PLOS ONE Publishes its 100,000th Article

PLOS ONE publishes its 100,000th article – a pretty major milestone for a journal that has seen its fair share of momentous events, and a perfect opportunity to reflect on this journey.

 PLOS ONE began seven and a half years ago. On the day of its launch – as has become the legend in the PLOS offices – there was an earthquake in the Bay Area, heralding the tremors that would be felt through the science world as a result of the disruptive innovation underway. PLOS ONE was an aspirational idea for PLOS from the very beginning: our founders always intended to launch a multi-disciplinary, broad-acceptance journal that would shake off the vestiges of the print tradition – no limits to the scope of research, number of pages, or potential growth.

And grow it did. After two years PLOS ONE had published over 4,000 articles, by four years it was the largest journal in the world, and now seven years after launch has published 100,000 articles. The revolutionary model of PLOS ONE has been emulated the world over: virtually every publisher now has its own equivalent “megajournal.”

PLOS ONE is now a major force in the scientific literature. The top 2% PLOS ONE papers (by number of views) have been collectively viewed nearly 39 million times, cited on Scopus over 80,000 times, bookmarked by Mendeley readers over 150,000 times, tweeted over 59,000 times, cited 2,800 times on Wikipedia, and recommended over 300 times on F1000 Prime.

The enduring value of PLOS ONE to the scientific process lies in the solid union between the three following factors: speed to publication, high standards of science, and unrestricted scope of research.

Speed to publication:

Faster time to publication was the founding principle of PLOS ONE. It doesn’t just entail going from submission to publication more quickly (although that is also important). It means dramatically reducing the time from an author’s decision to publish their findings to the time those results appear in public. That time is often years in the old system of review, where subjective opinions of significance and scope lead to unnecessary rejections and resubmission to different journals. With PLOS ONE, where scientific rigor alone is assessed, this time window shortens to a few months.

High standards:

PLOS ONE instituted rigorous standards from the start. As the volume exponentially increased and the quality of the submissions became more variable, these checks became more important and more rigorous. For every paper the journal staff (over 100 strong, including 14 editors) now check each of the following before a manuscript is sent for review:

  • Competing interests
  • Financial disclosures
  • Quality of English language
  • Ethical approval for animal experiments
  • IRB approval for human experiments
  • Protocols and CONSORT for clinical trials
  • PRISMA for systematic reviews and meta-analyses
  • Cell line provenance
  • Field sample provenance
  • Humane endpoints in animal studies
  • Data availability
  • Plagiarism

The care that we take in reporting and oversight is rooted in PLOS’ commitment to this editorial responsibility.

Because of these checks, every PLOS ONE citation on a researcher’s CV shows that their work has reached high standards of reporting and oversight – something that matters a great deal to funders and institutions as the need for reproducibility becomes increasingly a part of their overall mission. This is an area where we feel journals can take a lead: high standards of reporting are the best way for the scientific community to regain the trust of the public and politicians in the wake of the recent spate of failures in replicating high-profile discoveries.

Unrestricted scope:

So many of the delays in sharing results are a result of journals putting unnecessary restrictions on the scope of the research they are willing to publish. Journals often withhold the release of negative findings because they are likely to be cited less, and will therefore lower their impact factor. Or they exclude papers purely due to the application of disciplinary boundaries. In this digital age, with no space restrictions on what can be published, such artificial limits only impede the flow of information. At PLOS ONE, we have thrown out these notions and will consider vital research across all subject areas (even seemingly strange and multi-disciplinary).

A heartfelt 100k thank you

The impact of PLOS ONE on scientific publishing has been tremendous and revolutionary. The world of scientific communication is a different place because of it, and that is something PLOS and its entire community of collaborators should be proud of.

The extraordinary PLOS ONE Editorial Board, reviewers and authors – who believed in the PLOS mission to accelerate research communication and gave their own time to review, edit and revise manuscripts – were critical to this transformation and share in this milestone. To each and every one of them PLOS ONE is eternally grateful.

So here’s to the 100,000th PLOS ONE article. Though thrilled to have reached this milestone, we are even more excited to see where the next 100,000 will lead.

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Magnifying Power to the People with the Foldscope

The microscope holds a place on the short list of inventions that have changed the world and revolutionized our understanding of science. Microscopes are crucially important public health tools, allowing workers to identify pathogens and correctly diagnose the cause of illnesses. As educational tools, they can excite and engage students, revealing a world invisible to the naked eye. And, as many people who’d love a microscope but don’t have one can tell you, they are also expensive. Millions of doctors, health workers, and patients worldwide lack the resources to benefit from this vital tool, and millions of students have never seen a microscope before. In a dramatic step to address this problem, researchers from Stanford University have designed ultra-low-cost microscopes built from an inexpensive yet durable material: paper. They recently published their designs and data in PLOS ONE.

Foldscope template

Meet the Foldscope. Borrowing from the time-honored tradition of origami, the Foldscope is a multi-functional microscope that can be assembled much like a paper doll. Users cut the pieces from a pattern of cardstock, fold it according to the printed lines, and add the battery, LED, and lens, and−voilà−a microscope. Foldscope schematicClick here to watch a video of how one is assembled. Some of their coolest features are as follows:

  • Foldscopes are highly adaptable and can be configured for bright-field and dark-field microscopy, to hold multiple lenses, or to illuminate fluorescent stains (with a special LED).

Foldscope Configurations

  • They can be designed for low or high powers and are capable of magnifying an image more than 2,000-fold.
  • They accept standard microscope slides, and the viewer can move the lens back and forth across the slide by pushing or pulling on paper tabs.
  • Users can focus the microscope by pushing or pulling paper tabs that change the lens’ position.
  • Foldscopes are compact and light, especially when compared with conventional field microscopes. They also weigh less than 10 grams each, or about the weight of two nickels.
  • They are difficult to break. You can stomp on them without doing much damage, and they can survive harsh field environments and encounters with children.

Stepping on FoldscopeWhat’s the total cost, you ask? According to authors, it’s less than a dollar.  At that price, it’s easy to imagine widespread use of Foldscopes by many who previously could not afford traditional microscopes. In this TED Talk, Manu Prakash demonstrates the Foldscopes and explains his hopes for them. The authors envision mass producing them and distributing different designs optimized for detecting the pathogens that cause specific diseases, such as Leishmaniasis and E. coli.  They could even include simple instructions for how to treat and prepare slides for specific diagnostic tests or provide pathogen identification guides to help health workers in the field make diagnoses.  This is just one way in which the ability to see tiny things could make a huge difference in the world.

Related links:

Low-Cost Mobile Phone Microscopy with a Reversed Mobile Phone Camera Lens

Community Health Workers and Mobile Technology: A Systematic Review of the Literature

Citation: Cybulski JS, Clements J, Prakash M (2014) Foldscope: Origami-Based Paper Microscope. PLoS ONE 9(6): e98781. doi:10.1371/journal.pone.0098781

Images: Images are from Figures 1 and 2 of the published paper

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Music, Language, and the Brain: Are You Experienced?

Have you ever thought about everything that goes into playing music or speaking two languages? Musicians for example need to listen to themselves and others as they play, use this sensory information to call up learned actions, decide what is important and what isn’t for this specific moment, continuously integrate these decisions into their playing, and sync up with the players around them. Likewise, someone who is bilingual must decide based on context which language to use, and since both languages will be fairly automatic, suppress one while recalling and speaking the other, all while continuously modifying their behavior based on their interactions with another listener/speaker. All of this must happen quickly enough for the conversation or song to flow and sound natural and coherent. It sounds exhausting, yet it all happens in milliseconds!

Playing music or speaking two languages are challenging experiences and complex tasks for our brains. Past research has shown that learning to play music or speak a second language can improve brain function, but it is not known exactly how this happens. Psychology researchers in a recent PLOS ONE article examined how being either a musician or a bilingual changed the way the brain functions. Although we sometimes think of music as a universal language, their results indicate that the two experiences enhance brain function in different ways.

heat map

One way to test changes in brain function is by using Event Related Potentials (ERPs). ERPs are electrical signals (brain waves) our brains give off immediately after receiving a stimulus from the outside world. They occur in fairly predictable patterns with slight variations depending on the individual brain. These variations, visualized in the figure above with the darkest red and blue areas showing the most intense electrical signals, can clue researchers into how brain function differs between individuals and groups, in this case musicians and bilinguals.

The ERP experiment performed here consisted of a go/nogo task that is frequently used to study brain activity when it is actively suppressing a specific behavior, also called inhibition. In this study, the authors asked research participants to sit in front of a computer while simple shapes appeared on screen, and they were to press a key when the shape was white—the most common-colored shape in the task—but not when purple, the least frequent color in the task. In other words, they responded to some stimuli (go) and inhibited their response to others (nogo). This is a similar task to playing music or speaking a second language because the brain has to identify relevant external sensory information, call on a set of learned rules about that information, and make a choice about what action to take.

 waves

The authors combined and compared correct responses to each stimulus type in control (non-musician, non-bilingual) groups, musician groups, and bilingual groups. The figure above compares the brainwaves of different groups over time using stimulus related brainwave components called N2, P2, and LP. As can be seen above, these peaks and valleys were significantly different between the groups in the nogo instances. The N2 wave is associated with the brain’s initial recognition of the meaning or significance of the stimulus and was strongest in the bilingual group. The P2 on the other hand, is associated with the early stages of putting a stimulus into a meaningful context as it relates to an associated behavior, and was strongest in the musician group. Finally, the authors note a wave called LP wave, which showed a prolonged monitoring response in the bilingual group. The authors believe this may mean bilinguals take more time to make sure their initial reaction is correct.

In other words, given a task that involved identifying a specific target and subsequently responding or not responding based on learned rules, these results suggest that musicians’ brains may be better at quickly assigning context and an appropriate response to information because they have a lot of practice turning visual and auditory stimuli into motor responses. Bilinguals, on the other hand, show a strong activation response to stimuli along with prolonged regulation of competing behaviors, likely because of their experience with suppressing the less relevant language in any given situation. Therefore, despite both musicianship and bilingual experiences improving brain function relative to controls, the aspects of brain function they improve are different. As games and activities for the purpose of “brain training” become popular, the researchers hope this work will help with testing the effectiveness of brain training.

Citation: Moreno S, Wodniecka Z, Tays W, Alain C, Bialystok E (2014) Inhibitory Control in Bilinguals and Musicians: Event Related Potential (ERP) Evidence for Experience-Specific Effects. PLoS ONE 9(4): e94169. doi:10.1371/journal.pone.0094169 

Images are Figures 1 and 2 from the article.

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Signs of Change: Regional and Generational Variants in British Sign Language

British Sign Language chart

British Sign Language chart

As societies change, so too do its languages. In the English-speaking world, we often make note of changes in language by recognizing the rise of new words, like “selfie,” and the repurposing of familiar words, such as “because.” It may not be a surprise, then, to learn that this “evolution” isn’t limited to the spoken word: sign languages can also change over time. In a recent PLOS ONE study, scientists examined regional variations within British Sign Language (BSL), and found evidence that the language is evolving and moving away from regional variation.

To assist in this undertaking, the authors used data collected and recorded for the British Sign Language Corpus Project. About 250 participants took part in the project, recruited from eight regions in the UK. In addition to hailing from different parts of the country, participants came from various social, familial, and educational backgrounds.

When the first deaf schools were established across the UK in 1760, there was little standardization in signing conventions. Consequently, depending on the school you were attending, schools sometimes taught pupils to use different signs to convey the same concepts or words. The authors posit that this lack of standardization may be the basis for today’s regionalism in BSL.

The participants were given visual stimuli, such as colors or numbers, and then asked to provide the corresponding sign, one that they would normally use in conversation. The researchers also recorded participants engaging in unscripted conversations, a more formal interview, and in the delivery of a personal narrative, all of which were incorporated into the authors’ study and analyzed.

Example of the stimuli shown to participants.

Example of the stimuli shown to participants.

In their analysis, researchers focused on four concepts: UK place names, numbers, colors, and countries. The participants’ responses to the visual stimuli were compared to with their recorded conversation to control for any confounding variables, or unforeseen social pressure to sign in a particular way. The responses were also coded as being either “traditional” or “non-traditional” according to the regional signing conventions.

Results indicated that age may play a role in whether a participant uses traditional or non-traditional signs. Particularly when signing for countries, about half the responses given by younger participants were non-traditional signs. In addition, some participants—young and old—explained that they changed the country sign they used as they grew older. The researchers posit that this may be due to changing definitions of political correctness, in which older, more traditional signs are now perceived to be politically incorrect.

The authors also found that age may also play an important role in the participant’s use of color and number signs. As was the case for signing countries, younger participants were more likely to use non-traditional signs, and older participants more likely to use traditional signs. The researchers noted that younger participants using signs non-traditional to their region seemed to be adopting signing conventions from southern parts of the country, such as London, or from multiple regions. In other cases, younger participants responded by signing the first letter of the word, such as ‘p’ for purple. The authors attribute this generational shift to the participants’ increased exposure to different signing conventions, ushered in by technological developments, such as the Internet, and increased opportunities for travel.

Changing social norms, technologies, and opportunities—these are no strangers to us by now. As the world changes, so too do the ways in which we communicate, verbally and physically.

 

Citation:Stamp R, Schembri A, Fenlon J, Rentelis R, Woll B, et al. (2014) Lexical Variation and Change in British Sign Language. PLoS ONE 9(4): e94053. doi:10.1371/journal.pone.0094053

Image 1: British Sign Language chart by Cowplopmorris, Wikimedia Commons

Image 2: Figure 3 from article

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Statistics Predicted a Healthier Medieval London Following the Black Death

Black_Death

The Black Death, a pandemic at its height in Europe during the mid-14th century, was a virulent killer. It was so effective that it wiped out approximately one third of Europe’s population. Recent studies have shown that the elderly and the sick were most susceptible. But was the Black Death a “smart” killer?

A recent PLOS ONE study indicates that the Black Death’s virulence might have affected genetic variation in the surviving human population by reducing frailty, resulting in less virulent subsequent outbreaks of the plague. By examining the differences in survival rates and mortality risks in both pre-Black Death and post-Black Death samples of a London population—in combination with other, extrinsic factors, like differences in diet between the two groups—the researcher found that in London, on average, people lived longer following the plague than they did before it, despite repeated plague outbreaks. In other words, in terms of genetic variation, the Black Death positively affected the health of the surviving population.

To uncover differences in the health of medieval Londoners, Dr. Sharon DeWitte of the University of South Carolina examined 464 pre-Black Death individuals from three cemeteries and 133 post-Black Death individuals from one. She chose a diverse range of samples for a comprehensive view of the population, including both the rich and the poor, and women and children, but targeted one geographic location: London.

The ages-at-death of the samples were determined by calculating best estimates—in statistics these are called point estimates—based on particular indicators of age found on the skeletons’ hip and skull bones. Individuals’ ages were then evaluated against those in the Anthropological Database of Odense University, a pre-existing database comprising the Smithsonian’s Terry Collection and prior age-at-death data from 17th-century Danish parish records.

After estimating how old these individuals were when they died and comparing the age indicators against the Odense reference tool, the author conducted statistical analyses on the data to examine what the ages-at-death could tell us about the proportion of pre- and post- Black Death medieval Londoners who lived to a ripe old age, as well as the likelihood of death.

Survivorship was estimated using the Kaplan-Meier Estimator, a function used to indicate a quantity based on known data; in this case the function evaluated how long people lived in a given time period (pre-Black Death or post-Black Death). The calculated differences were significant: In particular, the proportion of adults who lived beyond the age of 50 from the post-Black Death group was much greater than those from the pre-Black Death group.

Age-at-death Distributions

Age-at-death Distributions

In the pre-Black Death group, death was most likely to occur between the ages of 10 and 19, as seen above.

The Kaplan-Meier survival plot shows how the chances of survival, which decrease with age, differ for Pre-Black Death and Post-Black Death groups, as seen below.

Survival Functions

Survival Functions

As the survival plot indicates, post-Black Death Londoners lived longer than there Pre-Black Death predecessors.

Finally, Dr. DeWitte estimated the risk of mortality by applying the age data to the statistical model known as the Gompertz hazard, which shows the typical pattern of increased risk in mortality with age. She found that overall post-Black Death Londoners faced lower risks of mortality than their pre-Black Death counterparts.

To make long and complicated methodology short, these analyses indicate that post-Black Death Londoners appear to have lived longer than pre-Black Death Londoners. The author estimates that the general population of London enjoyed a period of about 200 years of improved survivorship, based on these results.

The virulent killer, the Black Death, may have helped select for a healthier London by influencing genetic variation, at least in the short term. However, to better understand the improved quality of life of post-Black Death London, the author suggests further study to disentangle two major factors: the selectivity of the Black Death, coupled with improvements in lifestyle for post-Black Death individuals. For example, the massive depopulation in Europe resulted in increased wages for workers and improvements to diet following the plague, which also likely improved health for medieval Londoners. By unraveling intrinsic, biological changes in genetic variation from outside extrinsic factors like improvements in diet, it may be possible to better understand the aftermath of one of the most devastating killers in infectious disease history.

The EveryONE blog has more on the medieval killer here.

Citation: DeWitte SN (2014) Mortality Risk and Survival in the Aftermath of the Medieval Black Death. PLoS ONE 9(5): e96513. doi:10.1371/journal.pone.0096513

Image 1: The Black Death from Simple Wikipedia

Image 2: pone.0096513

Image 3: pone.0096513

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Modern Humans: Were We Really Better than Neanderthals, or Did We Just Get Lucky?

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We’ve all heard the story: dim-witted Neanderthals couldn’t quite keep up with our intelligent modern human ancestors, leading to their eventual downfall and disappearance from the world we know now. Apparently they needed more brain space for their eyes. The authors of a recent PLOS ONE paper are digging into the ideas behind this perception, and take a closer look at eleven common hypotheses for the demise of the Neanderthals, comparing each to the latest research in this field to convince us that Neanderthals weren’t the simpletons we’ve made them out to be.

The authors tackled ideas like the Neanderthal’s capacity for language and innovative ability, both often described as possible weaknesses leading to their decline. Analyzing the published research on each topic, they found that archaeologists often used their finds to “build scenarios” that agreed with the running theories of human superiority, and that some long-held truths have now been challenged by recent discoveries and ongoing research at the same excavation sites.

As one example, researchers who found shell beads and pieces of ochre and manganese in South Africa—­used as pigments—claimed them as evidence of the use of structured language in anatomically modern humans. While we can only guess when linking items like these to the presence of language, new findings at Neanderthal sites indicate that they also decorated objects with paints and created personal ornaments using feathers and claws. Whatever the anatomically modern humans were doing in South Africa, Neanderthals were also doing in Europe around the same time, negating the claim that this ability may have provided the anatomically modern humans with better survival prospects once they arrived in Europe.

Another set of South African artifacts led the archaeological community to believe that anatomically modern humans were capable of rapidly improving on their own technology, keeping them ahead of their Neanderthal contemporaries. Two generations of tools, created during the Stillbay and Howiesons Poort periods, were originally believed to have evolved in phases shorter than 10,000 years—a drop in the bucket compared to the Neanderthals’ use of certain tools, unchanged, for 200,000 years. However, new findings suggest that the Stillbay and Howiesons Poort periods lasted much longer than previously thought, meaning that the anatomically modern humans may not have been the great visionaries we had assumed. Additionally, while Neanderthals were not thought capable of crafting the adhesives used by anatomically modern humans to assemble weapons and tools, it is now known that they did, purifying plant resin through an intricate distillation process.

We’re all living proof that anatomically modern humans survived in the end. Perhaps in an effort to flatter our predecessors, we have been holding on to dated hypotheses and ignoring recent evidence showing that Neanderthals were capable of a lot more (and perhaps the anatomically modern humans of a lot less) skill-wise than previously believed. Genetic studies continue to support the idea that anatomically modern humans and Neanderthals interbred and show that the genome of modern humans with Asian or European ancestry contains nearly 2% Neanderthal genes, a substantial quantity considering 40,000 years and 2000 generations have passed since they ceased to exist. These genes may have helped modern humans adjust to life outside of Africa, possibly aiding in the development of our immune system and variation in skin color. Researchers believe that the concentration of Neanderthal genes in modern humans was once much higher, but genetic patterns in modern humans show that hybrid Neanderthal-Human males may have been sterile, leaving no opportunity for their genes to be passed to the next generation.

So, while they may not walk among us today, we have Neanderthals to thank for some major adaptations that allowed us to thrive and spread across the planet. Too bad they’re not here to see the wonderful things we were able to accomplish with their help.

Related links:

Picked Clean: Neanderthals’ Use of Toothpicks to Fight Toothache

Contextualizing the Hobbits

Sharing was Caring for Ancient Humans and Their Prehistoric Pups

Citation: Villa P, Roebroeks W (2014) Neandertal Demise: An Archaeological Analysis of the Modern Human Superiority Complex. PLoS ONE 9(4): e96424. doi:10.1371/journal.pone.0096424

Image 1: Neandertaler im Museum from Wikimedia Commons

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Satellite Telemetry Uncovers the Tracks of Tiny Ocean Giants

Pygmy Blue Whale

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.

Pygmy Blue Whale 2

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.

Filtered satellite tag derived locations of pygmy blue whales (n = 11) by month.

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.

Pygmy Blue Whale 3

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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Linking Isolated Languages: Linguistic Relationships of the Carabayo

Amazon Header

Like PLOS ONE, the English language is rapidly taking over the world (we kid). In 2010, English clocked in at over 360 million native speakers, and it is the third-most-commonly used native language, right behind Mandarin Chinese and Spanish. While these languages spread, however, other indigenous languages decline at an accelerated pace. A fraction of these enigmatic languages belong to uncontacted indigenous groups of the Amazonian rainforest, groups of people in South America who have little to no interaction with societies beyond their own. Many of these groups choose to remain uncontacted by the rest of the world. Because of their isolation, not much is known about these languages beyond their existence.

The researchers of a recent PLOS ONE paper investigated one such language, that of the Carabayo people who live in the Colombian Amazon rainforest. Working with the relatively scarce historical data that exists for the Carabayo language—only 50 words have been recorded over time—the authors identified similarities between Carabayo and Yurí and Tikuna, two known languages of South America that constitute the current language family, Ticuna-Yurí. Based on the correspondences, the authors posit a possible genealogical connection between these languages.

Few resources were available to the authors in this endeavor. They analyzed historical wordlists collected during the last encounter with the Carabayo people in 1969—the only linguistic data available from this group— against wordlists for the Yurí language. In addition, they sought the expertise of a native speaker of Tikuna, a linguist trained in Tikuna’s many dialects. Using these resources, the authors broke down the Carabayo words into their foundational forms, starting with consonants and vowels. They then compared them to similarly deconstructed words in Yurí and Tikuna.

The examination involved the evaluation of similarities in the basic building blocks of these words: the number of times a specific sound (or phoneme) appeared; the composition and patterns of the smallest grammatical units of a word (a morpheme); and the meanings attached to these words. When patterns appeared between Carabayo and either Yurí or Tikuna, the authors considered whether or not the languages’ similarities constituted stronger correspondences. They also paid attention to the ways in which these words would have been used by the Carabayo when the lists were originally made many years ago.

The Yurí language was first recorded in the 19th century, but it is thought to have become extinct since then. From these lists, five words stood out: in Carabayo, ao ‘father’, hono ‘boy’, hako ‘well!’, and a complex form containing both the Yurí word from warm, noré, and the Yurí word, t∫au, which corresponds in English to ‘I’ or ‘my’. Given the evidence, the authors contend that the strongest link between Carabayo and Yurí is found in the correspondence of t∫au. The study of other languages has indicated that first person pronouns are particularly resistant to “borrowing”, or the absorption of one language’s vocabulary into another. Therefore, the authors surmise it is unlikely in this instance that either of the languages absorbed t∫au from the other, but that they share a genealogical link.

Similarly, the comparison of Carabayo words to words of the living language of Tikuna provided a high number of matches, including in Carabayo gudda ‘wait’ and gu ‘yes’. The matches especially exhibit sound correspondences of Carabayo g (or k) and the loss of the letter n in certain circumstances. Table 7 from the article shows the full results (click to enlarge):

Carabayo-Tikuna correspondences

Carabayo-Tikuna correspondences

 

Although it is possible that the Carabayo language represents a language that had not yet been documented until the time of 1969, the results of the researchers’ evaluation have led them to conclude that Carabayo more likely belongs to the language family of Ticuna-Yurí. The relationship of Carabayo to Yurí and Tikuna changes the structure of the Ticuna-Yurí family by placing Carabayo on the map as a member of that family. The Tikuna language, once considered to be the sole surviving member of the Ticuna-Yurí family, might now have a sibling, and the identity of a barely known language has become that much more defined.

For the authors, this research is a complicated endeavor. The desire to advance our knowledge and understanding of these precious languages must be balanced with the desires of the uncontacted indigenous groups, some of whom voluntarily choose to remain in isolation. As the authors themselves express, the continued study of these uncontacted languages seeks to engender an awareness in the larger community of the people who speak these languages, and to reiterate their right to be left to live their lives as they wish—in isolation.

Citation: Seifart F, Echeverri JA (2014) Evidence for the Identification of Carabayo, the Language of an Uncontacted People of the Colombian Amazon, as Belonging to the Tikuna-Yurí Linguistic Family. PLoS ONE 9(4): e94814. doi:10.1371/journal.pone.0094814

Image 1: Sunset on the Amazon by Pedro Szekely

Image 2: pone.0094814

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For Yeast’s Sake: The Benefits of Eating Cheese, Chocolate, and Wine

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Yeast—including more than 1500 species that make up 1% of all known fungi—plays an important role in the existence of many of our favorite foods. With a job in everything from cheese making to alcohol production to cocoa preparation, humans could not produce such diverse food products without this microscopic, unicellular sous-chef. While we have long been aware of our dependence on yeast, new research in PLOS ONE suggests that some strains of yeast would not be the same without us, either.

Studies have previously shown how our historical use of yeast has affected the evolution of one of the most commonly used species, Saccharomyces cerevisiae, creating different strains that are used for different purposes (bread, wine, and so on). To further investigate our influence on yeast, researchers from the University of Bordeaux, France, took a look at a different yeast species of recent commercial interest, Torulaspora delbrueckii. In mapping the T. delbrueckii family tree, the authors show not only that human intervention played a major role in the shaping of this species, but they provide us with valuable information for further improving this yeast as a tool for food production.

The authors collected 110 strains of T. delbrueckii from global sources of wine grapes, baked goods, dairy products, and fermented beverages. Possible microsatellites, or repeating sequences of base pairs (like A-T and G-C), were found in one strain’s DNA and used to create tools that would identify similar sequences in the other strains. They used the results to pinpoint eight different microsatellite markers (base pair sequences) that were shared by some strains but not others to measure genetic variation in the T. delbrueckii family. The composition of each strain was measured using microchip electrophoresis, a process in which DNA fragments migrate through a gel containing an electric field, which helps researchers separate the fragments according to size. As each strain’s microsatellite markers were identified, the information was added to a dendrogram (a funny-looking graph, shown below) to illustrate the level of similarity between strains. The researchers also estimated the time it took different strains to evolve by comparing the average rate of mutation and reproduction time for T. delbrueckii to the level of genetic difference between each strain.

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The dendrogram shows four clear clusters of yeast strains heavily linked to each sample’s origin. Two groups contain most of the strains isolated from Nature, but can be distinguished from each other by those collected on the American continents (nature Americas group) and those collected in Europe, Asia, and Africa (nature Old World group). The other two clusters include strains collected from food and drink samples, but cannot be discriminated by geographic location. The grape/wine group contains 27 strains isolated from grape habitats in the major wine-producing regions of the world: Europe, California, Australia, New Zealand, and South America. The bioprocess group contains geographically diverse strains collected from other areas of food processing—such as bread products, spoiled food, and fermented beverages—and includes a subgroup of strains used specifically for dairy products. Further analysis of the variation between strains confirmed that, while the clusters don’t perfectly segregate the strains according to human usage, and geographic origin of the sample played some role in diversity, a large part of the population’s structure is explained by the material source of the strain.

Divergence times calculated for the different groups further emphasize the connection between human adoption of T. delbrueckii yeast and the continued evolution of this species. The grape/wine cluster of strains diverged from the Old World group approximately 1900 years ago, aligning with the expansion of the Roman Empire, and the spread of Vitis vinifera, or the common grape, alongside. The bioprocesses group diverged much earlier, an estimated four millennia ago (around the Neolithic era), showing that yeast was used for food production long before it was domesticated for wine making.

While T. delbrueckii has often been overlooked by winemakers in favor of the more common S. cerevisiae, it has recently been gaining traction for its ability to reduce levels of volatile compounds that negatively affect wine’s flavor and scent. It has also been shown to have a high freezing tolerance when used as a leavening agent, making it of great interest to companies attempting to successfully freeze and transport dough. Though attempts to develop improved strains of this yeast for commercial use have already begun, we previously lacked an understanding of its life-cycle and reproductive habits. In creating this T. delbrueckii family tree, the authors also gained a deeper understanding of the species’ existence, which may help with further development for technological use.

Yeast has weaseled its way into our hearts via our stomachs, and it seems that, in return, we have fully worked our way into its identity. With a bit of teamwork, and perhaps a splash of genetic tweaking, we can continue this fruitful relationship and pursue new opportunities in Epicureanism. I think we would all drink to that!

Related Links:

A Novel Strategy to Construct Yeast Saccharomyces cerevisiae Strains for Very High Gravity Fermentation

The Vineyard Yeast Microbiome, a Mixed Model Microbial Map

Reference: Albertin W, Chasseriaud L, Comte G, Panfili A, Delcamp A, et al. (2014) Winemaking and Bioprocesses Strongly Shaped the Genetic Diversity of the Ubiquitous Yeast Torulaspora delbrueckii. PLoS ONE 9(4): e94246. doi:10.1371/journal.pone.0094246

Image 1: Figure 1 from article

Image 2: Figure 3 from article

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