sharks may impact the shark population.

A second shark study analyzed the structure of a megamouth shark’s pectoral fin (image 2) to understand and predict their motion through the water. Discovered megamouth finin 1976, the megamouth is one of the rarest sharks in the world, and little is known about how they move through the water. We do know that the megamouth lives deep in the ocean and is a filter feeder, moving at very slow speeds to filter out a meal with its large mouth. But swimming slowly in the water is difficult in a similar way flying slowly in an airplane is difficult. Sharks need speed to control lift and movement.

To better understand the megamouth’s slow movement, the researchers measured the cartilage, skin histology, and skeletal structure of the pectoral fins of one female and one male megamouth shark, caught accidentally and preserved for research. The researchers found that the megamouth’s skin was highly elastic, and its cartilage was made of more ‘segments’ than any other known shark, which may provide added flexibility compared to other species. megamouth jointThe authors also suggest that the joint structure (image 3) of the pectoral fin may allow forward and backward rotation, motions that are largely restricted in most sharks.  The authors suggest that this flexibility and mobility of the pectoral fin may be specialized for controlling body posture and depth at slow swimming speeds. This is in contrast to the fins of fast-swimming sharks that are generally stiff and immobile.

In addition to the difficulties in exploring deep, dark seas, small sample sizes present challenges for many shark studies, including those described here. But whether studying the infamous great white shark or one of the rare megamouths, both contribute to a growing body of knowledge of these elusive fish.

Citations: Hamady LL, Natanson LJ, Skomal GB, Thorrold SR (2014) Vertebral Bomb Radiocarbon Suggests Extreme Longevity in White Sharks. PLoS ONE 9(1): e84006. doi:10.1371/journal.pone.0084006

Tomita T, Tanaka S, Sato K, Nakaya K (2014) Pectoral Fin of the Megamouth Shark: Skeletal and Muscular Systems, Skin Histology, and Functional Morphology. PLoS ONE 9(1): e86205. doi:10.1371/journal.pone.0086205

Images1: doi:10.1371/journal.pone.0084006.g001

Image 2: doi:10.1371/journal.pone.0086205.g003

Image 3: doi:10.1371/journal.pone.0086205.g004

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All Dried Up? Modeling the Effects of Climate Change in California’s River Basins

Mono Lake
Whether you are trapped inside because of it, or mourning the lack of it, water is on everyone’s mind right now. Too much snow in the Midwest and Northeast has been ruining travel plans, while too little snow is limiting Californians’ annual ski trips. No one wants to drive three hours only to find a rocky hillside where their favorite slope used to be.

It’s hard to deny that abnormal things are happening with the weather right now. Recently, Governor Jerry Brown officially declared a state of emergency in California due to the drought and suggested that citizens cut water usage by 20%. With no relief in sight, it is important not only to regulate our current water use, but also to reevaluate our local programs and policies that will affect water usage in the future. So, how do we go about making these decisions without being able to predict what’s next? A recently published PLOS ONE article may offer an answer in the form of a model that allows us to estimate how potential future climate scenarios could affect our water supply.

journal.pone.0084946.g001

Researchers from UC Berkeley and the Stockholm Environmental Institute’s (SEI) office in Davis, CA built a hydrology simulation model of the Tuolumne and Merced River basins, both located in California’s Central Valley (pictured above). Their focus was on modeling the sensitivity of California’s water supply to possible increases in temperature. When building the model, the authors chose to incorporate historical water data, current water use regulations, and geographical information to estimate seasonal water availability across the Central Valley and the San Francisco Bay Area. They then ran various water availability scenarios through the model to predict how the region could be affected by rising temperatures.

Using estimated temperature increases of 2°C, 4°C, and 6°C, the model predicted earlier snowmelts, leading to a peak water flow earlier in the year than in previous years. The model also forecasted a decreased river flow due to increased evapotranspiration (temperature, humidity, and wind speed). The water supply was also estimated to drop incrementally with each temperature increase, though it is somewhat cushioned by the availability of water stored in California’s reservoirs.

journal.pone.0084946.g002

The authors used an existing model as an initial structure, and built upon it to include information on local land surface characteristics, evapotranspiration, precipitation, and runoff potential. Surrounding water districts were modeled as nodes and assigned a priority according to California’s established infrastructure and legislation. Using this information, the authors state that the tool is equipped to estimate monthly water allocation to agricultural and urban areas and compare it to historical averages for the same areas.

Though a broad model, the authors present it as a case study that provides estimates of longer-term water availability for the Central Valley and Bay Area, and encourage other areas to modify its design to meet the needs of their unique locales. Those of us looking for more specific predictions can also use the tool to create models with additional information and refined approximations, allowing flexibility for future changes in land use and policy. For now, we might have a good long-term view of our changing water supply and a vital tool as we race to keep up with our ever-changing world.

Citation: Kiparsky M, Joyce B, Purkey D, Young C (2014) Potential Impacts of Climate Warming on Water Supply Reliability in the Tuolumne and Merced River Basins, California. PLoS ONE 9(1): e84946. doi:10.1371/journal.pone.0084946

Image 1 Credit: Mono Lake by Stuart Rankin

Image 2 Credit: Figure 1 pone.0084946

Image 3 Credit: Figure 2 pone.0084946

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The Missing Underwater Forests of Australia: Restoring Phyllospora comosa Around Sydney

restoration_Adriana Verges

Although seaweed is the dominant habitat-forming organism along temperate coastlines, one of the major macroalgae of Australia, Phyllospora comosa, has disappeared over the last forty years from the urban shores around Sydney, Australia. Human activity is likely related to the degradation of these habitats in urbanized areas: During the 1970s and 1980s, humans discharged large amounts of sewage from nearby cities along surrounding coasts. Unfortunately, despite significant improvements in water quality around Sydney since, Phyllospora has not returned. To test whether Phyllospora can ever be restored in reefs where it was once abundant, authors of a recent PLOS ONE paper transplanted Phyllospora into two reefs in the Sydney area. In this interview, corresponding author Dr. Alexandra Campbell from the University of New South Wales elaborates on the group’s research and the impact of these ‘missing underwater forests’:

You’ve said that “seaweeds are the ‘trees’ of the ocean”. Can you tell us a little more about your study organism, Phyllospora, and explain its importance for coastal ecosystems around Australia?

Phyllospora comosa (known locally as ‘crayweed’) grows up to 2.5 m in length and forms dense, shallow forests along the south-eastern coastline of Australia, from near Port Macquarie in New South Wales, around Tasmania to Robe in South Australia. Individuals appear to persist on reefs for around 2 years and are reproductive year round.

How do these ecosystems change with the reduction of seaweed forests?

Large, canopy-forming macroalgae provide structural complexity, food and habitat for coastal marine ecosystems and other marine organisms. When these habitat-formers decline or disappear, the ecosystem loses its complexity, biodiversity decreases and many ecosystem services are also lost. Losing large seaweeds from temperate reefs has analogous ecosystem-level implications to losing corals from tropical reefs.

We’re interested in learning more about how you got involved in this research. Can you tell us how you became interested in studying Phyllospora?

For my doctorate, I studied how changing environmental conditions may disrupt relationships between seaweeds and microorganisms – which are abundant and ubiquitous in marine environments – potentially leading to climate-mediated diseases. During my PhD, my colleagues (Coleman et al.) published a paper describing the disappearance of crayweed from the urbanised coastline of Sydney and hypothesised that the cause was the high volume, low treatment, near shore sewage outfalls that used to flow directly on to some beaches and bays in the city. I wondered whether this pollution may have disrupted the relationship between Crayweed and its microbial associates and that’s how I got involved in the project.

Why is the loss of canopy-forming macroalgae difficult to study retrospectively and how has this informed your current study?

Once an organism has disappeared from an ecosystem, it can be difficult to piece together the processes that caused its demise, particularly if the disappearance occurred several decades ago and the ecosystem state shifted dramatically as a consequence.  In our study, we hypothesized that poor water quality might have caused the decline of Phyllospora. There have been significant improvements in water quality in the region since the decline, but the species and ecosystems they used to support have failed to recover. To test whether the water quality has improved enough to allow recolonisation of this seaweed, we transplanted the seaweed back onto reefs where it was once abundant. The survival rates of transplanted seaweed were very good, suggesting that with a little help, this species may be able to recolonize Sydney’s reefs.

What were some of the difficulties you faced while conducting your research?

Moving hundreds of large seaweeds many kilometres from donor populations to the restoration sites was a big job. Thankfully, we received a great deal of help from many volunteers from the local community – mostly divers, with an interest in conserving and restoring the marine ecosystems they visit recreationally and value as a natural resource.

You’ve talked about Phyllospora ‘recruitment’ at one recipient site. Can you explain in greater detail what a ‘recruit’ is and how this is important for the success of a restoration site?

Phyllospora reproduces sexually, with gametes from male individuals fertilizing gametes from females, forming zygotes, which then attach themselves to the bottom (usually not very far from their parents) and grow into juvenile algae which we call ‘recruits’. In the context of restoration, the high level of recruitment (i.e. successful reproduction) we observed at our transplant site is very encouraging because it creates the possibility for the establishment of a self-sustaining population of Phyllospora at this site for the first time in many decades.

Why do seaweed forests receive less attention than other marine ecosystems, for example mangroves or coral reefs?

Most people don’t think about seaweeds very often. When they do, it’s usually because the sight, touch or smell of seaweed on the beach is annoying or offensive. Even the name “seaweed” conjures negative imagery so perhaps it’s a PR issue! Arguably, macroalgae have traditionally received less attention from marine ecologists than other marine ecosystems as well, with much more attention and funding going to coral reef research. With global patterns of declines of temperate, habitat-forming macroalgae, this needs to change and our understanding of the processes that affect seaweed populations needs to grow.

What would a successful restoration of underwater kelp forests mean for the ecosystem and for the local population?

It’s our hope that, by restoring habitat-forming macroalgae like Phyllospora, we will also enhance populations of other organisms that rely on this species for food or shelter. Detecting such follow-on benefits of our seaweed restoration program is the focus of ongoing research and our initial results are very encouraging.

You’ve mentioned that larger scale restoration would be a sound way of combating the grazing (herbivory) you saw. What is the next step forward for you?

Enhanced grazing may be another mechanism by which Phyllospora disappeared from these reefs (or perhaps why it’s failed to recover). The impacts of grazing we observed were site-specific, so further investigations in to why one place was so severely impacted by herbivores while the other was not, are needed. Our first step towards resolving this is to establish more numerous restoration patches of different sizes to see whether we can satiate the herbivores and whether smaller patches are more susceptible to grazing than larger patches.

For more PLOS ONE articles about the ‘trees of the ocean’, check out the way seaweed and coral interact in “Seaweed-Coral Interactions: Variance in Seaweed Allelopathy, Coral Susceptibility, and Potential Effects on Coral Resilience” and how ocean currents influence seaweed community organization in “The Footprint of Continental-Scale Ocean Currents on the Biogeography of Seaweeds”.

Citation: Campbell AH, Marzinelli EM, Vergés A, Coleman MA, Steinberg PD (2014) Towards Restoration of Missing Underwater Forests. PLoS ONE 9(1): e84106. doi:10.1371/journal.pone.0084106

Image: Adriana Vergés, co-author

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Unearthing the Environmental Impact of Cambodia’s Ancient City, Mahendraparvata

Angkor from the air

 

From the 9th to the mid-14th century, the region of Angkor in modern-day northern Cambodia was the capital of Khmer Empire and the largest preindustrial city in the world. Home to possibly more than three quarters of a million people, several different urban plans and reservoir systems, and impressive monuments like the temple of Angkor Wat (pictured from a bird’s-eye-view above), Angkor was the core of the Khmer Empire, which dominated Southeast Asia by the 11th century CE. Like many modern, booming cities, Angkor was fed by water sourced from another city.

Mahendraparvata, a hill-top site in the mountain range of Phnom Kulen, is significant as the birthplace of the Khmer Kingdom and as the seat of Angkor’s water supply. In 802 CE, Jayavarman II proclaimed himself the universal king of the Angkor region on the top of Mahendraparvata. Jayavarman’s ascension to power marked the unification of the Angkor region and the foundation of the Khmer Empire.

Figure1_PLOS_Pennyetal

 

Until recently, however, little was known about the urban settlement of Mahendraparvata; a dense forest canopy obscures a great deal of the area’s archaeological landscape. To determine the extent of land use around Mahendraparvata, the authors of a recent PLOS ONE paper examined soil core samples taken from one of the Phnom Kulen region’s reservoirs.

As Angkor’s source of water, Phnom Kulen’s archaeological landscape is littered with hydraulic structures, like dams, dykes, and reservoirs (points A, B, and E on the remote sensing digital image shown below), meant to store and direct Angkor’s water sources strategically. The researchers focused on an ancient reservoir upstream of the main river running north to south, now a swamp, to find evidence of intensive land use.

Remote sensing

 

Core samples taken from the sediment of this ancient reservoir, point F on the image above, provided the researchers with chronological layers of earth containing organic materials, like wood, pollens, and spores, which could be assessed using radiocarbon dating.

By analyzing the sediment cores, researchers found that the reservoir was likely in use for about 400 years. Although the age of the reservoir itself remains inconclusive, sediment samples suggest that the valley was flooded in the mid-to-late 8th century CE, around the time Jayavarman II unified the area.

The authors found that medium-to-coarse sand deposition in the sediment samples beginning in the mid-9th century points to the presence of continual soil erosion, either from the surrounding hills or from the dyke itself, likely caused by deforestation in the area. By analyzing samples from the late 11th century, the authors found that the last and largest episode of erosion occurred, a possible result of intensive land use.

The researchers suggest that deforestation, as evidenced by soil erosion, implies that “settlement on Mahendraparvata was not only spatially extensive but temporally enduring.” In other words, the estimated extent of deforestation by continual sand deposits from the mid-9th century to the late-11th century in core samples indicates that Mahendraparvata was home to a large and thriving urban network in need of resources.

However, an increase in pollen spores dated to the 11th century, followed by the establishment of swamp forests in the early to mid-12th century in the reservoir, reflects that, by this time, the reservoir had fallen out of use, perhaps linked to changes in water management throughout the broader area, and possible population decline nearby. According to mid-16th century samples, the swamp flora around this time appears to have developed into the swamp flora seen today in the ruins of Mahendraparvata.

For some 400 years, the Phnom Kulen mountains acted as the main source of water for the Angkor region. The change of water management practices in the Phnom Kulen region has implications for the water supply to Angkor itself. In sum, by examining core samples drawn from one of Phnom Kulen’s ancient reservoirs, authors were able to explore an archaeological landscape that is still largely hidden and a history still mainly obscured by time. The potential link between the rise and fall of urban life in the Angkor region and the use of reservoirs like the one used in this study helps to unearth a little bit more about the the Khmer Kingdom and the marked environmental impact of Mahendraparvata.

Citation: Penny D, Chevance J-B, Tang D, De Greef S (2014) The Environmental Impact of Cambodia’s Ancient City of Mahendraparvata (Phnom Kulen). PLoS ONE 9(1): e84252. doi:10.1371/journal.pone.0084252

Image 1: Angkor Wat by Mark McElroy

Image 2: journal.pone.0084252

Image 3: journal.pone.0084252

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