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So, let’s see what’s new in PLoS Genetics, PLoS Computational Biology, PLoS Pathogens, and PLoS Neglected Tropical Diseases this week. 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, 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:

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There are 10 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, 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:
Individually Unique Body Color Patterns in Octopus (Wunderpus photogenicus) Allow for Photoidentification:

Studies on the longevity and migration patterns of wild animals rely heavily on the ability to track individual adults. Non-extractive sampling methods are particularly important when monitoring animals that are commercially important to ecotourism, and/or are rare. The use of unique body patterns to recognize and track individual vertebrates is well-established, but not common in ecological studies of invertebrates. Here we provide a method for identifying individual Wunderpus photogenicus using unique body color patterns. This charismatic tropical octopus is commercially important to the underwater photography, dive tourism, and home aquarium trades, but is yet to be monitored in the wild. Among the adults examined closely, the configurations of fixed white markings on the dorsal mantle were found to be unique. In two animals kept in aquaria, these fixed markings were found not to change over time. We believe another individual was photographed twice in the wild, two months apart. When presented with multiple images of W. photogenicus, volunteer observers reliably matched photographs of the same individuals. Given the popularity of W. photogenicus among underwater photographers, and the ease with which volunteers can correctly identify individuals, photo-identification appears to be a practical means to monitor individuals in the wild.

Structural Relationships between Highly Conserved Elements and Genes in Vertebrate Genomes:

Large numbers of sequence elements have been identified to be highly conserved among vertebrate genomes. These highly conserved elements (HCEs) are often located in or around genes that are involved in transcription regulation and early development. They have been shown to be involved in cis-regulatory activities through both in vivo and additional computational studies. We have investigated the structural relationships between such elements and genes in six vertebrate genomes human, mouse, rat, chicken, zebrafish and tetraodon and detected several thousand cases of conserved HCE-gene associations, and also cases of HCEs with no common target genes. A few examples underscore the potential significance of our findings about several individual genes. We found that the conserved association between HCE/HCEs and gene/genes are not restricted to elements by their absolute distance on the genome. Notably, long-range associations were identified and the molecular functions of the associated genes do not show any particular overrepresentation of the functional categories previously reported. HCEs in close proximity are found to be linked with different set of gene/genes. The results reflect the highly complex correlation between HCEs and their putative target genes.

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There are 10 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, 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 Relative Influence of Competition and Prey Defenses on the Phenotypic Structure of Insectivorous Bat Ensembles in Southern Africa:

Deterministic filters such as competition and prey defences should have a strong influence on the community structure of animals such as insectivorous bats that have life histories characterized by low fecundity, low predation risk, long life expectancy, and stable populations. We investigated the relative influence of these two deterministic filters on the phenotypic structure of insectivorous bat ensembles in southern Africa. We used null models to simulate the random phenotypic patterns expected in the absence of competition or prey defences and analysed the deviations of the observed phenotypic pattern from these expected random patterns. The phenotypic structure at local scales exhibited non-random patterns consistent with both competition and prey defense hypotheses. There was evidence that competition influenced body size distribution across ensembles. Competition also influenced wing and echolocation patterns in ensembles and in functional foraging groups with high species richness or abundance. At the same time, prey defense filters influenced echolocation patterns in two species-poor ensembles. Non-random patterns remained evident even after we removed the influence of body size from wing morphology and echolocation parameters taking phylogeny into account. However, abiotic filters such as geographic distribution ranges of small and large-bodied species, extinction risk, and the physics of flight and sound probably also interacted with biotic filters at local and/or regional scales to influence the community structure of sympatric bats in southern Africa. Future studies should investigate alternative parameters that define bat community structure such as diet and abundance to better determine the influence of competition and prey defences on the structure of insectivorous bat ensembles in southern Africa.

Natural Disease Resistance in Threatened Staghorn Corals:

Disease epidemics have caused extensive damage to tropical coral reefs and to the reef-building corals themselves, yet nothing is known about the abilities of the coral host to resist disease infection. Understanding the potential for natural disease resistance in corals is critically important, especially in the Caribbean where the two ecologically dominant shallow-water corals, Acropora cervicornis and A. palmata, have suffered an unprecedented mass die-off due to White Band Disease (WBD), and are now listed as threatened under the US Threatened Species Act and as critically endangered under the IUCN Red List criteria. Here we examine the potential for natural resistance to WBD in the staghorn coral Acropora cervicornis by combining microsatellite genotype information with in situ transmission assays and field monitoring of WBD on tagged genotypes. We show that six percent of staghorn coral genotypes (3 out of 49) are resistant to WBD. This natural resistance to WBD in staghorn corals represents the first evidence of host disease resistance in scleractinian corals and demonstrates that staghorn corals have an innate ability to resist WBD infection. These resistant staghorn coral genotypes may explain why pockets of Acropora have been able to survive the WBD epidemic. Understanding disease resistance in these corals may be the critical link to restoring populations of these once dominant corals throughout their range.

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There are 13 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, from CiteULike, Connotea and Stumbleupon, to Facebook and Digg, with just one click. Here are my own picks for the week – you go and look for your own favourites:
The Absolute Threshold of Colour Vision in the Horse:

Arrhythmic mammals are active both during day and night if they are allowed. The arrhythmic horses are in possession of one of the largest terrestrial animal eyes and the purpose of this study is to reveal whether their eye is sensitive enough to see colours at night. During the day horses are known to have dichromatic colour vision. To disclose whether they can discriminate colours in dim light a behavioural dual choice experiment was performed. We started the training and testing at daylight intensities and the horses continued to choose correctly at a high frequency down to light intensities corresponding to moonlight. One Shetland pony mare, was able to discriminate colours at 0.08 cd/m2, while a half blood gelding, still discriminated colours at 0.02 cd/m2. For comparison, the colour vision limit for several human subjects tested in the very same experiment was also 0.02 cd/m2. Hence, the threshold of colour vision for the horse that performed best was similar to that of the humans. The behavioural results are in line with calculations of the sensitivity of cone vision where the horse eye and human eye again are similar. The advantage of the large eye of the horse lies not in colour vision at night, but probably instead in achromatic tasks where presumably signal summation enhances sensitivity.

Losing the Big Picture: How Religion May Control Visual Attention:

Despite the abundance of evidence that human perception is penetrated by beliefs and expectations, scientific research so far has entirely neglected the possible impact of religious background on attention. Here we show that Dutch Calvinists and atheists, brought up in the same country and culture and controlled for race, intelligence, sex, and age, differ with respect to the way they attend to and process the global and local features of complex visual stimuli: Calvinists attend less to global aspects of perceived events, which fits with the idea that people’s attentional processing style reflects possible biases rewarded by their religious belief system.

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There are 10 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. Here are my own picks for the week – you go and look for your own favourites:
Imitation of Body Movements Facilitated by Joint Attention through Eye Contact and Pointing in Japanese Monkey:

Eye contact and pointing are typical gestures in order to direct another individual’s attention toward a target. We previously investigated on Japanese monkeys whether joint attention ability encouraged by eye contact and pointing was associated with the imitation of human’s actions. The monkeys with the joint attention skills showed the imitation of human’s actions. In the current study, we investigated on a monkey whether joint attention ability also facilitated the imitation of human body-movements. Results showed that the monkey being taught eye contact and pointing showed the imitation of human body-movements. These results suggest that the monkeys have basic potential for following another individual’s motion, and that what imitation expresses depends on where the monkeys are paying attention. Thus, eye contact and pointing are suitable for directing the monkey’s attention toward the human.

Converting Endangered Species Categories to Probabilities of Extinction for Phylogenetic Conservation Prioritization:

Categories of imperilment like the global IUCN Red List have been transformed to probabilities of extinction and used to rank species by the amount of imperiled evolutionary history they represent (e.g. by the Edge of Existence programme). We investigate the stability of such lists when ranks are converted to probabilities of extinction under different scenarios. Using a simple example and computer simulation, we show that preserving the categories when converting such list designations to probabilities of extinction does not guarantee the stability of the resulting lists. Care must be taken when choosing a suitable transformation, especially if conservation dollars are allocated to species in a ranked fashion. We advocate routine sensitivity analyses.

Food Inequality Negatively Impacts Cardiac Health in Rabbits:

Individuals with lower socioeconomic status experience higher rates of mortality and are more likely to suffer from numerous diseases. While some studies indicate that humans who suffer from social inequality suffer generally worse health, to our knowledge no controlled experiments of this nature have been done in any species. Lipofuscin is a highly oxidized cross-linked aggregate consisting of oxidized protein and lipid clusters. This eminent terminal oxidation outcome accumulates within cells during aging process. Thirty two rabbits were assigned into four groups randomly of eight each. The first group encountered food deprivation for eight weeks and was kept in an isolated situation. The second group was food deprived for eight weeks but encountered to other groups continuously. The third group suffered two weeks of deprivation and then received free access to food. The fourth group had free access to diet without any deprivation. All hearts were removed for histopathological evaluation. Cross-sections of hearts were examined by light microscopy for the presence of yellow-brown Lipofuscin pigment granules. Here we show that relative food deprivation can cause accumulation of Lipofuscin pigmentation. We find that cardiac Lipofuscin deposition increases the most in the inequitable condition in which food deprived individuals observe well-fed individuals. Our findings demonstrate that a sense of inequality in food intake can promote aging more than food deprivation alone. These findings should be considered as a basis for further studies on the physiological mechanisms by which inequality negatively impacts health and well-being.

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So, let’s see what’s new in PLoS Genetics, PLoS Computational Biology, PLoS Pathogens, PLoS ONE and PLoS Neglected Tropical Diseases this week. 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 – you go and look for your own favourites:
The Evolutionary Dynamics of the Lion Panthera leo Revealed by Host and Viral Population Genomics:

The lion Panthera leo, a formidable carnivore with a complex cooperative social system, has fascinated humanity since pre-historical times, inspiring hundreds of religious and cultural allusions. Here, we use a comprehensive sample of 357 individuals from most of the major lion populations in Africa and Asia. We assayed appropriately informative autosomal, Y-chromosome, and mitochondrial genetic markers, and assessed the prevalence and genetic variation of the lion-specific feline immunodeficiency virus (FIVPle), a lentivirus analogous to human immunodeficiency virus (HIV) that causes AIDS-like immunodeficiency disease in domestic cats. We compare the large multigenic dataset from lions with patterns of genetic variation of the FIVPle to characterize the population-genomic legacy of lions. We refute the hypothesis that African lions consist of a single panmictic population, highlighting the importance of preserving populations in decline rather than prioritizing larger-scale conservation efforts. Interestingly, lion and FIVPle variation revealed evidence of unsuspected genetic diversity even in the well-studied lion population of the Serengeti Ecosystem, which consists of recently admixed animals derived from three distinct genetic groups.

Facilitated Variation: How Evolution Learns from Past Environments To Generalize to New Environments:

One of the striking features of evolution is the appearance of novel structures in organisms. The origin of the ability to generate novelty is one of the main mysteries in evolutionary theory. The molecular mechanisms that enhance the evolution of novelty were recently integrated by Kirschner and Gerhart in their theory of facilitated variation. This theory suggests that organisms have a design that makes it more likely that random genetic changes will result in organisms with novel shapes that can survive. Here we demonstrate how facilitated variation can arise in computer simulations of evolution. We propose a quantitative approach for studying facilitated variation in computational model systems. We find that the evolution of facilitated variation is enhanced in environments that change from time to time in a systematic way: the varying environments are made of the same set of subgoals, but in different combinations. Under such varying conditions, the simulated organisms store information about past environments in their genome, and develop a special modular design that can readily generate novel modules.

Emergence of Functional Hierarchy in a Multiple Timescale Neural Network Model: A Humanoid Robot Experiment:

Functional hierarchy in neural systems, defined as the principle that complex entities may be segmented into simpler elements and that simple elements may be integrated into a complex entity, is a challenging area of study in neuroscience. Such a functional hierarchy may be thought of intuitively in two ways: as hierarchy in space, and as hierarchy in time. An example of hierarchy in space is visual information processing, where elemental information in narrow receptive fields is integrated into complex features of a visual image in a larger space. Hierarchy in time is exemplified by auditory information processing, where syllable-level information within a short time window is integrated into word-level information over a longer time window. Although extensive investigations have illuminated the neural mechanisms of spatial hierarchy, those governing temporal hierarchy are less clear. In the current study, we demonstrate that functional hierarchy can self-organize through multiple timescales in neural activity, without explicit spatial hierarchical structure. Our results suggest that multiple timescales are an essential factor leading to the emergence of functional hierarchy in neural systems. This work could contribute to providing clues regarding the puzzling observation of such hierarchy in the absence of spatial hierarchical structure.

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