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

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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

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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

journal.pone.0094246.g001

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.

journal.pone.0094246.g003

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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Beating the Odds: Are Goats Better Gamers than Sheep?

goats

We’re all familiar with the shell game, though many may not recognize it by that name. Popular with street swindlers and sports fans at halftime, it has been annoying those unable to locate which cup the ball is under—most people—as long as anyone can remember. But, what if you were a small ruminant playing a modified version of the game, in which cups were not moved? Seems easier, right? Turns out it may depend on what kind of ruminant you are.

The authors of a recent PLOS ONE article updated this age-old game to find out whether goats and sheep, given information upfront about which cup the food was (or was not) under, could find the food again once the cups were replaced. The ability to connect an experience with an imagined result (“If I see that the cup is empty, the other must have the food!”) is called inferential reasoning, and has been tested in dogs, primates, and birds. Different levels of inferential reasoning, especially between two closely related species, may be linked to differences in the way they search for and find food. A deeper understanding of the different feeding behaviors found in ruminants could shed light on the evolutionary practices that shape these behaviors and help us understand how domesticated breeds have modified their behavior over time to better fit a farming environment.

In this study, researchers ran two rounds of testing with slightly different protocols to evaluate how the ruminants’ behavior would change in response to varied amounts of information. They created an experimental set with the animal separated by a series of bars from the researcher and a table (see image above) that held two cups, one with a piece of food hidden underneath. In the first test, researchers lifted one of the following:

  • both cups (full information)
  • the baited cup (direct information – shown in the video below)
  • the unbaited cup (indirect information)
  • no cups (no information)

The animal then chose a cup and was rewarded with food if found. The video below shows a sheep correctly identifying the baited cup after receiving direct information on the food’s location.

To minimize the possibility that animals would simply select the cup most recently moved by the researcher, the authors further modified the game for the second round of testing. A set of internal cups was added under each external cup, some transparent and some opaque, allowing the researchers to lift both external cups simultaneously while providing the same amount of information to the animals.

Animals participating in the test were again presented with two cups. Both external cups were removed simultaneously to reveal the inner set, which were one of the following:

  • both transparent (full information)
  • the baited cup transparent and the unbaited one opaque (direct information)
  • the baited cup opaque and the unbaited transparent (indirect information)
  • both opaque (no information)

In the same way as in the first experiment, animals were given a chance to select a cup and were rewarded with food if found.

When reviewing the results of all the sessions, the authors found that goats were more successful than sheep at identifying the baited cup when given full or direct information, although sheep also chose the baited cup more often under these circumstances. The second experiment showed that goats were also more successful at finding food when provided with indirect information. In both experiments, sheep did not guess better than chance when shown the empty contents of the unbaited cup or no cups at all, and goats did not guess better than chance when neither of the cups were lifted.

Though several factors varied between species populations used in this experiment—like the time of day experiments were completed, number of animals tested, or history of testing experience in goats—the authors saw no sign of improved performance due to learning in goats, and no differences in motivation as tests continued.

The researchers speculate that the different foraging behaviors used by goats and sheep allowed goats to get ahead in these experiments. Goats are dietary browsers, meaning they are more selective in what they eat and prefer low-fiber foods, like plant stems and leaves. Sheep, as dietary grazers, feed primarily on high fiber foods like grass, and are not at all particular about what they consume. If goats have evolved to be picky, selective eaters, then it makes sense that they might have a better memory for where they saw food in the past, and the insight to avoid an empty cup when they saw one. Future studies on this topic could provide insight on decision making and risk sensitivity in these animals, and give us a glimpse into the minds of a species that can actually beat the odds in the shell game.

Related links:

Citation: Nawroth C, von Borell E, Langbein J (2014) Exclusion Performance in Dwarf Goats (Capra aegagrus hircus) and Sheep (Ovis orientalis aries). PLoS ONE 9(4): e93534. doi:10.1371/journal.pone.0093534

Image: Figure 1 from article
Video: Video S3 from article

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Awl be Darned: Metal Arrived in the Southern Levant Long Before Previously Thought

The Copper Age, sometimes referred to as the Chalcolithic period, was a time of technological transition for humans. As stone tools gave way to metal ones, the Levant—which includes parts of modern-day Israel, Palestine, Jordan, Lebanon, and Syria—emerged as a significant hub of copper crafting. Important archaeological finds, like the cache of copper artifacts found in the Nahal Mishmar Cave, are testaments to a robust copper-working tradition in the region, dating back to at least 4500-3800 BC. Although little is known about the origin and proliferation of metallurgy, or metal-working, in the Near East, a recent study published in PLOS ONE may offer new evidence of the earliest known use of copper in the southern Levant.

The recently discovered awl

The recently discovered copper awl

In the study, archaeologists from institutions in Israel and Germany describe a copper awl they discovered at an archaeological dig in Tel Tsaf, Israel, that they estimate dates back to 5100-4600 BC. An awl is a sharp spike, generally attached to a handle, that can be used to pierce holes in leather or textiles. Residue at the base of the spike indicates that it initially was connected to a wooden handle.  Researchers found the awl at a complex of mud brick buildings, rectangular rooms, and large circular grain silos. In addition, a multitude of beads, intricately decorated pottery, obsidian objects, and more were also found on site, and they appear to have originated from locations as far away as Armenia, Syria, Mesopotamia, and Egypt.  The presence of objects from other regions suggests that the site was connected to far-reaching trade networks.  The awl in question was found in an elaborate burial with a woman of about forty years of age, along with an ornate necklace made from over 1,500 ostrich eggshell beads. Its favored place as part of a burial indicates that it would have been a highly prized item.

The awl was discovered in this burial of a woman of about 40

The awl was discovered in this burial of a woman of about 40. A necklace of ostrich eggshell beads is visible in the bottom left corner.

The estimated age of the awl may make it the first known copper artifact in the Levant. Its presence at the excavation site shows that metal tools and objects may have arrived in the southern Levant via long-distance trade networks hundreds of years earlier than previously thought, long before the technology to make it locally was widely understood and adopted in the region.

The authors of this study used X-ray spectroscopy, or the bombarding of a sample with a beam of high-energy particles, to determine the awl’s chemical composition by analyzing the unique signal that different elements emit in response. The spectroscopy revealed significant amounts of tin in the awl, an additive that creates bronze when mixed with copper. Bronze, like copper, is so important that it also gets its own Age (the Bronze Age). However, because this awl predates the advent of bronze by thousands of years, the authors speculate that the tin may have actually been incidental and naturally occurring.  Copper with traces of tin is known to occur naturally in the Caucuses, a range of mountains stretching between the Caspian and Black Seas, and the awl may have originated there and made its way through trade networks to where it was finally discovered in Tel Tsaf. Copper-working know-how may have proliferated along the same networks, paving the way for widespread local production of copper artifacts, and followed closely, no doubt, by the ever-present scourge of copper theft.

Related Links:

What Early Neolithic People Left Behind: Levantine Arrowheads Found in Saudi Arabia

Dressed-Up Donkey Discovered at Religious Burial Site

Citation: Garfinkel Y, Klimscha F, Shalev S, Rosenberg D (2014) The Beginning of Metallurgy in the Southern Levant: A Late 6th Millennium CalBC Copper Awl from Tel Tsaf, Israel. PLoS ONE 9(3): e92591. doi:10.1371/journal.pone.0092591

Images: Images are Figures 4 and 5 of the published article

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Meta-Analyses of Genetic Association Studies – PLOS ONE’s Approach

Meta-analysis can be a powerful way to reveal otherwise hidden or unclear associations, when done with care. In line with recent trends in biomedical literature (1), PLOS ONE has seen a consistent increase in submissions reporting meta-analyses of genetic association studies over the last few years. These submissions report analyses of potential associations between candidate gene variants (usually single nucleotide polymorphisms, or SNPs) and specific disease risks and outcomes in human populations, based on a search of the literature to identify published reports studying the association and statistical analyses that synthesize the results of the identified studies.

However, researchers in the community, among them members of our editorial board, have raised concerns about some of these meta-analyses, including the risk of false positives due to publication bias, incomplete searches of the literature, redundancy, and an insufficient assessment of the power and quality of the included studies. As noted a decade ago, “Meta-analysis is not a replacement for adequately powered genetic association studies” (2).  Many of these studies focus on a single gene variant, and many do not include data from relevant genome-wide association  studies (GWAS), some of which have failed to replicate previously reported associations between candidate genes and diseases.

While many meta-analyses of genetic association studies are still clinically relevant, especially those studying rare conditions where GWAS data are not available, and well-conducted meta-analyses can provide useful and valid clinical evidence, we strongly feel that meta-analyses of genetic association studies considered by PLOS ONE must have the rationale clearly explained and that authors must report their studies according to high standards.

In order to address these concerns and after consultation with PLOS ONE editorial board members, we are introducing a new process to handle meta-analyses of genetic association studies. Authors will now be asked to provide the following information:

  1. The rationale for conducting the meta-analysis;
  2. The contribution that the meta-analysis makes to knowledge in light of previously published related reports, including other meta-analyses and systematic reviews;
  3. Whether GWASs relevant to the meta-analysis have been published and whether these were included in the analysis;
  4. Full methodological details for the meta-analysis, including completion of a checklist that has been developed with reference to several published guidelines (3, 4, 5) and in consultation with members of the PLOS ONE editorial board.

The information supplied by the authors will be evaluated by the in-house editorial team as part of the checks undertaken on new submissions. Meta-analyses replicating studies in the literature without adequate justification will be rejected. For those manuscripts that proceed to review, PLOS ONE Academic Editors will be consulted on the adequacy of the methodological aspects of the study and the quality of the reporting in the manuscript.

This process underscores our commitment to maintaining high standards of quality and reporting in publications at PLOS ONE. We are grateful for the input we have received from our editorial board that led to this new process, and wish to thank the PLOS ONE Academic Editors who provided advice and guidance.

If you have any questions or feedback, or if you are an author who would like additional information about our requirements for meta-analyses of genetic association studies, please contact us at plosone@plos.org.

Posted on behalf of the in-house editors at PLOS ONE:

Associate Editors Adrian Aldcroft, Gina Alvino, Meghan Byrne, Christna Chap, Michelle Dohm, Renee Hoch, Matt Hodgkinson, Alejandra Clark and Nicola Stead; Senior Editors Eric Martens, Iratxe Puebla and Emma Veitch; and Editorial Director Damian Pattinson

  1. Ioannidis JPA, Chang CQ, Lam TK, Schully SD, Khoury MJ (2013) The Geometric Increase in Meta-Analyses from China in the Genomic Era. PLOS ONE 8(6): e65602. doi:10.1371/journal.pone.0065602
  2. Marcus R. Munafò and Jonathan Flint (2004) Meta-analysis of genetic association studies. Trends Genet. 20(9):439-44 doi:10.1016/j.tig.2004.06.014
  3. Sagoo GS, Little J, Higgins JPT (2009) Systematic Reviews of Genetic Association Studies. PLOS Med 6(3): e1000028. doi:10.1371/journal.pmed.1000028
  4. Minelli C, Thompson JR, Abrams KR, Thakkinstian A, Attia J: The quality of meta-analyses of genetic association studies: a review with recommendations. Am J Epidemiol. 2009 Dec 1;170(11):1333-43. doi: 10.1093/aje/kwp350
  5. Little J, Higgins JP, Ioannidis JP, Moher D, Gagnon F, et al. (2009) STrengthening the REporting of Genetic Association Studies (STREGA)- An Extension of the STROBE Statement. PLOS Med 6(2): e1000022. doi:10.1371/journal.pmed.1000022
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