Monthly Archives: October 2009

There are 19 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Dominance, Politics, and Physiology: Voters’ Testosterone Changes on the Night of the 2008 United States Presidential Election:

Background
Political elections are dominance competitions. When men win a dominance competition, their testosterone levels rise or remain stable to resist a circadian decline; and when they lose, their testosterone levels fall. However, it is unknown whether this pattern of testosterone change extends beyond interpersonal competitions to the vicarious experience of winning or losing in the context of political elections. Women’s testosterone responses to dominance competition outcomes are understudied, and to date, a clear pattern of testosterone changes in response to winning and losing dominance competitions has not emerged. The present study investigated voters’ testosterone responses to the outcome of the 2008 United States Presidential election. 183 participants provided multiple saliva samples before and after the winner was announced on Election Night. The results show that male Barack Obama voters (winners) had stable post-outcome testosterone levels, whereas testosterone levels dropped in male John McCain and Robert Barr voters (losers). There were no significant effects in female voters. The findings indicate that male voters exhibit biological responses to the realignment of a country’s dominance hierarchy as if they participated in an interpersonal dominance contest.

Oldest Evidence of Toolmaking Hominins in a Grassland-Dominated Ecosystem:

Major biological and cultural innovations in late Pliocene hominin evolution are frequently linked to the spread or fluctuating presence of C4 grass in African ecosystems. Whereas the deep sea record of global climatic change provides indirect evidence for an increase in C4 vegetation with a shift towards a cooler, drier and more variable global climatic regime beginning approximately 3 million years ago (Ma), evidence for grassland-dominated ecosystems in continental Africa and hominin activities within such ecosystems have been lacking. We report stable isotopic analyses of pedogenic carbonates and ungulate enamel, as well as faunal data from ~2.0 Ma archeological occurrences at Kanjera South, Kenya. These document repeated hominin activities within a grassland-dominated ecosystem. These data demonstrate what hitherto had been speculated based on indirect evidence: that grassland-dominated ecosystems did in fact exist during the Plio-Pleistocene, and that early Homo was active in open settings. Comparison with other Oldowan occurrences indicates that by 2.0 Ma hominins, almost certainly of the genus Homo, used a broad spectrum of habitats in East Africa, from open grassland to riparian forest. This strongly contrasts with the habitat usage of Australopithecus, and may signal an important shift in hominin landscape usage.

Discovery of the Largest Orbweaving Spider Species: The Evolution of Gigantism in Nephila:

More than 41,000 spider species are known with about 400-500 added each year, but for some well-known groups, such as the giant golden orbweavers, Nephila, the last valid described species dates from the 19th century. Nephila are renowned for being the largest web-spinning spiders, making the largest orb webs, and are model organisms for the study of extreme sexual size dimorphism (SSD) and sexual biology. Here, we report on the discovery of a new, giant Nephila species from Africa and Madagascar, and review size evolution and SSD in Nephilidae. We formally describe N. komaci sp. nov., the largest web spinning species known, and place the species in phylogenetic context to reconstruct the evolution of mean size (via squared change parsimony). We then test female and male mean size correlation using phylogenetically independent contrasts, and simulate nephilid body size evolution using Monte Carlo statistics. Nephila females increased in size almost monotonically to establish a mostly African clade of true giants. In contrast, Nephila male size is effectively decoupled and hovers around values roughly one fifth of female size. Although N. komaci females are the largest Nephila yet discovered, the males are also large and thus their SSD is not exceptional.

Evidence for Repeated Independent Evolution of Migration in the Largest Family of Bats:

How migration evolved represents one of the most poignant questions in evolutionary biology. While studies on the evolution of migration in birds are well represented in the literature, migration in bats has received relatively little attention. Yet, more than 30 species of bats are known to migrate annually from breeding to non-breeding locations. Our study is the first to test hypotheses on the evolutionary history of migration in bats using a phylogenetic framework. In addition to providing a review of bat migration in relation to existing hypotheses on the evolution of migration in birds, we use a previously published supertree to formulate and test hypotheses on the evolutionary history of migration in bats. Our results suggest that migration in bats has evolved independently in several lineages potentially as the need arises to track resources (food, roosting site) but not through a series of steps from short- to long-distance migrants, as has been suggested for birds. Moreover, our analyses do not indicate that migration is an ancestral state but has relatively recently evolved in bats. Our results also show that migration is significantly less likely to evolve in cave roosting bats than in tree roosting species. This is the first study to provide evidence that migration has evolved independently in bat lineages that are not closely related. If migration evolved as a need to track seasonal resources or seek adequate roosting sites, climate change may have a pivotal impact on bat migratory habits. Our study provides a strong framework for future research on the evolution of migration in chiropterans.

New Episodic Learning Interferes with the Reconsolidation of Autobiographical Memories:

It is commonly assumed that, with time, an initially labile memory is transformed into a permanent one via a process of consolidation. Yet, recent evidence indicates that memories can return to a fragile state again when reactivated, requiring a period of reconsolidation. In the study described here, we found that participants who memorized a story immediately after they had recalled neutral and emotional experiences from their past were impaired in their memory for the neutral (but not for the emotional) experiences one week later. The effect of learning the story depended critically on the preceding reactivation of the autobiographical memories since learning without reactivation had no effect. These results suggest that new learning impedes the reconsolidation of neutral autobiographical memories.

Five Years of Access and Activism:

In April 2009, we marked the five year anniversary of PLoS Medicine’s first call for papers with an editorial titled “A Medical Journal for the World’s Health Priorities” [1]. The editorial was a renewed and revitalized call for papers, announcing a “refocusing of the journal’s priorities.” Going forward, we said, we would prioritize papers addressing those diseases with the greatest global burden. We would also aim to be as broad a journal as possible, publishing papers that explored not just biological causes of illness, but also social, environmental, and political determinants of health. Six months later, as we now mark the journal’s official five-year anniversary (our launch issue was October 19, 2004), has our refocused scope had any impact on what we publish?

Male or Female? For Honeybees, a Single Gene Makes All the Difference:

Male or female? How genes send a developing embryo down one path or the other varies substantially among species. In honeybees, it boils down to whether a particular chromosomal location has the same version of a gene (called homozygous) or two different versions (heterozygous). Honeybees that have two different versions of the sex determination locus (SDL) develop female traits. Those that have two of the same version–or, more commonly, have only one version as a result of developing from an unfertilized egg–become male. This approach, known as complementary sex determination, is found in a number of social insects, yet is still poorly understood.

Sex Determination in Honeybees: Two Separate Mechanisms Induce and Maintain the Female Pathway:

Sexual differentiation is a fundamental process in the animal kingdom, and different species have evolved a bewildering diversity of mechanisms to generate the two sexes in the proper proportions. Sex determination in honeybees (Apis mellifera) provides an interesting and unusual system to study, as it is governed by heterozygosity of a single locus harbouring the complementary sex determiner gene (csd), in contrast to the well-studied sex chromosome system of Drosophila melanogaster. We show that the female sex determination pathway is exclusively induced by the csd gene in early embryogenesis. Later on and throughout development this inductive signal is maintained via a positive feedback loop of the feminizer (fem) gene, in which the Fem protein mediates its own synthesis. The findings reveal how the sex determination process in honeybees is realized by the regulation and function of two genes differing from Drosophila.

There are 19 new articles in PLoS ONE today.
But first, you need to look at the new Collection of articles – Structural Biology and Human Health: Medically Relevant Proteins from the SGC – in which you can see the protein structures in 3D, turn them around, zoom in and out, and do other manipulations of the embedded object, right there inside the articles. Read more about it in: A New Method for Publishing Three-Dimensional Content:

A new method for electronic publishing of articles with text linked to its interactive three dimensional content is described. The method is based on a single document containing a variety of objects such as formatted text, multiple three dimensional molecular objects, textured shapes and surfaces, data tables and graphs, chemical spreadsheets, alignments, etc. The 3D article can then be published for an online web delivery using the activeICM/active X components as well as be downloaded as a single file to be browsed with all its attached objects locally with the ICM browser. Both activeICM and ICM browser are freely available for the public. This method eliminates the need for multiple methods for the web and the local off-line delivery; it offers the dramatically enhanced, customizable and interactive delivery of article’s three dimensional content and data attachments in a single compact file.

See the explanation on everyONE blog and the first reactions by Dave Bath, Jean-Claude Bradley and Nick Anthis.

Also today – and as always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers – here are my own picks for the week:
Influenza A Gradual and Epochal Evolution: Insights from Simple Models:

The recurrence of influenza A epidemics has originally been explained by a “continuous antigenic drift” scenario. Recently, it has been shown that if genetic drift is gradual, the evolution of influenza A main antigen, the haemagglutinin, is punctuated. As a consequence, it has been suggested that influenza A dynamics at the population level should be approximated by a serial model. Here, simple models are used to test whether a serial model requires gradual antigenic drift within groups of strains with the same antigenic properties (antigenic clusters). We compare the effect of status based and history based frameworks and the influence of reduced susceptibility and infectivity assumptions on the transient dynamics of antigenic clusters. Our results reveal that the replacement of a resident antigenic cluster by a mutant cluster, as observed in data, is reproduced only by the status based model integrating the reduced infectivity assumption. This combination of assumptions is useful to overcome the otherwise extremely high model dimensionality of models incorporating many strains, but relies on a biological hypothesis not obviously satisfied. Our findings finally suggest the dynamical importance of gradual antigenic drift even in the presence of punctuated immune escape. A more regular renewal of susceptible pool than the one implemented in a serial model should be part of a minimal theory for influenza at the population level.

Temporal-Difference Reinforcement Learning with Distributed Representations:

Temporal-difference (TD) algorithms have been proposed as models of reinforcement learning (RL). We examine two issues of distributed representation in these TD algorithms: distributed representations of belief and distributed discounting factors. Distributed representation of belief allows the believed state of the world to distribute across sets of equivalent states. Distributed exponential discounting factors produce hyperbolic discounting in the behavior of the agent itself. We examine these issues in the context of a TD RL model in which state-belief is distributed over a set of exponentially-discounting “micro-Agents”, each of which has a separate discounting factor (γ). Each µAgent maintains an independent hypothesis about the state of the world, and a separate value-estimate of taking actions within that hypothesized state. The overall agent thus instantiates a flexible representation of an evolving world-state. As with other TD models, the value-error (δ) signal within the model matches dopamine signals recorded from animals in standard conditioning reward-paradigms. The distributed representation of belief provides an explanation for the decrease in dopamine at the conditioned stimulus seen in overtrained animals, for the differences between trace and delay conditioning, and for transient bursts of dopamine seen at movement initiation. Because each µAgent also includes its own exponential discounting factor, the overall agent shows hyperbolic discounting, consistent with behavioral experiments.

Balancing with Vibration: A Prelude for ‘Drift and Act’ Balance Control:

Stick balancing at the fingertip is a powerful paradigm for the study of the control of human balance. Here we show that the mean stick balancing time is increased by about two-fold when a subject stands on a vibrating platform that produces vertical vibrations at the fingertip (0.001 m, 15-50 Hz). High speed motion capture measurements in three dimensions demonstrate that vibration does not shorten the neural latency for stick balancing or change the distribution of the changes in speed made by the fingertip during stick balancing, but does decrease the amplitude of the fluctuations in the relative positions of the fingertip and the tip of the stick in the horizontal plane, A(x,y). The findings are interpreted in terms of a time-delayed “drift and act” control mechanism in which controlling movements are made only when controlled variables exceed a threshold, i.e. the stick survival time measures the time to cross a threshold. The amplitude of the oscillations produced by this mechanism can be decreased by parametric excitation. It is shown that a plot of the logarithm of the vibration-induced increase in stick balancing skill, a measure of the mean first passage time, versus the standard deviation of the A(x,y) fluctuations, a measure of the distance to the threshold, is linear as expected for the times to cross a threshold in a stochastic dynamical system. These observations suggest that the balanced state represents a complex time-dependent state which is situated in a basin of attraction that is of the same order of size. The fact that vibration amplitude can benefit balance control raises the possibility of minimizing risk of falling through appropriate changes in the design of footwear and roughness of the walking surfaces.

Some cool papers tonight in 4 out of 7 PLoS journals. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Short Telomeres in Hatchling Snakes: Erythrocyte Telomere Dynamics and Longevity in Tropical Pythons:

Telomere length (TL) has been found to be associated with life span in birds and humans. However, other studies have demonstrated that TL does not affect survival among old humans. Furthermore, replicative senescence has been shown to be induced by changes in the protected status of the telomeres rather than the loss of TL. In the present study we explore whether age- and sex-specific telomere dynamics affect life span in a long-lived snake, the water python (Liasis fuscus). Erythrocyte TL was measured using the Telo TAGGG TL Assay Kit (Roche). In contrast to other vertebrates, TL of hatchling pythons was significantly shorter than that of older snakes. However, during their first year of life hatchling TL increased substantially. While TL of older snakes decreased with age, we did not observe any correlation between TL and age in cross-sectional sampling. In older snakes, female TL was longer than that of males. When using recapture as a proxy for survival, our results do not support that longer telomeres resulted in an increased water python survival/longevity. In fish high telomerase activity has been observed in somatic cells exhibiting high proliferation rates. Hatchling pythons show similar high somatic cell proliferation rates. Thus, the increase in TL of this group may have been caused by increased telomerase activity. In older humans female TL is longer than that of males. This has been suggested to be caused by high estrogen levels that stimulate increased telomerase activity. Thus, high estrogen levels may also have caused the longer telomeres in female pythons. The lack of correlation between TL and age among old snakes and the fact that longer telomeres did not appear to affect python survival do not support that erythrocyte telomere dynamics has a major impact on water python longevity.

‘Glocal’ Robustness Analysis and Model Discrimination for Circadian Oscillators:

Robustness is an intrinsic property of many biological systems. To quantify the robustness of a model that represents such a system, two approaches exist: global methods assess the volume in parameter space that is compliant with the proper functioning of the system; and local methods, in contrast, study the model for a given parameter set and determine its robustness. Local methods are fundamentally biased due to the a priori choice of a particular parameter set. Our ‘glocal’ analysis combines the two complementary approaches and provides an objective measure of robustness. We apply this method to two prominent, recent models of the cyanobacterial circadian oscillator. Our results allow discriminating the two models based on this analysis: both global and local measures of robustness favor one of the two models. The ‘glocal’ method also identifies key factors that influence robustness. For instance, we find that in both models the most fragile reactions are the ones that affect the concentration of the feedback component.

The Rewarding Aspects of Music Listening Are Related to Degree of Emotional Arousal:

Listening to music is amongst the most rewarding experiences for humans. Music has no functional resemblance to other rewarding stimuli, and has no demonstrated biological value, yet individuals continue listening to music for pleasure. It has been suggested that the pleasurable aspects of music listening are related to a change in emotional arousal, although this link has not been directly investigated. In this study, using methods of high temporal sensitivity we investigated whether there is a systematic relationship between dynamic increases in pleasure states and physiological indicators of emotional arousal, including changes in heart rate, respiration, electrodermal activity, body temperature, and blood volume pulse. Twenty-six participants listened to self-selected intensely pleasurable music and “neutral” music that was individually selected for them based on low pleasure ratings they provided on other participants’ music. The “chills” phenomenon was used to index intensely pleasurable responses to music. During music listening, continuous real-time recordings of subjective pleasure states and simultaneous recordings of sympathetic nervous system activity, an objective measure of emotional arousal, were obtained. Results revealed a strong positive correlation between ratings of pleasure and emotional arousal. Importantly, a dissociation was revealed as individuals who did not experience pleasure also showed no significant increases in emotional arousal. These results have broader implications by demonstrating that strongly felt emotions could be rewarding in themselves in the absence of a physically tangible reward or a specific functional goal.

Multilevel Selection in Models of Prebiotic Evolution II: A Direct Comparison of Compartmentalization and Spatial Self-Organization:

The origin of life has ever been attracting scientific inquiries. The RNA world hypothesis suggests that, before the evolution of DNA and protein, primordial life was based on RNA-like molecules both for information storage and chemical catalysis. In the simplest form, an RNA world consists of RNA molecules that can catalyze the replication of their own copies. Thus, an interesting question is whether a system of RNA-like replicators can increase its complexity through Darwinian evolution and approach the modern form of life. It is, however, known that simple natural selection acting on individual replicators is insufficient to account for the evolution of complexity due to the evolution of parasite-like templates. Two solutions have been suggested: compartmentalization of replicators by membranes (i.e., protocells) and spatial self-organization of a replicator population. Here, we make a direct comparison of the two suggestions by computer simulations. Our results show that the two suggestions can lead to unanticipated and contrasting consequences in the long-term evolution of replicating molecules. The results also imply a novel advantage in the spatial self-organization for the evolution of complexity in RNA-like replicator systems.

On the Track of DNA Methylation: An Interview with Adrian Bird:

The day school let out for the summer, my daughter and I packed our bags for Britain, where we had lived for a few months in 2006. Annie was eager to reconnect with her friends there, and I had arranged to conduct three interviews. In desperation and with the clock ticking, I struggled to fit my bulky recorder into my wheelie when it dawned on me that the “talk app” on my daughter’s iphone should be up to the job. You can imagine the reluctance and skepticism on the part of my 15-year-old, but she managed to get into the spirit and acquiesced.
First up on my schedule was Adrian Bird (Image 1), who holds the Buchanan Chair of Genetics at the University of Edinburgh and is also Director of the Wellcome Trust Centre for Cell Biology. Long before the word “epigenome” was coined, Bird began mapping the distribution of DNA methylation (occurring at the cytosine of CpG dinucleotides) in the genomes of a variety of species. His work emerged just as agarose gels, restriction enzymes, and Southern blots were being developed. Bird later spawned the idea of CpG islands, pockets of DNA rich in unmethylated CpGs and frequently found in conjunction with the promoter regions of mammalian genes. Bird’s observation provided a roadmap for disease gene discovery for about 15 years, until human genome draft sequences began to emerge.

There are 17 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Circadian Modulation of Gene Expression, but not Glutamate Uptake, in Mouse and Rat Cortical Astrocytes:

Circadian clocks control daily rhythms including sleep-wake, hormone secretion, and metabolism. These clocks are based on intracellular transcription-translation feedback loops that sustain daily oscillations of gene expression in many cell types. Mammalian astrocytes display circadian rhythms in the expression of the clock genes Period1 (Per1) and Period2 (Per2). However, a functional role for circadian oscillations in astrocytes is unknown. Because uptake of extrasynaptic glutamate depends on the presence of Per2 in astrocytes, we asked whether glutamate uptake by glia is circadian. We measured glutamate uptake, transcript and protein levels of the astrocyte-specific glutamate transporter, Glast, and the expression of Per1 and Per2 from cultured cortical astrocytes and from explants of somatosensory cortex. We found that glutamate uptake and Glast mRNA and protein expression were significantly reduced in Clock/Clock, Per2- or NPAS2-deficient glia. Uptake was augmented when the medium was supplemented with dibutyryl-cAMP or B27. Critically, glutamate uptake was not circadian in cortical astrocytes cultured from rats or mice or in cortical slices from mice. We conclude that glutamate uptake levels are modulated by CLOCK, PER2, NPAS2, and the composition of the culture medium, and that uptake does not show circadian variations.

Social Structure Predicts Genital Morphology in African Mole-Rats:

African mole-rats (Bathyergidae, Rodentia) exhibit a wide range of social structures, from solitary to eusocial. We previously found a lack of sex differences in the external genitalia and morphology of the perineal muscles associated with the phallus in the eusocial naked mole-rat. This was quite surprising, as the external genitalia and perineal muscles are sexually dimorphic in all other mammals examined. We hypothesized that the lack of sex differences in naked mole-rats might be related to their unusual social structure. We compared the genitalia and perineal muscles in three African mole-rat species: the naked mole-rat, the solitary silvery mole-rat, and the Damaraland mole-rat, a species considered to be eusocial, but with less reproductive skew than naked mole-rats. Our findings support a relationship between social structure, mating system, and sexual differentiation. Naked mole-rats lack sex differences in genitalia and perineal morphology, silvery mole-rats exhibit sex differences, and Damaraland mole-rats are intermediate. The lack of sex differences in naked mole-rats is not an attribute of all African mole-rats, but appears to have evolved in relation to their unusual social structure and reproductive biology.

Nutrient Enrichment and Food Web Composition Affect Ecosystem Metabolism in an Experimental Seagrass Habitat:

Food web composition and resource levels can influence ecosystem properties such as productivity and elemental cycles. In particular, herbivores occupy a central place in food webs as the species richness and composition of this trophic level may simultaneously influence the transmission of resource and predator effects to higher and lower trophic levels, respectively. Yet, these interactions are poorly understood. Using an experimental seagrass mesocosm system, we factorially manipulated water column nutrient concentrations, food chain length, and diversity of crustacean grazers to address two questions: (1) Does food web composition modulate the effects of nutrient enrichment on plant and grazer biomasses and stoichiometry? (2) Do ecosystem fluxes of dissolved oxygen and nutrients more closely reflect above-ground biomass and community structure or sediment processes? Nutrient enrichment and grazer presence generally had strong effects on biomass accumulation, stoichiometry, and ecosystem fluxes, whereas predator effects were weaker or absent. Nutrient enrichment had little effect on producer biomass or net ecosystem production but strongly increased seagrass nutrient content, ecosystem flux rates, and grazer secondary production, suggesting that enhanced production was efficiently transferred from producers to herbivores. Gross ecosystem production (oxygen evolution) correlated positively with above-ground plant biomass, whereas inorganic nutrient fluxes were unrelated to plant or grazer biomasses, suggesting dominance by sediment microbial processes. Finally, grazer richness significantly stabilized ecosystem processes, as predators decreased ecosystem production and respiration only in the zero- and one- species grazer treatments. Overall, our results indicate that consumer presence and species composition strongly influence ecosystem responses to nutrient enrichment, and that increasing herbivore diversity can stabilize ecosystem flux rates in the face of perturbations.

There are 23 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Chimpanzees Help Each Other upon Request:

The evolution of altruism has been explained mainly from ultimate perspectives. However, it remains to be investigated from a proximate point of view how and in which situations such social propensity is achieved. We investigated chimpanzees’ targeted helping in a tool transfer paradigm, and discuss the similarities and differences in altruism between humans and chimpanzees. Previously it has been suggested that chimpanzees help human experimenters by retrieving an object which the experimenter is trying to reach. In the present study, we investigated the importance of communicative interactions between chimpanzees themselves and the influence of conspecific partner’s request on chimpanzees’ targeted helping. We presented two tool-use situations (a stick-use situation and a straw-use situation) in two adjacent booths, and supplied non-corresponding tools to paired chimpanzees in the two booths. For example, a chimpanzee in the stick-use situation was supplied with a straw, and the partner in the straw-use situation possessed a stick. Spontaneous tool transfer was observed between paired chimpanzees. The tool transfer events occurred predominantly following recipients’ request. Even without any hope of reciprocation from the partner, the chimpanzees continued to help the partner as long as the partner required help. These results provide further evidence for altruistic helping in chimpanzees in the absence of direct personal gain or even immediate reciprocation. Our findings additionally highlight the importance of request as a proximate mechanism motivating prosocial behavior in chimpanzees whether between kin or non-kin individuals and the possible confounding effect of dominance on the symmetry of such interactions. Finally, in contrast to humans, our study suggests that chimpanzees rarely perform acts of voluntary altruism. Voluntary altruism in chimpanzees is not necessarily prompted by simple observation of another’s struggle to attain a goal and therefore an accurate understanding of others’ desires in the absence of communicative signals.

Understanding Ancient Hominin Dispersals Using Artefactual Data: A Phylogeographic Analysis of Acheulean Handaxes:

Reconstructing the dispersal patterns of extinct hominins remains a challenging but essential goal. One means of supplementing fossil evidence is to utilize archaeological evidence in the form of stone tools. Based on broad dating patterns, it has long been thought that the appearance of Acheulean handaxe technologies outside of Africa was the result of hominin dispersals, yet independent tests of this hypothesis remain rare. Cultural transmission theory leads to a prediction of a strong African versus non-African phylogeographic pattern in handaxe datasets, if the African Acheulean hypothesis is to be supported. Here, this prediction is tested using an intercontinental dataset of Acheulean handaxes and a biological phylogenetic method (maximum parsimony). The analyses produce a tree consistent with the phylogeographic prediction. Moreover, a bootstrap analysis provides evidence that this pattern is robust, and the maximum parsimony tree is also shown to be statistically different from a tree constrained by stone raw materials. These results demonstrate that nested analyses of behavioural data, utilizing methods drawn from biology, have the potential to shed light on ancient hominin dispersals. This is an encouraging prospect for human palaeobiology since sample sizes for lithic artefacts are many orders of magnitude higher than those of fossil data. These analyses also suggest that the sustained occurrence of Acheulean handaxe technologies in regions such as Europe and the Indian subcontinent resulted from dispersals by African hominin populations.

Understanding Others’ Regret: A fMRI Study:

Previous studies showed that the understanding of others’ basic emotional experiences is based on a “resonant” mechanism, i.e., on the reactivation, in the observer’s brain, of the cerebral areas associated with those experiences. The present study aimed to investigate whether the same neural mechanism is activated both when experiencing and attending complex, cognitively-generated, emotions. A gambling task and functional-Magnetic-Resonance-Imaging (fMRI) were used to test this hypothesis using regret, the negative cognitively-based emotion resulting from an unfavorable counterfactual comparison between the outcomes of chosen and discarded options. Do the same brain structures that mediate the experience of regret become active in the observation of situations eliciting regret in another individual? Here we show that observing the regretful outcomes of someone else’s choices activates the same regions that are activated during a first-person experience of regret, i.e. the ventromedial prefrontal cortex, anterior cingulate cortex and hippocampus. These results extend the possible role of a mirror-like mechanism beyond basic emotions.

Mapping Oil and Gas Development Potential in the US Intermountain West and Estimating Impacts to Species:

Many studies have quantified the indirect effect of hydrocarbon-based economies on climate change and biodiversity, concluding that a significant proportion of species will be threatened with extinction. However, few studies have measured the direct effect of new energy production infrastructure on species persistence. We propose a systematic way to forecast patterns of future energy development and calculate impacts to species using spatially-explicit predictive modeling techniques to estimate oil and gas potential and create development build-out scenarios by seeding the landscape with oil and gas wells based on underlying potential. We illustrate our approach for the greater sage-grouse (Centrocercus urophasianus) in the western US and translate the build-out scenarios into estimated impacts on sage-grouse. We project that future oil and gas development will cause a 7-19 percent decline from 2007 sage-grouse lek population counts and impact 3.7 million ha of sagebrush shrublands and 1.1 million ha of grasslands in the study area. Maps of where oil and gas development is anticipated in the US Intermountain West can be used by decision-makers intent on minimizing impacts to sage-grouse. This analysis also provides a general framework for using predictive models and build-out scenarios to anticipate impacts to species. These predictive models and build-out scenarios allow tradeoffs to be considered between species conservation and energy development prior to implementation.

Species-Specific Traits Rather Than Resource Partitioning Mediate Diversity Effects on Resource Use:

The link between biodiversity and ecosystem processes has firmly been established, but the mechanisms underpinning this relationship are poorly documented. Most studies have focused on terrestrial plant systems where resource use can be difficult to quantify as species rely on a limited number of common resources. Investigating resource use at the bulk level may not always be of sufficient resolution to detect subtle differences in resource use, as species-specific nutritional niches at the biochemical level may also moderate diversity effects on resource use. Here we use three co-occurring marine benthic echinoderms (Brissopsis lyrifera, Mesothuria intestinalis, Parastichopus tremulus) that feed on the same phytodetrital food source, to determine whether resource partitioning is the principal mechanism underpinning diversity effects on resource use. Specifically we investigate the use of phytodetrital pigments (chlorophylls and carotenoids) because many of these are essential for biological functions, including reproduction. Pigments were identified and quantified using reverse-phase high performance liquid Chromatography (HPLC) and data were analysed using a combination of extended linear regression with generalised least squares (GLS) estimation and standard multivariate techniques. Our analyses reveal no species-specific selectivity for particular algal pigments, confirming that these three species do not partition food resources at the biochemical level. Nevertheless, we demonstrate increased total resource use in diverse treatments as a result of selection effects and the dominance of one species (B. lyrifera). Overall, we found no evidence for resource partitioning at the biochemical level, as pigment composition was similar between individuals, which is likely due to plentiful food availability. Reduced intra-specific competition in the species mixture combined with greater adsorption efficiency and differences in feeding behaviour likely explain the dominant use of resources by B. lyrifera.

Ecological Equivalence: A Realistic Assumption for Niche Theory as a Testable Alternative to Neutral Theory:

Hubbell’s 2001 neutral theory unifies biodiversity and biogeography by modelling steady-state distributions of species richness and abundances across spatio-temporal scales. Accurate predictions have issued from its core premise that all species have identical vital rates. Yet no ecologist believes that species are identical in reality. Here I explain this paradox in terms of the ecological equivalence that species must achieve at their coexistence equilibrium, defined by zero net fitness for all regardless of intrinsic differences between them. I show that the distinction of realised from intrinsic vital rates is crucial to evaluating community resilience. An analysis of competitive interactions reveals how zero-sum patterns of abundance emerge for species with contrasting life-history traits as for identical species. I develop a stochastic model to simulate community assembly from a random drift of invasions sustaining the dynamics of recruitment following deaths and extinctions. Species are allocated identical intrinsic vital rates for neutral dynamics, or random intrinsic vital rates and competitive abilities for niche dynamics either on a continuous scale or between dominant-fugitive extremes. Resulting communities have steady-state distributions of the same type for more or less extremely differentiated species as for identical species. All produce negatively skewed log-normal distributions of species abundance, zero-sum relationships of total abundance to area, and Arrhenius relationships of species to area. Intrinsically identical species nevertheless support fewer total individuals, because their densities impact as strongly on each other as on themselves. Truly neutral communities have measurably lower abundance/area and higher species/abundance ratios. Neutral scenarios can be parameterized as null hypotheses for testing competitive release, which is a sure signal of niche dynamics. Ignoring the true strength of interactions between and within species risks a substantial misrepresentation of community resilience to habitat loss.

Lots of interesting articles in PLoS Biology, PLoS Medicine, PLoS Neglected Tropical Diseases and PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
The Perfect Family: Decision Making in Biparental Care:

Previous theoretical work on parental decisions in biparental care has emphasized the role of the conflict between evolutionary interests of parents in these decisions. A prominent prediction from this work is that parents should compensate for decreases in each other’s effort, but only partially so. However, experimental tests that manipulate parents and measure their responses fail to confirm this prediction. At the same time, the process of parental decision making has remained unexplored theoretically. We develop a model to address the discrepancy between experiments and the theoretical prediction, and explore how assuming different decision making processes changes the prediction from the theory. We assume that parents make decisions in behavioral time. They have a fixed time budget, and allocate it between two parental tasks: provisioning the offspring and defending the nest. The proximate determinant of the allocation decisions are parents’ behavioral objectives. We assume both parents aim to maximize the offspring production from the nest. Experimental manipulations change the shape of the nest production function. We consider two different scenarios for how parents make decisions: one where parents communicate with each other and act together (the perfect family), and one where they do not communicate, and act independently (the almost perfect family). The perfect family model is able to generate all the types of responses seen in experimental studies. The kind of response predicted depends on the nest production function, i.e. how parents’ allocations affect offspring production, and the type of experimental manipulation. In particular, we find that complementarity of parents’ allocations promotes matching responses. In contrast, the relative responses do not depend on the type of manipulation in the almost perfect family model. These results highlight the importance of the interaction between nest production function and how parents make decisions, factors that have largely been overlooked in previous models.

Bayesian Estimation of Animal Movement from Archival and Satellite Tags:

The reliable estimation of animal location, and its associated error is fundamental to animal ecology. There are many existing techniques for handling location error, but these are often ad hoc or are used in isolation from each other. In this study we present a Bayesian framework for determining location that uses all the data available, is flexible to all tagging techniques, and provides location estimates with built-in measures of uncertainty. Bayesian methods allow the contributions of multiple data sources to be decomposed into manageable components. We illustrate with two examples for two different location methods: satellite tracking and light level geo-location. We show that many of the problems with uncertainty involved are reduced and quantified by our approach. This approach can use any available information, such as existing knowledge of the animal’s potential range, light levels or direct location estimates, auxiliary data, and movement models. The approach provides a substantial contribution to the handling uncertainty in archival tag and satellite tracking data using readily available tools.

Dynamic Coupling of Pattern Formation and Morphogenesis in the Developing Vertebrate Retina:

The vertebrate brain contains a point-to-point representation of sensory input from the eye. This visual map forms during embryonic development, by neuronal cells of the retina sending targeted axon projections to the brain. Since the projection needs to wire up neighboring cell positions in the retina to neighboring target areas in the brain, all retinal cells must harbor a defined spatial coordinate as prerequisite for map formation. How such a retinal coordinate system is established and maintained in the dynamically evolving embryo is a fundamental, but unresolved, question. By combining genetic analysis and in vivo imaging in zebrafish embryos, we have tracked the developmental origin of cell coordinates in the retina. We find that three related Fgf signals emanating from outside the eye define relative cell positions in the retina very early, already at the onset of its formation. But the absolute position of retinal cells relative to the body axes is greatly rearranged during subsequent development. In this phase, surprisingly, the same Fgf signals that at first defined retinal cell positions now balance asymmetric cell movements and cell shape changes, which are required for harmonic retinal growth and the final alignment of cell coordinates in the eye.

The Comparative Oncology Trials Consortium: Using Spontaneously Occurring Cancers in Dogs to Inform the Cancer Drug Development Pathway:

Despite evidence of drug efficacy in mouse models of cancer, many novel anti-cancer agents fail in human cancer patients because of unacceptable toxicity or poor efficacy [1]. Naturally occurring tumors in dogs and other animals have clinical and biological similarities to human cancers that are difficult to replicate in other model systems. A recently launched cooperative effort, the National Cancer Institute’s (NCI’s) Comparative Oncology Trials Consortium (COTC; http://ccr.cancer.gov/resources/cop/COTC​.asp ), now provides infrastructure and resources needed to integrate these naturally occurring cancer models into the development of new human cancer drugs, devices, and imaging techniques.

Let’s look back at the week and see what’s cool. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
ECG Response of Koalas to Tourists Proximity: A Preliminary Study:

Koalas operate on a tight energy budget and, thus, may not always display behavioral avoidance reaction when placed in a stressful condition. We investigated the physiological response of captive koalas Phascolarctos cinereus in a conservation centre to the presence of tourists walking through their habitat. We compared, using animal-attached data-recorders, the electrocardiogram activity of female koalas in contact with tourists and in a human-free area. One of the koalas in the tourist zone presented elevated heart rate values and variability throughout the recording period. The remaining female in the exhibit area showed a higher field resting heart rates during the daytime than that in the isolated area. In the evening, heart rate profiles changed drastically and both the koalas in the exhibit and in the tourist-free zones displayed similar field resting heart rates, which were lower than those during the day. In parallel, the autonomic nervous systems of these two individuals evolved from sympathetic-dominant during the day to parasympathetic-dominant in the evening. Our results report ECG of free-living koalas for the first time. Although they are preliminary due to the difficulty of having sufficient samples of animals of the same sex and age, our results stress out the importance of studies investigating the physiological reaction of animals to tourists.

Packages of Care for Mental, Neurological, and Substance Use Disorders in Low- and Middle-Income Countries: PLoS Medicine Series:

This Perspective introduces a new series in PLoS Medicine on mental health disorders in low- and middle-income countries that reviews the evidence for packages of care for ADHD, alcohol misuse disorders, dementia, depression, epilepsy, and schizophrenia.

Identification of Plasmodium malariae, a Human Malaria Parasite, in Imported Chimpanzees:

It is widely believed that human malaria parasites infect only man as a natural host. However, earlier morphological observations suggest that great apes are likely to be natural reservoirs as well. To identify malaria parasites in great apes, we screened 60 chimpanzees imported into Japan. Using the sequences of small subunit rRNA and the mitochondrial genome, we identified infection of Plasmodium malariae, a human malaria parasite, in two chimpanzees that were imported about thirty years ago. The chimpanzees have been asymptomatic to the present. In Japan, indigenous malaria disappeared more than fifty years ago; and thus, it is most likely inferred that the chimpanzees were infected in Africa, and P. malariae isolates were brought into Japan from Africa with their hosts, suggesting persistence of parasites at low level for thirty years. Such a long term latent infection is a unique feature of P. malariae infection in humans. To our knowledge, this is the first to report P. malariae infection in chimpanzees and a human malaria parasite from nonhuman primates imported to a nonendemic country.

Plasticity of the Chemoreceptor Repertoire in Drosophila melanogaster:

Rapid adaptation and phenotypic plasticity to the chemical environment are essential prerequisites for survival; and, consequently, large families of genes that mediate the recognition of olfactory and gustatory cues have evolved. We asked how flexible the expression of these genes is in the face of rapidly changing conditions encountered during an individual’s lifetime. We used the fruit fly, Drosophila melanogaster, to address this question, since both the genetic composition and environmental rearing conditions can be controlled precisely in this experimentally amenable model organism. By measuring expression levels of all chemosensory genes simultaneously, we identified genes that show altered expression at different developmental stages, during aging, in males and females, following mating, and in different social conditions. We asked whether chemosensory genes are regulated independently or whether their regulation is structured. We found that chemosensory genes that are located in close proximity to one another on the chromosome are often regulated independently. However, statistical analysis showed that groups of chemosensory genes are coordinately expressed in response to a range of environmental conditions, revealing an underlying modular organization of the phenotypic plasticity of the chemosensory receptor repertoire.

Long-Term GPS Tracking of Ocean Sunfish Mola mola Offers a New Direction in Fish Monitoring:

Satellite tracking of large pelagic fish provides insights on free-ranging behaviour, distributions and population structuring. Up to now, such fish have been tracked remotely using two principal methods: direct positioning of transmitters by Argos polar-orbiting satellites, and satellite relay of tag-derived light-level data for post hoc track reconstruction. Error fields associated with positions determined by these methods range from hundreds of metres to hundreds of kilometres. However, low spatial accuracy of tracks masks important details, such as foraging patterns. Here we use a fast-acquisition global positioning system (Fastloc GPS) tag with remote data retrieval to track long-term movements, in near real time and position accuracy of <70 m, of the world's largest bony fish, the ocean sunfish Mola mola. Search-like movements occurred over at least three distinct spatial scales. At fine scales, sunfish spent longer in highly localised areas with faster, straighter excursions between them. These 'stopovers' during long-distance movement appear consistent with finding and exploiting food patches. This demonstrates the feasibility of GPS tagging to provide tracks of unparalleled accuracy for monitoring movements of large pelagic fish, and with nearly four times as many locations obtained by the GPS tag than by a conventional Argos transmitter. The results signal the potential of GPS-tagged pelagic fish that surface regularly to be detectors of resource 'hotspots' in the blue ocean and provides a new capability for understanding large pelagic fish behaviour and habitat use that is relevant to ocean management and species conservation.