There are 37 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:
First Known Feeding Trace of the Eocene Bottom-Dwelling Fish Notogoneus osculus and Its Paleontological Significance:
The Green River Formation (early Eocene, about 42-53 Ma) at and near Fossil Butte National Monument in Wyoming, USA, is world famous for its exquisitely preserved freshwater teleost fish in the former Fossil Lake. Nonetheless, trace fossils attributed to fish interacting with the lake bottom are apparently rare, and have not been associated directly with any fish species. Here we interpret the first known feeding and swimming trace fossil of the teleost Notogoneus osculus Cope (Teleostei: Gonorynchidae), which is also represented as a body fossil in the same stratum. A standard description of the trace fossil, identified as Undichna cf. U. simplicatas, was augmented by high-resolution digital images and spatial and mathematical analyses, which allowed for detailed interpretations of the anatomy, swimming mode, feeding behavior, and body size of the tracemaker. Our analysis indicates that the tracemaker was about 45 cm long; used its caudal, anal, and pelvic fins (the posterior half of its body) to make the swimming traces; and used a ventrally oriented mouth to make overlapping feeding marks. We hypothesize that the tracemaker was an adult Notogoneus osculus. Our results are the first to link a specific teleost tracemaker with a trace fossil from the Green River Formation, while also interpreting the size and relative age of the tracemaker. The normal feeding and swimming behaviors indicated by the trace fossil indicate temporarily oxygenated benthic conditions in the deepest part of Fossil Lake, counter to most paleoecological interpretations of this deposit. Lastly, our spatial and mathematical analyses significantly update and advance previous approaches to the study of teleost trace fossils.
Read the interview with one of the authors: Part I and Part II.
Four New Vining Species of Solanum (Dulcamaroid Clade) from Montane Habitats in Tropical America:
Solanum (Solanaceae), with approximately 1500 species, is one of the largest genera of flowering plants, and has a centre of diversity in the New World tropics. The genus is divided into 13 major clades, of which two, the Dulcamaroid clade and the “African Non-Spiny” clade, exhibit vine morphology with twining petioles. I am currently preparing a worldwide monograph of these two groups, comprising some 70 species. I formally describe here four new species of Solanum from montane Mexico and South America all belonging to the Dulcamaroid clade (including the traditionally recognised section Jasminosolanum Bitter). Descriptions, discussions of closely related species and preliminary conservation assessments are provided for all species; all species are illustrated. This paper is also a test case for the electronic publication of new names in flowering plants. These new species are all relatively rare, but not currently of conservation concern. Solanum aspersum sp. nov. is distributed in Colombia and Ecuador, S. luculentum sp. nov. in Colombia and Venezuela, S. sanchez-vegae sp. nov. is endemic to northern Peru and S. sousae sp. nov. to southern Mexico. Solanum luculentum has the morphology of a dioecious species; this is the first report of this breeding system in the Dulcamaroid clade.
Read the acommpanying blog post.
3-D Modelling of Megaloolithid Clutches: Insights about Nest Construction and Dinosaur Behaviour:
Megaloolithid eggs have long been associated with sauropod dinosaurs. Despite their extensive and worldwide fossil record, interpretations of egg size and shape, clutch morphology, and incubation strategy vary. The Pinyes locality in the Upper Cretaceous Tremp Formation in the southern Pyrenees, Catalonia provides new information for addressing these issues. Nine horizons containing Megaloolithus siruguei clutches are exposed near the village of Coll de Nargó. Tectonic deformation in the study area strongly influenced egg size and shape, which could potentially lead to misinterpretation of reproductive biology if 2D and 3D maps are not corrected for bed dip that results from tectonism. Detailed taphonomic study and three-dimensional modelling of fossil eggs show that intact M. siruguei clutches contained 20-28 eggs, which is substantially larger than commonly reported from Europe and India. Linear and grouped eggs occur in three superimposed levels and form an asymmetric, elongate, bowl-shaped profile in lateral view. Computed tomography data support previous interpretations that the eggs hatched within the substrate. Megaloolithid clutch sizes reported from other European and Indian localities are typically less than 15 eggs; however, these clutches often include linear or grouped eggs that resemble those of the larger Pinyes clutches and may reflect preservation of incomplete clutches. We propose that 25 eggs represent a typical megaloolithid clutch size and smaller egg clusters that display linear or grouped egg arrangements reported at Pinyes and other localities may represent eroded remnants of larger clutches. The similarity of megaloolithid clutch morphology from localities worldwide strongly suggests common reproductive behaviour. The distinct clutch geometry at Pinyes and other localities likely resulted from the asymmetrical, inclined, and laterally compressed titanosaur pes unguals of the female, using the hind foot for scratch-digging during nest excavation.
Familiarity Breeds Contempt: Kangaroos Persistently Avoid Areas with Experimentally Deployed Dingo Scents:
Whether or not animals habituate to repeated exposure to predator scents may depend upon whether there are predators associated with the cues. Understanding the contexts of habituation is theoretically important and has profound implication for the application of predator-based herbivore deterrents. We repeatedly exposed a mixed mob of macropod marsupials to olfactory scents (urine, feces) from a sympatric predator (Canis lupus dingo), along with a control (water). If these predator cues were alarming, we expected that over time, some red kangaroos (Macropus rufous), western grey kangaroos (Macropus fuliginosus) and agile wallabies (Macropus agilis) would elect to not participate in cafeteria trials because the scents provided information about the riskiness of the area. We evaluated the effects of urine and feces independently and expected that urine would elicit a stronger reaction because it contains a broader class of infochemicals (pheromones, kairomones). Finally, we scored non-invasive indicators (flight and alarm stomps) to determine whether fear or altered palatability was responsible for the response. Repeated exposure reduced macropodid foraging on food associated with 40 ml of dingo urine, X = 986.75±3.97 g food remained as compared to the tap water control, X = 209.0±107.0 g (P<0.001). Macropodids fled more when encountering a urine treatment, X = 4.50±2.08 flights, as compared to the control, X = 0 flights (P0.5). Macropodids did not habituate to repeated exposure to predator scents, rather they avoided the entire experimental area after 10 days of trials (R2 = 83.8; P<0.001). Responses to urine and feces were indistinguishable; both elicited fear-based responses and deterred foraging. Despite repeated exposure to predator-related cues in the absence of a predator, macropodids persistently avoided an area of highly palatable food. Area avoidance is consistent with that observed from other species following repeated anti-predator conditioning, However, this is the first time this response has been experimentally observed among medium or large vertebrates − where a local response is observed spatially and an area effect is revealed over time.
Virtue or Pretense? Looking behind Self-Declared Innocence in Doping:
Social science studies of doping practices in sport rely predominantly on self-reports. Studies of psychoactive drug use indicate that self-reporting is characterised by under-reporting. Likewise doping practice is likely to be equally under-reported, if not more so. This calls for more sophisticated methods for such reporting and for independent, objective validation of its results. The aims of this study were: i) to contrast self-reported doping use with objective results from chemical hair analysis and ii) to investigate the influence of the discrepancy on doping attitudes, social projection, descriptive norms and perceived pressure to use doping. A doping attitudes questionnaire was developed and combined with a response latency-based implicit association test and hair sample analysis for key doping substances in 14 athletes selected from a larger sample (N = 82) to form contrast comparison groups. Results indicate that patterns of group differences in social projection, explicit attitude about and perceived pressure to use doping, vary depending on whether the user and non-user groups are defined by self-report or objectively verified through hair analysis. Thus, self-confessed users scored higher on social projection, explicit attitude to doping and perceived pressure. However, when a doping substance was detected in the hair of an athlete who denied doping use, their self-report evidenced extreme social desirability (negative attitude, low projection and low perceived pressure) and contrasted sharply with a more positive estimate of their implicit doping attitude. Hair analysis for performance enhancing substances has shown considerable potential in validating athletes’ doping attitude estimations and admissions of use. Results not only confirm the need for improved self-report methodology for future research in socially-sensitive domains but also indicate where the improvements are likely to come from: as chemical validation remains expensive, a more realistic promise for large scale studies and online data collection efforts is held by measures of implicit social cognition.
Is the Spatial Distribution of Mankind’s Most Basic Economic Traits Determined by Climate and Soil Alone?:
Several authors, most prominently Jared Diamond (1997, Guns, Germs and Steel), have investigated biogeographic determinants of human history and civilization. The timing of the transition to an agricultural lifestyle, associated with steep population growth and consequent societal change, has been suggested to be affected by the availability of suitable organisms for domestication. These factors were shown to quantitatively explain some of the current global inequalities of economy and political power. Here, we advance this approach one step further by looking at climate and soil as sole determining factors. As a simplistic ‘null model’, we assume that only climate and soil conditions affect the suitability of four basic landuse types – agriculture, sedentary animal husbandry, nomadic pastoralism and hunting-and-gathering. Using ecological niche modelling (ENM), we derive spatial predictions of the suitability for these four landuse traits and apply these to the Old World and Australia. We explore two aspects of the properties of these predictions, conflict potential and population density. In a calculation of overlap of landuse suitability, we map regions of potential conflict between landuse types. Results are congruent with a number of real, present or historical, regions of conflict between ethnic groups associated with different landuse traditions. Furthermore, we found that our model of agricultural suitability explains a considerable portion of population density variability. We mapped residuals from this correlation, finding geographically highly structured deviations that invite further investigation. We also found that ENM of agricultural suitability correlates with a metric of local wealth generation (Gross Domestic Product, Purchasing Power Parity). From simplified assumptions on the links between climate, soil and landuse we are able to provide good predictions on complex features of human geography. The spatial distribution of deviations from ENM predictions identifies those regions requiring further investigation of potential explanations. Our findings and methodological approaches may be of applied interest, e.g., in the context of climate change.
Student Behavior during a School Closure Caused by Pandemic Influenza A/H1N1:
Many schools were temporarily closed in response to outbreaks of the recently emerged pandemic influenza A/H1N1 virus. The effectiveness of closing schools to reduce transmission depends largely on student/family behavior during the closure. We sought to improve our understanding of these behaviors. To characterize this behavior, we surveyed students in grades 9-12 and parents of students in grades 5-8 about student activities during a weeklong closure of a school during the first months after the disease emerged. We found significant interaction with the community and other students-though less interaction with other students than during school-with the level of interaction increasing with grade. Our results are useful for the future design of social distancing policies and to improving the ability of modeling studies to accurately predict their impact.
An Analysis of Genetic Changes during the Divergence of Drosophila Species:
It has been long appreciated that speciation involves changes in body plans and establishes genetic, reproductive, developmental and behavioral incompatibilities between populations. However, little is still known about the genetic components involved in these changes or the sequence and scale of events that lead to the differentiation of species. In this paper, we investigated the genetic changes in three closely related species of Drosophila by making pair-wise comparisons of their genomes. We focused our analysis on the modern relatives of the alleles likely to be segregating in pre-historic populations at the time or after the ancestor of D. simulans became separated from the ancestor of D. melanogaster. Some of these genes were previously implicated in the genetics of reproduction and behavior while the biological functions of others are not yet clear. Together these results identify different classes of genes that might have participated in the beginning of segregation of these species millions of years ago in Africa.
Phenex: Ontological Annotation of Phenotypic Diversity:
Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge. Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices. Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.
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