There are 62 new articles in PLoS ONE 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:
Diurnal and Circadian Rhythms in the Tomato Transcriptome and Their Modulation by Cryptochrome Photoreceptors:

Circadian clocks are internal molecular time-keeping mechanisms that provide living organisms with the ability to adjust their growth and physiology and to anticipate diurnal environmental changes. Circadian clocks, without exception, respond to light and, in plants, light is the most potent and best characterized entraining stimulus. The capacity of plants to respond to light is achieved through a number of photo-perceptive proteins including cryptochromes and phytochromes. There is considerable experimental evidence demonstrating the roles of photoreceptors in providing light input to the clock. In order to identify genes regulated by diurnal and circadian rhythms, and to establish possible functional relations between photoreceptors and the circadian clock in tomato, we monitored the temporal transcription pattern in plants entrained to long-day conditions, either by large scale comparative profiling, or using a focused approach over a number of photosensory and clock-related genes by QRT-PCR. In parallel, focused transcription analyses were performed in cry1a- and in CRY2-OX tomato genotypes. We report a large series of transcript oscillations that shed light on the complex network of interactions among tomato photoreceptors and clock-related genes. Alteration of cryptochrome gene expression induced major changes in the rhythmic oscillations of several other gene transcripts. In particular, over-expression of CRY2 had an impact not only on day/night fluctuations but also on rhythmicity under constant light conditions. Evidence was found for widespread diurnal oscillations of transcripts encoding specific enzyme classes (e.g. carotenoid biosynthesis enzymes) as well as for post-transcriptional diurnal and circadian regulation of the CRY2 transcript.

Postglacial Colonisation Patterns and the Role of Isolation and Expansion in Driving Diversification in a Passerine Bird:

Pleistocene glacial cycles play a major role in diversification and speciation, although the relative importance of isolation and expansion in driving diversification remains debated. We analysed mitochondrial DNA sequence data from 15 great reed warbler (Acrocephalus arundinaceus) populations distributed over the vast Eurasian breeding range of the species, and revealed unexpected postglacial expansion patterns from two glacial refugia. There were 58 different haplotypes forming two major clades, A and B. Clade A dominated in Western Europe with declining frequencies towards Eastern Europe and the Middle East, but showed a surprising increase in frequency in Western and Central Asia. Clade B dominated in the Middle East, with declining frequencies towards north in Central and Eastern Europe and was absent from Western Europe and Central Asia. A parsimonious explanation for these patterns is independent postglacial expansions from two isolated refugia, and mismatch distribution analyses confirmed this suggestion. Gene flow analyses showed that clade A colonised both Europe and Asia from a refugium in Europe, and that clade B expanded much later and colonised parts of Europe from a refugium in the Middle East. Great reed warblers in the eastern parts of the range have slightly paler plumage than western birds (sometimes treated as separate subspecies; A. a. zarudnyi and A. a. arundinaceus, respectively) and our results suggest that the plumage diversification took place during the easterly expansion of clade A. This supports the postglacial expansion hypothesis proposing that postglacial expansions drive diversification in comparatively short time periods. However, there is no indication of any (strong) reproductive isolation between clades and our data show that the refugia populations became separated during the last glaciation. This is in line with the Pleistocene speciation hypothesis invoking that much longer periods of time in isolation are needed for speciation to occur.

Evolution of Skull and Mandible Shape in Cats (Carnivora: Felidae):

The felid family consists of two major subgroups, the sabretoothed and the feline cats, to which all extant species belong, and are the most anatomically derived of all carnivores for predation on large prey with a precision killing bite. There has been much controversy and uncertainty about why the skulls and mandibles of sabretoothed and feline cats evolved to become so anatomically divergent, but previous models have focused on single characters and no unifying hypothesis of evolutionary shape changes has been formulated. Here I show that the shape of the skull and mandible in derived sabrecats occupy entirely different positions within overall morphospace from feline cats, and that the evolution of skull and mandible shape has followed very different paths in the two subgroups. When normalised for body-size differences, evolution of bite forces differ markedly in the two groups, and are much lower in derived sabrecats, and they show a significant relationship with size and cranial shape, whereas no such relationship is present in feline cats. Evolution of skull and mandible shape in modern cats has been governed by the need for uniform powerful biting irrespective of body size, whereas in sabrecats, shape evolution was governed by selective pressures for efficient predation with hypertrophied upper canines at high gape angles, and bite forces were secondary and became progressively weaker during sabrecat evolution. The current study emphasises combinations of new techniques for morphological shape analysis and biomechanical studies to formulate evolutionary hypotheses for difficult groups.

Dinosaurian Soft Tissues Interpreted as Bacterial Biofilms:

A scanning electron microscope survey was initiated to determine if the previously reported findings of “dinosaurian soft tissues” could be identified in situ within the bones. The results obtained allowed a reinterpretation of the formation and preservation of several types of these “tissues” and their content. Mineralized and non-mineralized coatings were found extensively in the porous trabecular bone of a variety of dinosaur and mammal species across time. They represent bacterial biofilms common throughout nature. Biofilms form endocasts and once dissolved out of the bone, mimic real blood vessels and osteocytes. Bridged trails observed in biofilms indicate that a previously viscous film was populated with swimming bacteria. Carbon dating of the film points to its relatively modern origin. A comparison of infrared spectra of modern biofilms with modern collagen and fossil bone coatings suggests that modern biofilms share a closer molecular make-up than modern collagen to the coatings from fossil bones. Blood cell size iron-oxygen spheres found in the vessels were identified as an oxidized form of formerly pyritic framboids. Our observations appeal to a more conservative explanation for the structures found preserved in fossil bone.

From Plants to Birds: Higher Avian Predation Rates in Trees Responding to Insect Herbivory:

An understanding of the evolution of potential signals from plants to the predators of their herbivores may provide exciting examples of co-evolution among multiple trophic levels. Understanding the mechanism behind the attraction of predators to plants is crucial to conclusions about co-evolution. For example, insectivorous birds are attracted to herbivore-damaged trees without seeing the herbivores or the defoliated parts, but it is not known whether birds use cues from herbivore-damaged plants with a specific adaptation of plants for this purpose. We examined whether signals from damaged trees attract avian predators in the wild and whether birds could use volatile organic compound (VOC) emissions or net photosynthesis of leaves as cues to detect herbivore-rich trees. We conducted a field experiment with mountain birches (Betula pubescens ssp. czerepanovii), their main herbivore (Epirrita autumnata) and insectivorous birds. Half of the trees had herbivore larvae defoliating trees hidden inside branch bags and half had empty bags as controls. We measured predation rate of birds towards artificial larvae on tree branches, and VOC emissions and net photosynthesis of leaves. The predation rate was higher in the herbivore trees than in the control trees. This confirms that birds use cues from trees to locate insect-rich trees in the wild. The herbivore trees had decreased photosynthesis and elevated emissions of many VOCs, which suggests that birds could use either one, or both, as cues. There was, however, large variation in how the VOC emission correlated with predation rate. Emissions of (E)-DMNT [(E)-4,8-dimethyl-1,3,7-nonatriene], β-ocimene and linalool were positively correlated with predation rate, while those of highly inducible green leaf volatiles were not. These three VOCs are also involved in the attraction of insect parasitoids and predatory mites to herbivore-damaged plants, which suggests that plants may not have specific adaptations to signal only to birds.

Temperature-Dependent Sex Determination in Fish Revisited: Prevalence, a Single Sex Ratio Response Pattern, and Possible Effects of Climate Change:

In gonochoristic vertebrates, sex determination mechanisms can be classified as genotypic (GSD) or temperature-dependent (TSD). Some cases of TSD in fish have been questioned, but the prevalent view is that TSD is very common in this group of animals, with three different response patterns to temperature. We analyzed field and laboratory data for the 59 fish species where TSD has been explicitly or implicitly claimed so far. For each species, we compiled data on the presence or absence of sex chromosomes and determined if the sex ratio response was obtained within temperatures that the species experiences in the wild. If so, we studied whether this response was statistically significant. We found evidence that many cases of observed sex ratio shifts in response to temperature reveal thermal alterations of an otherwise predominately GSD mechanism rather than the presence of TSD. We also show that in those fish species that actually have TSD, sex ratio response to increasing temperatures invariably results in highly male-biased sex ratios, and that even small changes of just 1-2°C can significantly alter the sex ratio from 1:1 (males:females) up to 3:1 in both freshwater and marine species. We demonstrate that TSD in fish is far less widespread than currently believed, suggesting that TSD is clearly the exception in fish sex determination. Further, species with TSD exhibit only one general sex ratio response pattern to temperature. However, the viability of some fish populations with TSD can be compromised through alterations in their sex ratios as a response to temperature fluctuations of the magnitude predicted by climate change.

And more:

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Piecing Together An Extinct Lemur, Large As A Big Baboon:

Penn State researchers have used computed tomography (CT) technology to virtually glue newly-discovered skull fragments of a rare extinct lemur back into its partial skull, which was discovered over a century ago. Alan Walker, Evan Pugh Professor of Anthropology and Biology at Penn State, and Research Associate in Anthropology Timothy Ryan, led the research. The different fragments of this lemur’s skull are separated by thousands of miles, with the partial skull in Vienna and the pieces of frontal bone in the United States.

Insect Biodiversity In Amazon May Be Result Of Ice Age Climate Change And Ancient Flooding, Not River Barriers:

Ice age climate change and ancient flooding–but not barriers created by rivers–may have promoted the evolution of new insect species in the Amazon region of South America, a new study suggests.

Unexpected Key To Flowering Plants’ Diversity:

What began with an off-the-cuff curiosity eventually led Joe Williams to hang from the limbs of a tree 80 feet above the soil of northeastern Australia. The things Williams, a University of Tennessee, Knoxville, researcher found there may help explain the amazing diversity in the world’s flowering plants, a question that has puzzled scientists from the time of Charles Darwin to today.

Uncertain Future For Elephants Of Thailand:

Worries over the future of Thailand’ s famous elephants have emerged following an investigation by a University of Manchester team.

Endangered European Wild Cat May Protected By Proposed Network Of Corridors:

For the first time an international researcher team has developed a model, which identifies potential habitats and corridors for the European wildcat (Felis silvestris silvestris). Using Rheinland-Pfalz as an example, it was demonstrated that almost half of this German federal state could be suitable for wildcats, enabling a maximum population of 1600 females.

What’s new in PLoS Biology and PLoS Medicine this week? Among else:

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Birdsong Not Just For The Birds: Bio-acoustic Method Also Hears Nature’s Cry For Help:

Switch on the mike, start the recording, the stage is set for the local fauna!

Explosion In Marine Biodiversity Explained By Climate Change:

A global change in climate could explain the explosion in marine biodiversity that took place 460 million years ago. Researchers from Lyon (1) and Canberra (Australia) (2) have found evidence of a progressive ocean cooling of about 15°C over a period of 40 million years during the Ordovician (3). Until now, this geologic period had been associated with a “super greenhouse effect” on our planet.

Plant Steroids Offer New Paradigm For How Hormones Work:

Steroids bulk up plants just as they do human athletes, but the playbook of molecular signals that tell the genes to boost growth and development in plant cells is far more complicated than in human and animal cells.

Acidification Of The Sea Hampers Reproduction Of Marine Species: Decreasing pH The Biggest Threat To Marine Animal Life For Thousands Of Years:

By absorbing carbon dioxide from the atmosphere, and from the human use of fossil fuels, the world’s seas function as a giant buffer for the Earth’s life support system. The chemical balance of the sea has long been regarded as immovable.

Bacteria Reveal Secret Of Adaptation At Evolution Canyon:

Bacteria living on opposite sides of a canyon have evolved to cope with different temperatures by altering the make-up of their ‘skin’, or cell membranes. Scientists have found that bacteria change these complex and important structures to adapt to different temperatures by looking at the appearance of the bacteria as well as their genes. The researchers hope their study, published in the August issue of Microbiology, will start a new trend in research.

Diversity In Primary Schools Promotes Harmony, Study Finds:

For the first time, children as young as 5 have been shown to understand issues regarding integration and separation. The research confirms that the ethnic composition of primary schools has a direct impact on children’s attitudes towards those in other ethnic groups and on their ability to get on with their peers.

Who’s More Likely To Do Sports? White, Middle Class, And Middle-aged:

The comfortably off, white, and middle aged are the most likely to participate in sporting activities, reveals a 10 year study published ahead of print in the British Journal of Sports Medicine.

Older People May Need Less Sleep, Study Finds:

Along with all the other changes that come with age, healthy older people also lose some capacity for sleep, according to a new report published online on July 24th in Current Biology. When asked to stay in bed for 16 hours in the dark each day for several days, younger people get an average of 9 hours of shuteye compared to 7.5 for older people, the researchers report.

Frequent Family Meals Might Reduce Teen Substance Use:

Parents who have regular meals with their adolescent children might help lessen the chances they will start drinking or smoking later in their teen years, according to new research.

Energy Drinks Linked To Risk-taking Behaviors Among College Students:

Over the last decade, energy drinks — such as Red Bull, Monster and Rockstar — have become nearly ubiquitous on college campuses. The global market for these types of drinks currently exceeds $3 billion a year and new products are introduced annually.

New Roadside Beautification Concept Studied:

Travel America’s highways or drive down any city street this summer and you’ll probably see them. From small, manicured beds of flowers maintained by community volunteers to extensive landscaping projects along America’s byways, roadside gardens are taking root.