Jumping and gliding rodents: Mitogenomic affinities of Pedetidae and Anomaluridae deduced from an RNA-Seq approach

An RNA-Seq strategy was used to obtain the complete set of protein-coding mitochondrial genes from two rodent taxa. Thanks to the next generation sequencing (NGS) 454 approach, we determined the complete mitochondrial DNA genome from Graphiurus kelleni (Mammalia: Rodentia: Gliridae) and partial mitogenome from Pedetes capensis (Pedetidae), and compared them with published rodent and outgroup mitogenomes. We finished the mitogenome sequencing by a series of amplicons using conserved PCR primers to fill the gaps corresponding to tRNA, rRNA and control regions. Phylogenetic analyses of the mitogenomes suggest a well-supported rodent phylogeny in agreement with nuclear gene trees. Pedetes groups with Anomalurus into the clade Anomaluromorpha, while Graphiurus branches within the squirrel-related clade. Moreover, Pedetes + Anomalurus branch with Castor into the mouse-related clade. Our study demonstrates the utility of NGS for obtaining new mitochondrial genomes as well as the importance of choosing adequate models of sequence evolution to infer the phylogeny of rodents.     

Dealing with uncertain absences in habitat modelling: a case study of a rare ground-dwelling parrot

In the development of a species distribution model based on regression techniques such as generalized linear or additive modelling (GLM/GAM), a basic assumption is that records of species presence and absence are real. However, a common concern in many studies examining species distributions is that absences cannot be inferred with certainty. This is particularly the case where the species is rare, difficult to detect and/or does not occupy all available habitat considered suitable. The western ground parrot ( Pezoporus wallicus flaviventris ) of southern Western Australia, Australia, is a case in point, as not only is it rare and difficult to detect, but it is also unlikely to occupy all available suitable habitat. A recent survey of ground parrots provided the opportunity to develop a predictive distribution model. As the data were susceptible to false absences, these were replaced with randomly selected 'pseudo' absences and modelled using GLM. As a comparison, presence-only information was modelled using a relatively new approach, MAXENT, a machine-learning technique that has been shown to perform comparatively well. The predictive performance of both models, as assessed by the receiver operating characteristic plot (ROC) was high (AUC > 0.8), with MAXENT performing only marginally better than the GLM. These approaches both indicated that the ground parrot prefers areas relatively high in altitude, distant from rivers, gently sloping to level habitat, with an intermediate cover of vegetation and where there is a mosaic of vegetation ages. In this case, the use of presence-only information resulted in the identification of important environmental attributes defining the occurrence of the ground parrot, but additional factors that account for the inability of the bird to occupy all suitable habitat should be a component of model refinement.     

Multimodel inference in ecology and evolution: challenges and solutions

Information theoretic approaches and model averaging are increasing in popularity, but this approach can be difficult to apply to the realistic, complex models that typify many ecological and evolutionary analyses. This is especially true for those researchers without a formal background in information theory. Here, we highlight a number of practical obstacles to model averaging complex models. Although not meant to be an exhaustive review, we identify several important issues with tentative solutions where they exist (e.g. dealing with collinearity amongst predictors; how to compute model-averaged parameters) and highlight areas for future research where solutions are not clear (e.g. when to use random intercepts or slopes; which information criteria to use when random factors are involved). We also provide a worked example of a mixed model analysis of inbreeding depression in a wild population. By providing an overview of these issues, we hope that this approach will become more accessible to those investigating any process where multiple variables impact an evolutionary or ecological response.     

Does phylogeny matter? Assessing the impact of phylogenetic information in ecological meta‐analysis

Meta-analysis is increasingly used in ecology and evolutionary biology. Yet, in these fields this technique has an important limitation: phylogenetic non-independence exists among taxa, violating the statistical assumptions underlying traditional meta-analytic models. Recently, meta-analytical techniques incorporating phylogenetic information have been developed to address this issue. However, no syntheses have evaluated how often including phylogenetic information changes meta-analytic results. To address this gap, we built phylogenies for and re-analysed 30 published meta-analyses, comparing results for traditional vs. phylogenetic approaches and assessing which characteristics of phylogenies best explained changes in meta-analytic results and relative model fit. Accounting for phylogeny significantly changed estimates of the overall pooled effect size in 47% of datasets for fixed-effects analyses and 7% of datasets for random-effects analyses. Accounting for phylogeny also changed whether those effect sizes were significantly different from zero in 23 and 40% of our datasets (for fixed- and random-effects models, respectively). Across datasets, decreases in pooled effect size magnitudes after incorporating phylogenetic information were associated with larger phylogenies and those with stronger phylogenetic signal. We conclude that incorporating phylogenetic information in ecological meta-analyses is important, and we provide practical recommendations for doing so.     

The response of the pediatric head to impacts onto a rigid surface

The study of pediatric head injury relies heavily on the use of finite element models and child anthropomorphic test devices (ATDs). However, these tools, in the context of pediatric head injury, have yet to be validated due to a paucity of pediatric head response data. The goal of this study is to investigate the response and injury tolerance of the pediatric head to impact.Twelve pediatric heads were impacted in a series of drop tests. The heads were dropped onto five impact locations (forehead, occiput, vertex and right and left parietal) from drop heights of 15 and 30 cm. The head could freely fall without rotation onto a flat 19 mm thick platen. The impact force was measured using a 3-axis piezoelectric load cell attached to the platen.Age and drop height were found to be significant factors in the impact response of the pediatric head. The head acceleration (14%–15 cm; 103–30 cm), Head Injury Criterion (HIC) (253%–15 cm; 154%–30 cm) and impact stiffness (5800%–15 cm; 3755%–30 cm) when averaged across all impact locations increased with age from 33 weeks gestation to 16 years, while the pulse duration (66%–15 cm; 53%–30 cm) decreased with age. Increases in head acceleration, HIC and impact stiffness were also observed with increased drop height, while pulse duration decreased with increased drop height.One important observation was that three of the four cadaveric heads between the ages of 5-months and 22-months sustained fractures from the 15 cm and 30 cm drop heights. The 5-month-old sustained a right parietal linear fracture while the 11- and 22-month-old sustained diastatic linear fractures.     

ATPase and Protease Domain Movements in the Bacterial AAA+ Protease FtsH Are Driven by Thermal Fluctuations

AAA+ proteases are essential players in cellular pathways of protein degradation. Elucidating their conformational behavior is key for understanding their reaction mechanism and, importantly, for elaborating our understanding of mutation-induced protease deficiencies. Here, we study the structural dynamics of the Thermotoga maritima AAA+ hexameric ring metalloprotease FtsH (TmFtsH). Using a single-molecule Förster resonance energy transfer approach to monitor ATPase and protease inter-domain conformational changes in real time, we show that TmFtsH—even in the absence of nucleotide—is a highly dynamic protease undergoing sequential transitions between five states on the second timescale. Addition of ATP does not influence the number of states or change the timescale of domain motions but affects the state occupancy distribution leading to an inter-domain compaction. These findings suggest that thermal energy, but not chemical energy, provides the major driving force for conformational switching, while ATP, through a state reequilibration, introduces directionality into this process. The TmFtsH A359V mutation, a homolog of the human pathogenic A510V mutation of paraplegin (SPG7) causing hereditary spastic paraplegia, does not affect the dynamic behavior of the protease but impairs the ATP-coupled domain compaction and, thus, may account for protease malfunctioning and pathogenesis in hereditary spastic paraplegia.     

Describing size-related mortality and size distribution by nonparametric estimation and model selection using the Akaike Bayesian Information Criterion

When we calculate mortality along a gradient such as size, dividing into size classes and calculating rates for every class often involves a trade-off: fine class intervals produce fluctuating rates along the gradient, whereas broad ones may miss some trends within an interval. The same trade-off occurs when we want to illustrate size distribution by a histogram. This paper introduces nonparametric methods, published in a statistical journal, into forest ecology, in which the fine-class strategy is used in an extreme way: (1) a smoothly changing pattern is approximated by a fine step function, (2) the goodness-of-fit to the data and the smoothness along the gradient are formulated as a weighting sum within a Bayesian framework, (3) the Akaike Bayesian Information Criterion (ABIC) selects the weighting system that most appropriately balances the two demands, and (4) the values of the step function are optimized by the maximum likelihood method. The nonparametric estimates enable us to represent various patterns visually and, unlike parametric modeling, calculations do not demand the determination of a functional form. Mortality and size distribution analyses were conducted on 12-year forest tree monitoring data from a 4 ha permanent plot in an old-growth warm–temperate evergreen broad-leaved forest in Japan. From trees of 11 evergreen species with a diameter at breast height (DBH) greater than 5 cm, we found three types of trend with increasing DBH: decreasing, ladle-shaped and constant mortality. These patterns reflect variations in life history particular to each species.     

Plant morphometric traits and climate gradients in northern China: a meta-analysis using quadrat and flora data

Background and Aims

The collection of field data on plant traits is time consuming and this makes it difficult to examine changing patterns of traits along large-scale climate gradients. The present study tests whether trait information derived from regional floras can be used in conjunction with pre-existing quadrat data on species presence to derive meaningful relationships between specific morphometric traits and climate.

Methods

Quadrat records were obtained for 867 species in 404 sites from northern China (38–49°N, 82–132°E) together with information on the presence/absence of key traits from floras. Bioclimate parameters for each site were calculated using the BIOME3 model. Principal component analysis and correlation analysis were conducted to determine the most important climate factors. The Akaike Information Criterion was used to select the best relationship between each trait and climate. Canonical correspondence analysis was used to explore the relationships between climate and trait occurrence.

Key Results

The changing abundance of life form, leaf type, phenology, photosynthetic pathway, leaf size and several other morphometric traits are determined by gradients in plant-available moisture (as measured by the ratio of actual to potential evapotranspiration: α), growing-season temperature (as measured by growing degree-days on a 0 ° base: GDD₀) or a combination of these. Different plant functional types (PFTs, as defined by life form, leaf type and phenology) reach maximum abundance in distinct areas of this climate space: for example, evergreen trees occur in the coldest, wettest environments (GDD₀ < 2500 °Cd, α > 0·38), and deciduous scale-leaved trees occur in drier, warmer environments than deciduous broad-leaved trees. Most leaf-level traits show similar relationships with climate independently of PFT: for example, leaf size in all PFTs increases as the environment becomes wetter and cooler. However, some traits (e.g. petiole length) display different relationships with climate in different PFTs.

Conclusions

Based on presence/absence species data and flora-based trait assignments, the present study demonstrates ecologically plausible trends in the occurrence of key plant traits along climate gradients in northern China. Life form, leaf type, phenology, photosynthetic pathway, leaf size and other key traits reflect climate. The success of these analyses opens the possibility of using quadrat- and flora-based trait analyses to examine climate–trait relationships in other regions of the world.     

Independent effects of song quality and experience with photostimulation on expression of the immediate,early gene ZENK (EGR‐1) in the auditory telencephalon of female European starlings

Age influences behavioral decisions such as reproductive timing and effort. In photoperiodic species, such age effects may be mediated, in part, by the individual's age‐accrued experience with photostimulation. In female European starlings (Sturnus vulgaris) that do not differ in age, experimental manipulation of photostimulation experience (photoexperience) affects hypothalamic, pituitary, and gonadal activity associated with reproductive development. Does photoexperience also affect activity in forebrain regions involved in processing a social cue, the song of males, which can influence mate choice and reproductive timing in females? Female starlings prefer long songs over short songs in a mate‐choice context, and, like that in other songbird species, their auditory telencephalon plays a major role in processing these signals. We manipulated the photoexperience of female starlings, photostimulated them, briefly exposed them to either long or short songs, and quantified the expression of the immediate‐early gene ZENK (EGR‐1) in the caudomedial nidopallium as a measure of activity in the auditory telencephalon. Using an information theoretic approach, we found higher ZENK immunoreactivity in females with prior photostimulation experience than in females experiencing photostimulation for the first time. We also found that long songs elicited greater ZENK immunoreactivity than short songs did. We did not find an effect of the interaction between photoexperience and song length, suggesting that photoexperience does not affect forebrain ZENK‐responsiveness to song quality. Thus, photoexperience affects activity in an area of the forebrain that processes social signals, an effect that we hypothesize mediates, in part, the effects of age on reproductive decisions in photoperiodic songbirds. © 2009 Wiley Periodicals, Inc. Develop Neurobiol 2009