Carrie Dolan is an Assistant Professor in the Department of Health Sciences at William and Mary in Williamsburg, Virginia.. What first drew you to your field of research? My experience as
Category Archives: Author Spotlight
EveryONE: Yvonne Fondufe-Mittendorf
Note: this is the second of a series of posts in which you’ll get a glimpse into the important work that PLOS ONE authors are performing. Today we’re showcasing Yvonne Fondufe-Mittendorf from the department of
Zoom-Enhance: Identifying Trends in Article-Level Metrics
In late December 2013, PLOS ONE published an article from UK-based Psychologists Rob Jenkins and Christie Kerr titled “Identifiable Images of Bystanders Extracted from Corneal Reflections”. Using high-resolution photography, Jenkins, from the University of York, and Kerr, from the University … Continue reading
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Canada’s Species at Risk Rarely Recover: The Story Behind the PLOS ONE Article
Post By Caroline Fox & Brett Favaro Most scientists are passionate about their work, but enthusiasm can sometimes be hard to maintain over a long project. What if we could inject the fun back into science—take away the emotional baggage … Continue reading
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Satellite Telemetry Uncovers the Tracks of Tiny Ocean Giants
The pygmy blue whale, cousin to the more well-known Antarctic blue whale, has an enigmatic history. Pygmy blue whales dwell in vast expanses of the Indian and southern Pacific oceans, and are a highly mobile species. The species was identified in 1966—although it’s likely to have been confused with its cousin the “true” blue whale prior to 1966—so it’s only in recent years that we’ve been able to catch glimpses of these elusive cetaceans during their migrations to and from breeding and feeding grounds. The researchers of a recent PLOS ONE paper tested out a new method of tracking these whales: satellite telemetry (described below). Using this method, the researchers mapped the migration of pygmy blue whales as they moved from the coast of Australia to the waters of Indonesia. We caught up with author Virginia Andrews-Goff to get some additional details on what it’s like to track these tiny giants.
How did you become interested in pygmy blue whales, and how did you get involved in mapping their migratory movements?
This research was carried out by the Australian Marine Mammal Centre, a national research centre focused on understanding, protecting and conserving whales, dolphins, seals, and dugongs in the Australian region. The work we carry out aims to provide scientific research and advice that underpins Australia’s marine mammal conservation and policy initiatives. We, therefore, have a keen interest in all whales that migrate through Australian waters including pygmy blue, right and humpback whales.
Pygmy blue whales are of particular interest, however, as so little is known in regard to their movements and population status. Large scale movements of whales are particularly hard to study and what we do know about pygmy blue whales we have mainly learnt from examining whaling records. Fortunately, pygmy blue whales were targeted by the whaling industry for only a very short period of time in the late 1950s and early 1960s just prior to the IWC banning the hunting of all blue whales in 1966.
What are the challenges of better understanding whale migration in general?
Large-scale, long-term whale movements are challenging to study as it is impractical to do so by direct observation. Therefore, we need to use devices, such as satellite tags, that can be attached to the whale to provide real-time location information.
What is satellite telemetry and how did it enable your findings?
In this case, satellite telemetry refers to the use of a satellite-linked tag attached to the whale. This tag communicates with the Argos satellite system when the antenna breaks the surface of the water. A location can then be determined when multiple Argos satellites receive the tag’s transmissions. We then receive this location data in almost real time via the Argos website, which allows us to track the movement of the tagged whale.
Based on your tracking, you found that the pygmy blue whales traveled from the west coast of Australia north to breeding grounds in Indonesia. Can you give readers a sense of why they travel this route?
Generally, whales migrate between productive feeding grounds (at high latitudes) in the summer to warmer breeding grounds (at low latitudes) during the winter. The exact reason for this general pattern is unclear, though quite a few theories exist, including to avoid predators, to assist the thermoregulatory ability of the calf, and to birth in relatively calm waters. Because of the timing of this migration, we believe these animals travel to Indonesian waters to calve. Usually it is assumed that whales fast outside of the summer when no longer located in the productive feeding grounds. Interestingly, these pygmy blue whales travel from productive feeding grounds off Western Australia to productive breeding grounds in Indonesia and therefore, probably have the opportunity to feed (and not fast) on the breeding grounds.
Satellite tag derived locations of pygmy blue whales by month.
You’ve mentioned that pygmy blue whale migratory routes correspond with shipping routes. How does this interaction impact the whales?
Baleen whales (whales that use filters to feed instead of teeth) use sound for communication and to gain information about the environment they occupy. When pygmy blue whale movements correspond to shipping routes, there is potential for the noise generated by the ships to play some role in altering calling rates associated with social encounters and feeding.
Why is it important for us to better understand pygmy blue whale migration, and how does mapping their migratory movements help conservation efforts for this endangered animal?
Our coauthor, Trevor Branch, hypothesised in 2007 that pygmy blue whales occupying Australian waters traveled into Indonesian waters. However, prior to this study, we didn’t actually know that this was the case. As such, conservation efforts relevant to the pygmy blue whales that use Australian waters are required outside of Australian waters too. We can also now gain some understanding of risks within the pygmy blue whale migratory range, such as increased ambient noise from development, shipping, and fishing, and therefore assist in mitigating these risks.
What’s next for you and your research team?
A question mark still remains over the movements of the pygmy blue whales that utilise the Bonney Upwelling feeding grounds off southern Australia. Genetic evidence indicates mixing between the animals in the feeding areas of the Perth Canyon (the animals that were tagged in this study) and the Bonney Upwelling. This indicates the potential for individuals from the Bonney Upwelling to follow a similar migration route to those animals feeding in the Perth Canyon. However, it is also thought that Bonney Upwelling animals may utilise the subtropical convergence region south of Australia. We plan to collaborate on a research project that aims to tag the pygmy blue whales of the Bonney Upwelling and ascertain whether these animals move through the same areas and are therefore exposed to the same risks as the Perth Canyon animals.
We look forward to seeing more from Dr. Andrews-Goff and her team in the future. In the meantime, read more about the elusive worlds of southern Pacific Ocean whales here at the EveryONE blog.
Citation: Double MC, Andrews-Goff V, Jenner KCS, Jenner M-N, Laverick SM, et al. (2014) Migratory Movements of Pygmy Blue Whales (Balaenoptera musculus brevicauda) between Australia and Indonesia as Revealed by Satellite Telemetry. PLoS ONE 9(4): e93578. doi:10.1371/journal.pone.0093578
Image 1: IA19847 Blue pygmy whale
Photograph © Mike Double/Australian Antarctic Division
Image 2: IA19850 Blue pygmy whale
Photograph © Mike Double/Australian Antarctic Division
Image 3: pone.0093578
Image 4: IA19851 Blue pygmy whale off Western Australian coast near Perth, Western Australia, Australia Photograph © Mike Double/Australian Antarctic Division
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The Missing Underwater Forests of Australia: Restoring Phyllospora comosa Around Sydney
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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Plant Roots May Lie Beneath Namibian Fairy Circles
Circles of barren land, ranging from one to several feet in diameter, appear and disappear spontaneously in Namibian grasslands. The origins of these ‘fairy circles’ remain obscure, and have been attributed to causes ranging from the fantastic (the poisonous breath of a subterranean dragon) to those backed by more evidence, such as the work of a soil termite. A recent PLOS ONE paper suggests another possibility: Patterns that emerge during normal plant growth. Author Michael Cramer elaborates on the results of this study:
How did you become interested in studying the Namibian fairy circles, and are similar circles seen elsewhere?
It would be hard not to be intrigued by these mysterious barren circles on the edge of the spectacular Namibian sand sea! These circles are also reminiscent of soil mounds in other places, for example mima mounds in the US, “heuweltjies” in South Africa and “campos de murundus” in South America that have primarily been ascribed to faunal activity. Like fairy circles, these mounds may, however, represent a distinct product of patterns formed by vegetation. My co-author, Nichole Barger, became intrigued by both these phenomena while I was on sabbatical in her lab.
Many other scientific ideas have been proposed to explain the occurrence of these circles. What’s missing from these explanations?
Any explanation of fairy circles has to provide a plausible mechanism for regular spacing of these relatively large circles in the landscape. The most common explanation to date has been that termites cause the circles. While it is undoubtedly true that ants, termites and other fauna do occur in the circles and may play a role in maintenance of the circles, we suggest that inter-plant competition is the primary cause that drives circle formation. This places plant competition in focus as a possible mechanism for determining the shape, size and distribution of the circles.
What made you think the patterns could be formed by plant growth patterns themselves?
We stood on the shoulders of giants! Previous studies have alluded to vegetation patterning as a possible cause. Other researchers have also produced computer models to predict fairy circle occurrence and found plant growth may play a role. More generally, understanding of spatial patterns formed by plants and the realization that this emergent phenomenon is common in arid landscapes has increased recently. Several groups have produced mathematical models that explain the production of vegetation patterns (gaps, bands and spots) and show that increasing aridity can result in transition from one pattern to another.
How did you analyze the fairy circles?
We adopted two approaches. We used Google Earth to obtain images of sites across Namibia, analyzed these to determine circle morphological characteristics, and then combined the images with environmental data to predict the distribution of fairy circles. We performed ground surveys to measure circle morphology and collect soil samples. Soils were sampled at various depths and regular intervals inside and outside the circles and analyzed for water and nutrient contents.
What did you find?
We found that we could predict, with 95% accuracy, the distribution of fairy circles based on just three variables. Rainfall strongly determined their distribution, and differences in rainfall from year to year may thus explain why circles dynamically appear and disappear in this landscape. The patterns of moisture depletion across the circles are also consistent with plant roots foraging for water in the circle-soil. The size and density of the circles is inversely related to resource availability, indicating that bigger circles occur in drier areas and where soil nitrogen is lower.
Do the data in this study strengthen previous results or disprove any older explanations for the circles?
Our results corroborate previous results and extend them, but we have interpreted the results in a novel manner. Since our study was correlative, i.e: we correlated the occurrence of fairy circles with certain environmental conditions, it does not disprove existing hypotheses. Direct experiments that result in fairy circles being created or closing up are perhaps the only way to prove or disprove any of these ideas.
Do these results have implications for other ecosystems? For example, could similar ecological conditions cause fairy circles to form in other grasslands around the world?
Circular grass rings do occur in many contexts. For example, Stipagrostis ciliata in the Negev and Muhlenbergia torreyi (ring muhly) in the US (e.g. New Mexico, Utah) form rings. The distinction is that these are much smaller (ca. < 1 – 2 m diameter) and less regularly spaced than fairy circles. Nevertheless, their origins may have some commonalities with fairy circles. The special circumstance that results in the spectacular Namibian fairy circles may be the fact that the soils are very sandy and homogenous.
More generally, the fairy circles represent an example of how patterns formed by growing plants can create heterogenous spaces in otherwise homogenous grassland. Differences in soil moisture or composition across the span of a fairy circle can provide habitat for both grasses and fauna that would otherwise not thrive in this arid environment.
Citation: Cramer MD, Barger NN (2013) Are Namibian “Fairy Circles” the Consequence of Self-Organizing Spatial Vegetation Patterning? PLoS ONE 8(8): e70876. doi:10.1371/journal.pone.0070876
Images: fairy circles by Vernon Swanepoel (top); images below from 10.1371/journal.pone.0070876
Contextualizing the Hobbits
18,000 years ago, the remote Indonesian island of Flores was home to a population of tiny humans. They stood only about 3.5 feet tall on their large feet, and their skulls housed unusually small brains approximately the size of a grapefruit. The identity of these ‘hobbits’ has been hotly debated for years: Were they modern humans suffering a disease, or a new species, Homo floresiensis?
Biological anthropologist Karen Baab first studied a model of LB1, the only skull recovered from the site, at the American Museum of Natural History in 2005. In a recently published PLOS ONE study, she and other researchers compare this specimen to a range of other modern human and extinct hominin skulls to get closer to settling the identity of Homo floresiensis, or ‘Flores man’.
The origins of ‘Flores man’ have been debated for quite a while now. What are the possible origins that are being discussed, and why the uncertainty?
The primary debate has centered on whether LB1 (and possibly the other individuals found on Flores) represents a new species that descended from an extinct species of the genus Homo or whether it is instead a pathological modern Homo sapiens, i.e the same species as us. If the Flores remains do in fact represent a distinct species, then the next question is whether they descended from Homo erectus, a species that may be our direct ancestor, or an even more primitive species. The latter scenario implies an otherwise undocumented migration out of Africa.
What makes it so hard to settle the argument one way or the other?
One of the difficulties in settling this particular argument is that most studies have focused on one or the other of these ideas and compared the Flores remains to either fossil hominins or to pathological modern humans, each using a different set of features. This makes it challenging to compare the alternative hypotheses side-by-side.
What kind of diseases might have caused modern humans to have features similar to these ‘hobbits’?
The three that have been discussed most prominently (and the three we looked at) are microcephaly, endemic hypothyroidism (“cretinism”) and Laron Syndrome. Microcephaly is not a disease per se, but rather a symptom of many different disorders. It refers to having an abnormally small brain and therefore skull. “Cretins” suffer from a lack of thyroid hormone before and after birth, which leads to stunted growth and possibly a slight decrease in skull size. Laron Syndrome individuals produce growth hormone, but their bodies do not properly recognize it, again leading to stunted growth and other developmental issues.
Only a few specimens of this hominin have been found, and there’s only one known skull, from the specimen named LB1. Are there reasons why these specimens have not been discovered elsewhere?
If Homo floresiensis descended from Homo erectus, then their closest relative lived just “next door” on the nearby island of Java. In this case, the unique features of the Homo floresiensis species probably evolved in the isolated island environment of Flores. If, however, the ancestor was a more primitive species, and Homo floresiensis didn’t branch off from H.erectus, it is possible that they might have migrated earlier than known, and we could still find older sites in mainland Asia containing this ancestral species.
You compared the morphology of the LB1 skull to many hominin ancestors and modern human populations from around the world. What were some of the most striking similarities and differences?
The LB1 skull is very distinct from the typical modern human’s, as it has a lower, more elongated silhouette when viewed from the side, , greater width at the rear of the braincase, and a flatter frontal bone (the bone underlying the forehead) with a more pronounced brow ridge. Interestingly, these are some of the same features that distinguish archaic species like Homo erectus from modern humans.
Specimens of Laron Syndrome and “cretin” skulls from modern Homo sapiens presented large, round, globular braincases, which are very different from the smaller, lower and less rounded braincase of LB1. The microcephalic human skulls present a closer comparison to LB1, but still show clear distinctions from LB1 in much the same way that they differ from species like Homo erectus or Homo habilis.
Overall, the LB1 braincase is most similar in its overall shape to small-brained Homo erectus from Eurasia that are 1.8 million years old.
How does this analysis add to, or change, what we knew about Flores man?
This analysis provides a unique opportunity to evaluate these evolutionary and pathological hypotheses side-by-side based on the same criterion – of cranial shape similarity. The results support a stronger affiliation of LB1 with fossil Homo than with any of the proposed pathologies. This study also offers an improvement over previous assessments of the microcephaly hypothesis by using a more extensive sample that better captures the variability in this disorder.
Do these results conclusively settle the discussion? What other possibilities still exist for the origins of H. floresiensis?
While very little in paleoanthropology is ever “settled,” I do think this study represents an important step forward in terms of putting the pathological hypotheses to rest. The question that remains to be answered definitively is which species of archaic Homo is the most likely ancestor of Homo floresiensis – Homo erectus or an earlier and more primitive species of Homo?
Citation: Baab KL, McNulty KP, Harvati K (2013) Homo floresiensis Contextualized: A Geometric Morphometric Comparative Analysis of Fossil and Pathological Human Samples. PLoS ONE 8(7): e69119. doi:10.1371/journal.pone.0069119
Images: Homo floresiensis by Ryan Somma, Cave where the remains of Homo Floresiensis where discovered in 2003, Liang Bua, Flores, Indonesia by Rosino
Balancing nutrient diets determines how ecosystems age
From rainforests to rocky glaciers, the life of an ecosystem is rooted in the balance of nutrients in its soil. Shifting levels of soil nitrogen (N) and phosphorus (P) define how ecosystems evolve, and understanding the dynamics of these key nutrients can help ecologists identify crucial factors to help mitigate climate change.
A new model to understand N and P dynamics over different time scales was described in the PLOS ONE paper, “Nitrogen and Phosphorus Limitation over Long-term Ecosystem Development in Terrestrial Ecosystems”. Recently awarded the Ecological Society of America’s prize for an outstanding theoretical ecology paper, the study determines whether N or P are more likely to limit the productivity of ecosystems over short, intermediate and long timescales. Author Duncan Menge explains the background and results of their study:
How do N and P levels change with the age of an ecosystem like a rainforest?
A good question. Levels of both N and P are very low in very young ecosystems (which typically have rocky soils; see picture above), higher in intermediate-aged ecosystems (see picture), and often lower in old ecosystems. How N levels change relative to P, though, is a trickier subject. The best-studied sites show relatively low N in younger ecosystems and relatively high N in older ecosystems, but there are some places that show opposing trends.
Prior to your research, how did theoretical models assess the impact of these two nutrients on ecosystem dynamics?
Prior to our work there were a series of conceptual developments, which I will call “the classic model,” but there was no previous mathematical model of N and P dynamics during long-term ecosystem development. The classic model states that ecosystems should progress from N deficiency in younger ecosystems to P deficiency in older ecosystems, as is seen on the best-studied sites. According to the classic model, this happens because of the differences in where N and P come from. P is present in most rocks, whereas N is not, so P inputs are largely controlled by the weathering of rocks. Consequently, very young ecosystems have large P inputs, whereas very old ecosystems have small P inputs. On the other hand, N comes primarily from rain, so N inputs don’t necessarily depend on ecosystem age.
Your paper mentions that these models don’t account for several possible trajectories of ecosystem evolution. What was missing?
There are a number of missing elements that jumped out as potentially important. First, the input side of the story isn’t as simple as “P comes from rocks, N comes from rain.” P also comes from dust that is blown in from upwind, whereas N can also come from organisms like soybean or alder that “fix” N from the air. Second, N and P losses from ecosystems should be as important as inputs in determining N and P levels, but these weren’t the focus of the classic model. These facts have been known for a long time in the scientific community, but no one had looked at what their implications might be for ecosystem development.
What was your new model and how did it cover these aspects?
Our model is novel for a couple of reasons. First, we considered a broader set of N and P input and loss dynamics than the classic model, which made for a richer set of possible ecosystem trajectories. Second, the type of mathematical analysis we did was unlike anything previous researchers had done in this particular field, and made it possible to pin down the types of conditions that might lead to different soil conditions.
What were some of the key data accounted for in your model that were overlooked in previous analyses?
Aside from the input and loss dynamics mentioned above, one piece of data we keyed in on was that microbes in the soil have an easier time accessing P than N in dead plant material. Again, this “preferential P mineralization” is something that has been known for a long time, but we thought that the effects of this quirk might not be fully appreciated.
What were the main findings of your analyses?
In addition to the classic “N limitation to P limitation” path, our model shows that many other trajectories are feasible. For example, if dust deposition is high and N-fixing organisms are abundant in young ecosystems (as they often are), an ecosystem might start out P limited and end N limited. One of the more surprising findings was that the levels of N and P in soil organic matter (mostly dead plant material) don’t necessarily correspond to N versus P limitation in an intuitive way.
What are some of the practical applications of this model- for example, for developmental activities in rainforests, or human activities planned in other ecosystems?
Whether N or P has a greater effect in an ecosystem has important implications for many environmental issues. The most important application is enhancing our climate models. Excess N can be transformed into a greenhouse gas, whereas P cannot. So, a better understanding of nutrient levels will improve predictions about the extent of climate change.
Congratulations to the authors on receiving an ESA award for this outstanding research paper!
Citation: Menge DNL, Hedin LO, Pacala SW (2012) Nitrogen and Phosphorus Limitation over Long-Term Ecosystem Development in Terrestrial Ecosystems. PLoS ONE 7(8): e42045. doi:10.1371/journal.pone.0042045
Photos by Duncan Menge:
top: the rocky soil of a very young ecosystem, Franz Josef glacier in New Zealand. The rainforests in the valley formed by the Franz Josef glacier are some of the best studied ecosystem development sites in the world.
below: a rainforest on 500 year old soil near the Franz Josef glacier.
Meet Vectidraco, a European pterosaur the size of a crow
Fossil records show that pterosaurs of all sizes and shapes flew through the skies of China and Central Asia about 145 to 66 million years ago. A new species of small pterosaurs described in a PLOS ONE paper reveals that western Europe may have had a similar diversity of these ancient animals. Author Darren Naish discusses the importance of the new species, named Vectidraco.
How did you begin studying dinosaurs (or pterosaurs in particular)?
Most of my research is and has been based on the Lower Cretaceous fossils that come from the Isle of Wight and elsewhere in southern England. The rocks here are famous for their dinosaurs, but fossil crocodilians, marine reptiles like plesiosaurs and rare pterosaurs are found here too. I’ve always been interested in pterosaurs and for several years have had a special research interest in a highly peculiar pterosaur group called the azhdarchoids – I’ve been working continuously on this group since 2007 or so and have been especially interested in their ecology, functional anatomy and evolutionary relationships. The finding of a new azhdarchoid in the Lower Cretaceous rocks of the Isle of Wight thus combined several of my special interests.
Where and how did you find the new fossil described in your study?
Most Cretaceous Isle of Wight fossils come from a rock unit termed the Wealden Supergroup. The new specimen – we’ve called it Vectidraco – is from a different, younger unit called the Atherfield Clay Formation, and as such it’s (so far as we know) only the second pterosaur reported from this unit.
I should say that the discovery of Vectidraco itself is interesting in that the find was made by a young girl, Daisy Morris (aged just 5 at the time!), while she was on holiday with her family. Daisy’s family wanted this fossil to be studied and cared for properly, so they did what I and many of my colleagues would say is “the right thing” and donated it to The Natural History Museum in London. So, we only know of Vectidraco thanks to Daisy: for this reason we named it in her honour. It’s full name is Vectidraco daisymorrisae.
What was previously known about this group of flying reptiles, the azhdarchoid pterosaurs?
So far as we know right now, azhdarchoids are unique to the Cretaceous period (that is, they were alive between about 145 and 66 million years ago) and all were toothless. They’re actually a pretty diverse group of pterosaurs, with some – like the tapejarids – being relatively small, withwingspans of about 3 feet or slightly less and others – namely the azhdarchids – being gigantic, withwingspans of more than 32 feet.
Tapejarids have short, deep snouts while azhdarchids have incredibly long, pointed jaws, and other kinds of azhdarchoid were intermediate between these two groups. Particularly good azhdarchoid fossils are known from South and North America and China, but their remains have been found right across Europe, Asia and Africa too.
Working out what azhdarchoids did when they were alive has been one of the great questions about the group, but it seems that they were mostly omnivores or carnivores that lived in terrestrial environments.
The paper describes the new fossil as “small-bodied”. How much larger are other known pterosaurs of this kind usually?
Azhdarchoids span a diversity of species that range from ‘small-bodied’ all the way up to gigantic. The biggest kinds – like the famous Quetzalcoatlus from Texas – were something like 10 feettall at the shoulder and over 450 pounds heavy while small ones, and Vectidraco is one of them, had wingspans of just 30 inches or so and would have been similar in size to crows or gulls. I would say that Vectidraco belonged to an azhdarchoid group where small size was normal and widespread, with large and even giant size evolving in other azhdarchoid lineages.
How did you determine that the new fossil belonged to the same group as these other specimens?
Vectidraco is known only from its pelvis, but even with only a pelvis to go on, we could see several features of the new specimen that made it especially azhdarchoid-like, mostly to do with the weird anatomy of the big, T-shaped bony structure that projects upwards and backwards from the rear part of the pelvis. In an effort to better test the idea that Vectidraco is an azhdarchoid, we included it in a few different phylogenetic analyses and it came out as an azhdarchoid in these too. It also has several unique features, not seen in any other pterosaurs, and for these reasons we were able to name it as a new species.
How does this discovery change what we know about this group of pterosaurs?
We’ve known for a while that small-bodied azhdarchoids lived in western Europe during the Early Cretaceous: a new species called Europejara olcadesorum was described in PLOS ONE last year. Now we’ve found that Vectidraco lived in the same region during the same period, so we’re seeing a pattern: small-bodied azhdarchoids were living alongside longer-snouted, small-bodied pterosaurs and also alongside large, toothy kinds called ornithocheiroids.
This is essentially the same kind of pterosaur community that we see in Chinese rocks of the same age – the great difference is that the Chinese fossils are relatively numerous, and frequently preserved as complete or near-complete skeletons. In fact, one of the things that we comment on in our paper is the fact that western Europe’s pterosaur assemblage looks far less rich than that of China due to differences in the way these fossils were preserved. Chinese pterosaur and small dinosaur fossils were buried rapidly by volcanic ash and hence preserved whole, while those of western Europe were usually broken apart on floodplains, extensively scavenged, and eventually preserved in fragmentary form.
The western European and Chinese assemblages might actually have contained similar sorts of species, but the conditions local to both places meant that their fossil records ended up being very different.
Read more about this exciting new fossil at Darren Naish’s own blog, Tetrapod Zoology.
Citation: Naish D, Simpson M, Dyke G (2013) A New Small-Bodied Azhdarchoid Pterosaur from the Lower Cretaceous of England and Its Implications for
Pterosaur Anatomy, Diversity and Phylogeny. PLoS ONE 8(3): e58451. doi:10.1371/journal.pone.0058451
Vullo R, Marugán-Lobón J, Kellner AWA, Buscalioni AD, Gomez B, et al. (2012) A New Crested Pterosaur from the Early Cretaceous of Spain: The First European Tapejarid (Pterodactyloidea: Azhdarchoidea). PLoS ONE 7(7): e38900. doi:10.1371/journal.pone.0038900
Images: Specimen and speculative reconstruction of Vectidraco from 10.1371/journal.pone.0058451, Life restoration of the head of Europejara from 10.1371/journal.pone.0038900
A floral ‘map’ to nectar discourages bumblebee robbers
In the business of survival, the bright colors of blooming flowers mark a serious transaction. Their nectar, color and fragrances are all designed to attract pollinators to come hither and transfer pollen to help plants reproduce but occasionally, these plans go awry. Some bees choose to avoid the pollen and tunnel into flowers to steal nectar instead. A study published in PLOS ONE last week explains how plants deter these robbers by providing them a map to reach nectar more quickly. Author Anne Leonard explains their results:
How did you become interested in studying floral guide patterns?
I think many people are intrigued by the fact that bees see the patterns on flowers differently than we do. I was studying color learning in bumble bees, and as I looked through the literature I realized there were still many unanswered questions about how these patterns affect bees’ behavior. Living in Tucson, I started to photograph the dazzling variety of nectar guides on Sonoran desert wildflowers, slowing down many a hike in the process. Between all the reading and photography, I clearly had nectar guides on the brain.
Why do flowers have nectar guide patterns?
The patterns of nectar guides appear to be very attractive to many bee species. Bright colors, high color contrasts and star-like outlines could simply help a plant increase visits from pollinators. It’s even been suggested that these visual features might have evolved to mimic rewards, for example bright yellows and oranges might resemble protein-rich pollen to the insects. Secondly, plants that produce distinctive and memorable patterns might also benefit because they provide an identifying feature for pollinators to learn, remember, and return to.
Third, a nectar guide may reduce the overall time the bee spends on the flower. If bees are sensitive to the time costs associated with visiting different flowers, then they should prefer to visit flowers they can handle quickly. Finally, our research suggests a novel benefit: the pattern can reduce a bee’s tendency to rob nectar. In this case, the pattern benefits the plant by incentivizing the bee to access nectar “legitimately,” in a way that is most likely to transfer pollen.
Can you explain what nectar robbing refers to and what a ‘legitimate’ way of getting nectar looks like?
If you take a moment and imagine a bee visiting a trumpet-shaped flower like a morning glory, what you’re picturing is most likely what we call a “legitimate” visit. The bee lands on a petal, and walks forward to probe down to the nectar located in the tube-like part of the flower. In the process, she is likely to pick up pollen or transfer pollen from her body to the flower. This exchange of nectar for pollen transfer forms the basis of the relationship between plant and bee. We refer to this type of nectar for pollen transfer via the floral opening as a “legitimate” visit, from the plant’s perspective.
In a second type of visit, the bee lands on the flower but instead of going the legitimate route, it bites a hole in the side of the flower to access nectar, without necessarily depositing pollen or picking up new pollen. Because the plant has lost nectar to the bee without gaining pollen transfer, this type of visit is termed ‘nectar robbing’.
Why do bees indulge in ‘nectar robbing’? Is this behavior seen with other insects and birds?
Although observations of bees nectar robbing date back to at least the 18th century writings of Sprengel, we are still studying why bees do it. Some species, like carpenter bees, have a reputation as frequent robbers. Others like honey bees and the bumble bee species I study, Bombus impatiens, are better known as opportunistic nectar robbers. They’ll rob some plant species but not others; propensity to rob seems to also vary somewhat across individuals. Some studies show that bees may be more likely to rob if a previous visitor has already created the access hole. Likewise, our research suggests that if the flower doesn’t have a nectar guide pattern to direct the bee to the floral opening, they are more likely to stray and encounter an access hole left by a previous robber.
In your paper, you found that when a flower had a guide pattern, bees were less likely to rob nectar. How did you test the bees’ behavior?
We use an array of specially designed artificial flowers that my co-author Josh Brent spent many hours trouble-shooting. These flowers had nectar available in two different ways. The bee could either land on the top of the flower and access nectar “legitimately” from a small central well, or she could land on the underside of the flower, and “rob” nectar from a small well located on the side of the floral tube.
We kept bee colonies in the lab so they were naïve with respect to experience with real flowers. We let bees into the arena one at a time, and recorded their visits to the flowers on the array. Half the bees were given blue flowers with yellow star-shaped guides, and the other half saw only plain blue flowers with no patterns. We noted whether the bee robbed or visited each flower legitimately, and we were also able to measure how quickly she located the nectar after landing in each case.
We found that bees robbed less frequently when the flowers had nectar guides and also landed more quickly on flowers with guides than those without them. This suggests the bees indeed found the nectar guide more attractive to land upon than the plain flower top, and that the guide helped them find nectar faster.
Does this discovery have applications for bee-keepers or horticulturists?
We’d need a few more of the pieces of the puzzle before claiming that our research on floral patterns might yield better honey or healthier honeybees, but our research suggests that the stripes and dots that provide color patterns pleasing to the human eye can also affect the way the bee interacts with the flower.
Typically, varieties of nursery plants are bred for human aesthetics. Given a choice, planting a variety with a dramatic nectar guide pattern might allow an observant gardener the satisfaction of seeing more pollen transferred by bees. On the other hand, those gardeners eager to see nectar robbing in action might select a relatively plain variety. The committed backyard scientist might be inspired to plant varieties with different types of patterns, sit back, and watch what happens. Of course, flowers of different plants can also differ in many other aspects that might affect a bee’s propensity to rob nectar (such as floral scent or nectar chemistry) and keep in mind that some may have UV patterns that the human eye can’t see.
Citation and images: Leonard AS, Brent J, Papaj DR, Dornhaus A (2013) Floral Nectar Guide Patterns Discourage Nectar Robbing by Bumble Bees. PLoS ONE 8(2): e55914. doi:10.1371/journal.pone.0055914
New fossil suggests giant ‘killer walrus’ was just a toothy fish-eater
Sea lions, otters, humpback whales and harbor seals are familiar sights to most native Californians today, but the waters off this coastline once harbored a much stranger fauna: giant bony-toothed birds, sharks the size of whales, flightless penguin-like auks, sea cows and giant predatory sperm whales.
Several species of walruses also lived among these animals, but only one survived to the present-day. Robert Boessenecker, author of a paper published in PLOS ONE today, explains what one rare fossil of an extinct walrus reveals about life on Sharkstooth Hill about 15 million years ago:
How did you become interested in studying extinct walruses?
I was always interested in paleontology as a kid, but where I grew up in California, there aren’t any dinosaurs – so I went out collecting shark teeth in high school. As an undergraduate, my adviser encouraged me to start a field-based research project, so I began studying fossil sharks, birds, and marine mammals from the San Francisco region. This turned me on to marine mammal paleontology in general, and I started looking at fossil walruses from other areas in California and Oregon.
What was previously known about the extinct walrus Pelagiarctos?
Pelagiarctos, and close relatives – probably looked a bit more like a sea lion than the modern walrus, as they lacked long tusks.
The first fossils of Pelagiarctos included just the “chin” end of the jaw, and a handful of large teeth, and were discovered in the 1980′s at the famous Sharktooth Hill fossil site near Bakersfield, California. The jaw fragment is very large and the two jawbones were fused at the chin – like humans, but not typical for pinnipeds. The large teeth are somewhat similar to those of terrestrial “bone-cracking” carnivores like hyenas, and so Pelagiarctos was interpreted as an apex predator that was adapted to feed upon warm blooded prey, perhaps including smaller pinnipeds and marine birds, in addition to the typical pinniped diet of fish. The large size and fusion of the lower jaws also suggested that Pelagiarctos could produce a large bite force – also pointing towards it being an apex predator, or “killer walrus” if you will.
Lastly, fossils of Pelagiarctos are extremely rare. Although there are hundreds of specimens of other pinnipeds from Sharktooth Hill – there are only seven known specimens of Pelagiarctos from that site.
In your paper, you describe the discovery of a new jaw bone with teeth. What did this reveal about this walrus’ feeding habits?
The discovery of a more complete specimen allowed us to test the hypothesis that Pelagiarctos was a “killer walrus”. When we examined the new specimen and the original fossils, we found that the teeth really weren’t that sharp at all – in fact, the teeth looked like scaled up versions of the teeth of a much smaller sea lion. This told us that the tooth shape is really just a consequence of Pelagiarctos retaining primitive teeth, rather than being a feeding adaptation.
What about body size? My coauthor, Morgan Churchill, developed a method to reconstruct body size of fossil pinnipeds based on the size of the lower jaw. As mentioned already, Pelagiarctos was indeed large, about the size of large male sea lions. However, when you try to correlate the weight of modern pinnipeds with what they eat , there isn’t really any distinct trend. This is because most modern pinnipeds are generalists, and tend to eat fish, squid, and even krill and mollusks. Even the modern walrus, a mollusk specialist and an exception to the generalist ‘rule’ occasionally kills and eats marine birds and even other pinnipeds. The only pinniped to regularly hunt warm blooded prey – the leopard seal – spends a good deal of the year feeding on krill.
These alternative interpretations and observations – combined with the lack of feeding adaptations, suggests Pelagiarctos was also a generalist fish eater rather than a “killer walrus” that only hunted marine birds and warm blooded prey.
Does this tell us anything about the walruses that exist today?
This new find and reinterpretation of Pelagiarctos as a fish-eater gives us a slightly more accurate picture of the evolutionary background of the modern walrus. Right now, there is only one modern walrus species but back then, walruses were a very diverse group. Many of these other extinct walruses had strange adaptations – such as the development of upper and lower tusks, gigantic body size, ultradense bones, unusually short forelimbs, and even the loss of all teeth aside from tusks. The myriad types of extinct walruses – Pelagiarctos included – beautifully demonstrate the often convoluted path that evolution can take.
What is the most important aspect of your results?
Pelagiarctos lived roughly 15-18 million years ago; this period is also referred to as the “middle Miocene Climatic Optimum”, and global temperatures increased for a little while. After the optimum, the earth began to cool again.
Any information we can get that improves our knowledge of extinct marine mammal food webs – especially during times of climatic change – is a step forward towards putting together a “deep time” context for understanding modern marine mammal ecology.
Read more about this fossil at the author’s blog.
Image: Artist’s restoration of Pelagiarctos, Robert Boessenecker
Citation: Boessenecker RW, Churchill M (2013) A Reevaluation of the Morphology, Paleoecology, and Phylogenetic Relationships of the Enigmatic Walrus Pelagiarctos. PLoS ONE 8(1): e54311. doi:10.1371/journal.pone.0054311
Fixing siRNAs by creating an anti-siRNA
Small pieces of RNA in our cells can act like molecular switches that turn genes off by binding to them. These pieces, called small interfering RNAs (siRNAs) are also used by researchers to design experiments to understand what certain genes do.
Scientists can design siRNA molecules aimed at turning off specific genes they are trying to study. Though such siRNA ‘switches’ can be very useful, they are often non-specific, turning off hundreds of genes that they should not have an effect on. As a result, it is difficult for a biologist to conclude whether an experimentally observed effect is due to turning off the gene they meant to turn off or the hundreds that they didn’t (called “off-target effects”). Eugen Buehler of the National Center for Advancing Translational Sciences (NCATS), a new center at the NIH, describes an alternate approach to dealing with these off-target effects of siRNAs in his recent PLOS ONE paper. Read on to find out more about this research:
How did you become interested in improving siRNA experiments?
I’ve been working on siRNAs for about the last five years. When I would talk to my wife (a cell biologist) about my research, I would go on and on about all the problems created by these non-specific effects. Since she uses siRNAs in her research, she would ask, “Well, what should I do to avoid it?”
I didn’t have an answer. All the methods I had involved a statistical analysis of a large number of results from high-throughput screens, which look at several thousand genes at once. They couldn’t be applied to experiments that only involved one or a few genes, which is what many researchers do. It frustrated me not being able to help her, and so this question of what to do about off-target effects in small-scale experiments kept nagging me, until I found an answer.
And what was that answer?
As is often the case, the answer involved looking at the problem a different way. For years, people have been trying to solve the problem by getting rid of the non-specific effects. There are many ways to do this, but they still have a high incidence of these effects.
So, rather than trying to eliminate the off-target activity, we took the opposite approach. We changed three points (bases 9-11) where an siRNA makes contact with its target, so it couldn’t have the effect it was designed for. In this way, we created the C911 version, an anti-siRNA of sorts, which had all the off-target effects but none of the on-target effects.
So if an siRNA has an effect in a cell that is different from what the C911 version of the same siRNA has, we can conclude that the effect is because it silenced the intended target.
Which figure in the manuscript do you think best summarizes your results?
Definitely Figure 3B. Here, we compare siRNAs that appear to have specific effects but don’t (false positives), with ones that do have a specific action on a target gene. We took ten of each kind and created C911 versions for all twenty.
When we compared the two we found that for the false positives, the siRNA and the anti-siRNA had the same effects (left hand panel). But for the siRNAs which really did have an effect on their target, there was a big difference between the siRNA and its C911 version. As it happened, the C911 controls worked perfectly for all twenty siRNAs we had selected for the experiment.
Where do you hope to go from here?
For a tool as well established as siRNA, it will take a while to change the way we design our experiments. The first step is for there to be a reasonable alternative, and that is what this paper is meant to supply. The next is to make that alternative easy to choose. Part of that will involve getting companies that manufacture siRNAs to eventually make negative controls like this, so that negative controls like C911 can be easily and affordably obtained for any siRNA.
My hope is that someday when a researcher orders an siRNA, they won’t even have to ask; they’ll get a tube with their siRNA and a tube with the appropriate negative control by default.
Read about Nobel-winning research on interfering RNAs, and explore more PLOS ONE research about siRNAs here and here.
Citation: Buehler E, Chen Y-C, Martin S (2012) C911: A Bench-Level Control for Sequence Specific siRNA Off-Target Effects. PLoS ONE 7(12): e51942. doi:10.1371/journal.pone.0051942
Image: Target by Ivan McClellan on flickr
Using Virtual Reality to Understand Human Perception: An Author Spotlight on Andrew Glennerster
How do we visualize the world around us? To answer this question, researchers are using virtual reality to gain insight into how we perceive our surroundings. At the University of Reading, Dr. Andrew Glennerster and his international team are utilizing this technology to study how people generate a three-dimensional representation of the world around them. His recently published PLoS ONE article, A Demonstration of ‘Broken’ Visual Space, tests the theory on whether there is a one-to-one match between reference points in our internal representation of the world and those in our actual surroundings. In this author spotlight, Dr. Glennerster answers questions about his background, his research and his PLoS ONE manuscript.
Let’s start off with your background. How did you become interested in studying human vision and what role does virtual reality play in assisting your research?
I originally studied medicine at Cambridge. It was an exciting time for vision research there, and in my 3rd year I was taught by lots of the big names in vision like Horace Barlow and John Robson. I found it fascinating and went back to studying vision after I had finished my clinical training.
I have set up a virtual reality lab because it allows us to study people’s 3D vision as they move around. It is a much more difficult technical challenge than studying 3D vision from binocular stereopsis, like in a 3D movie, but moving around is the main way that animals see in 3D. To study this process systematically, you need virtual reality.
In your paper, you mention that most theories on three-dimensional vision suggest that the way we represent space in our visual systems assumes that we generate a one-to-one model of space in our brains. Why did your team test this theory and what did you find?
We tested this theory because, for a long time, it has been the dominant one in the literature. It is very easy to believe people have something like a ‘model of the world’ in their heads, but by itself that is not a good argument. We need to move away from accounts that are easy to imagine yet hard to explain at a neural level and toward ones that are based on operations we know the brain can carry out even if they are more conceptually challenging. We do not yet have a well worked out alternative to the one-to-one, ‘reconstruction’ model, but there are some promising beginnings.
When a three-dimensional illusion is depicted in a two-dimensional picture, certain paradoxes occur that wouldn’t be possible to replicate in real life. Given this, how does the Penrose staircase illusion, included in Figure 1 of your paper, compare to your experiment? Where there any similarities?
The similarity between the Penrose staircase and people’s representation of space is that if you tried to build a real 3D model of either you would fail. You cannot make sense of people’s responses in this experiment using a real 3D model. People believe they are in a stable room during the whole experiment. Anyone who suggests that a stable perception comes from the observer having an unchanging 3D ‘model’ of the environment in their head has a difficult time explaining these data. If you try to pick coordinates in some perceptual space for each of the objects in the experiment then you get tangled up in just the same way that you do with the Penrose staircase: you cannot say whether one object is in front of or behind another one. The solution is to give up trying to assign coordinates to each of the objects.
How does your research help further our understanding of human perception? Does it have real world applications?
There is an increasing focus within visual neuroscience on the issue of stability: what is it in the brain that remains constant as we move our eyes around and, even more problematically, as we walk around?
What’s next? Where do you hope to go from here?
This paper attacks the current dominant model, but the next, more positive, stage is to build coherent alternative models. I believe that working with colleagues in computer vision is a good way to do this as robots have to deal with images arriving in real time and react accordingly. Currently in computer vision, new types of representation are being developed that are not at all like a reconstruction. These can act as an inspiration for testable models of human vision. Equally, if neuroscientists produce good evidence about how the brain represents a scene, it could influence the way that mobile robots are programmed.
To learn more about University of Reading’s Virtual Reality Research Group and Dr. Andrew Glennerster’s work, click here. To find more PLoS ONE research on human vision and virtual reality click here.
The “responsible conduct of research” is not limited to properly obtained consent
Today we published the article,Willingness to Share Research Data Is Related to the Strength of the Evidence and the Quality of Reporting of Statistical Results, by Wicherts et al. In the manuscript, the authors show that weaker evidence in a psychology paper published in a journal requiring signed agreements to share data is associated with a failure to comply with this signed agreement to share.
Rochelle Tractenberg
In the following opinion piece, Rochelle Tractenberg, the academic editor who handled the peer review of Wicherts et al., discusses the ways in which “research ethics” and the “responsible conduct of research” go beyond human subjects protection, to include data sharing, professional conduct, and the careful, correct and complete reporting of all analyses in published research. Rochelle is a biostatistician and research methodologist at Georgetown University.
The article by Wicherts et al. describes their study of 1148 “statistically significant results” that were published in 49 different papers within two psychology journals. As it was being reviewed and revised, this paper sparked a vigorous debate among PLoS ONE editors and reviewers for two very different, ethics-oriented, reasons. These reasons were:
- Disciplines differ in their requirements that data analyzed and published should be made available to any scientist that requests the data. In some cases, the data cannot be properly de-identified, which violates a key feature of human subjects protections that all scientists are supposed to commit to whenever they carry out scientific work involving living persons. The Ethics Committee of the authors’ institution explicitly required them NOT to publicize the authors who refused to share data – and whose work was identified as being weak in terms of evidence and/or quality of results.
- The readers of published work are totally dependent on the quality and accuracy of the statistical results presented –and described – in any manuscript they wish to utilize as evidence in their own argument or scientific endeavor. The option to re-analyze data is critical to check the reliability of published designs, results, or conclusions. Time is a precious commodity; knowing what work is most likely to require replication prior to its use would limit our reliance on work likely to include mis-analyzed data, misinterpreted results, or both.
These considerations highlight diverse conceptualizations of the “responsible conduct of research”: in the first conceptualization, the protection of human subjects –the authors who did and did not share their data, whose published work was analyzed in this paper – is the sole concern. The second conceptualization involves the responsibility of the authors of the reviewed published papers to fulfill their professional ethical obligations as well as their contractual agreements. Wicherts et al. did obtain permission from their Ethics Committee to provide a list of authors who failed to share data – if specifically requested, but are NOT permitted to identify which authors were compliant and defiant within their paper, nor to place their data file, as is, into a public archive. Wicherts et al. analyzed the contents of published articles, and then requested the data these papers represented. The journals’ and APA ethics policies are public and require data sharing, so neither the requests nor the failures to comply with those requests can be considered privileged. In short, no feature of the data in this manuscript can be considered to be privileged. The responsible conduct of research is much more than protecting study subjects and obtaining informed consent, but the Ethics Committee did not act like it is.
As the editor shepherding this article through the review process, I applaud the effort by Wicherts and colleagues, and disagree with the Ethics Committee decision. I believe that every journal should document requests for data and the failures of authors to provide the requested data as part of the publication record. This compliance information should be accessible to all reviewers for journals and grants, and to scientists who look to the published literature for replicable, reliable, ethically obtained results.
A prior report by Wicherts et al. in 2006 found that, while journals published by the APA all require authors to sign an agreement to share their data, 73% of authors who were contacted for that study failed to do so. These 73% defied their written agreement, and professional obligation (see APA Ethical principle 8.05), to share their data. This is not responsible conduct of research; this is unethical behavior and every scientist is entitled to know whether or not an author is responsible in their conduct –and reporting – of their research. As critical as these features are to responsible conduct of research, the review of manuscripts and grants for “ethical considerations” cannot be limited to the inclusion of women and minorities, balance between male and female subjects, and properly obtaining informed consent.
Wicherts et al. conclude that policies for data archiving should be strengthened/more widespread, even though their 2006 findings that, in defiance of their signed agreements, the journals’ publishing policy, and the professional association policy on data sharing, nearly ¾ of APA published authors refused to share data when contacted. In their current study, the refusal rate was “only” 57%.
A survey of geneticists working at 100 universities in the US led to an estimate of 47% failure to share. The challenge is clearly widespread and has a prevalence rate in the 47-73% range. By contrast, in her survey of the prevalence of “unethical” or “questionable” scientific behavior, Fanelli arrived at far smaller estimates – possibly because of a lack of awareness among her respondents that a failure to share data or research resources constitutes irresponsible –not merely questionable – research practice.
A broader appreciation of how critical transparency and replicability are for good science could support the cultural shift necessary to promote the idea that the “responsible conduct of research” is not limited to properly obtained consent. A mechanism for documenting failures in these key features of responsible conduct of research would also support this shift. Every reviewer should have this information about the likelihood that an applicant or author will violate sharing policies and/or defy contracts they’ve signed and/or professional ethical science standards they should be held to.
The responsible conduct of research includes conscientious protection of human subjects. In the book, “Scientific Integrity”, Macrina also notes, “(s)haring research materials published in the peer reviewed literature has been a traditional practice that follows from the expectation that scientific research must be amenable to replication” (p. 81) and that “…written communication is an essential part of scientific research.” (p. 83) (see also National Research Council, 1992; Board on Life Sciences, 2003). As such, these should be just as conscientiously executed as other aspects of the research enterprise. Refusals to share data harms science and constitutes violations of our obligations to be responsible conductors of research.
Rochelle Tractenberg has also written a companion piece to this article, which can be found in the comments section of the Wicherts et al. manuscript. In the second piece, she interprets the association between weak evidence and failures to comply with data sharing requirements in a different way. Instead of supporting mandatory archiving of data, Dr. Tractenberg concludes that readers and reviewers of manuscripts and grant proposals should be notified of the author’s/applicant’s history of compliance with data sharing mandates and policies. She believes that such documentation will do more to change the culture towards one promoting science and data sharing than mandatory data archiving. To read this post, please click here.
References
Board on Life Sciences (2003). Sharing Publication-Related Data and
Materials: Responsibilities of Authorship in the Life Sciences.
Washington, DC: National Academy Press.
Campbell, E. G., Clarridge, B. R., Gokhale, M., Birenbaum, L.,
Hilgartner, S., Holtzman, N. A., et al. (2002). Data withholding in
academic genetics: Evidence from a national survey. Journal of the
American Medical Association, 287, 473–480.
Fanelli D (2009) How Many Scientists Fabricate and Falsify Research? A
Systematic Review and Meta-Analysis of Survey Data. PLoS ONE 4(5):
e5738. doi:10.1371/journal.pone.0005738
Macrina FL. (2005). Scientific Integrity: Text and Cases in
Responsible Conduct of Research, 3E. Washington, DC: American Society
for Microbiology Press.
National Research Council (1992). Responsible Science, Vol 1: Ensuring
the Integrity of the Research Process. Washington, DC: National
Academy Press.
Wicherts JM, Borsboom D, Kats J, Molenaar D (2006) The poor
availability of psychological research data for reanalysis. American
Psychologist 61:726-728.
Wicherts JM, Bakker M, Molenaar D (2011) Willingness to Share Research Data Is Related to the Strength of the Evidence and the Quality of Reporting of Statistical Results. PLoS ONE 6(11): e26828. doi: http://dx.plos.org/10.1371/journal.pone.0026828