A regional interpretation of rules and good practice for greenhouse accounting : Northern Australian savanna systems

Land-use change, particularly clearing of forests for agriculture, has contributed significantly to the observed rise in atmospheric carbon dioxide concentration. Concern about the impacts on climate has led to efforts to monitor and curtail the rapid increase in concentrations of carbon dioxide and other greenhouse gases in the atmosphere. Internationally, much of the current focus is on the Kyoto Protocol to the United Nations Framework Convention on Climate Change (UNFCCC). Although electing to not ratify the Protocol, Australia, as a party to the UNFCCC, reports on national greenhouse gas emissions, trends in emissions and abatement measures. In this paper we review the complex accounting rules for human activities affecting greenhouse gas fluxes in the terrestrial biosphere and explore implications and potential opportunities for managing carbon in the savanna ecosystems of northern Australia. Savannas in Australia are managed for grazing as well as for cultural and environmental values against a background of extreme climate variability and disturbance, notably fire. Methane from livestock and non-CO2 emissions from burning are important components of the total greenhouse gas emissions associated with management of savannas. International developments in carbon accounting for the terrestrial biosphere bring a requirement for better attribution of change in carbon stocks and more detailed and spatially explicit data on such characteristics of savanna ecosystems as fire regimes, production and type of fuel for burning, drivers of woody encroachment, rates of woody regrowth, stocking rates and grazing impacts. The benefits of improved biophysical information and of understanding the impacts on ecosystem function of natural factors and management options will extend beyond greenhouse accounting to better land management for multiple objectives.

Adaptations to a subterranean environment and longevity revealed by the analysis of mole rat genomes

Subterranean mammals spend their lives in dark, unventilated environments that are rich in carbon dioxide and ammonia and low in oxygen. Many of these animals are also long-lived and exhibit reduced aging-associated diseases, such as neurodegenerative disorders and cancer. We sequenced the genome of the Damaraland mole rat (DMR, Fukomys damarensis) and improved the genome assembly of the naked mole rat (NMR, Heterocephalus glaber). Comparative genome analyses, along with the transcriptomes of related subterranean rodents, revealed candidate molecular adaptations for subterranean life and longevity, including a divergent insulin peptide, expression of oxygen-carrying globins in the brain, prevention of high CO2-induced pain perception, and enhanced ammonia detoxification. Juxtaposition of the genomes of DMR and other more conventional animals with the genome of NMR revealed several truly exceptional NMR features: unusual thermogenesis, an aberrant melatonin system, pain insensitivity, and unique processing of 28S rRNA. Together, these genomes and transcriptomes extend our understanding of subterranean adaptations, stress resistance, and longevity.

Molecular phylogeny, biogeography, and habitat preference evolution of marsupials

Marsupials exhibit great diversity in ecology and morphology. However, compared to their sister group, the placental mammals, our understanding of many aspects of marsupial evolution remains limited. We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species. This tree allows us to analyze the evolution of habitat preference and geographic distributions of marsupial species through time. We found a pattern of mesic-adapted lineages evolving to use more arid and open habitats, which is broadly consistent with regional climate and environmental change. However, contrary to the general trend, several lineages subsequently appear to have reverted from drier to more mesic habitats. Biogeographic reconstructions suggest that current views on the connectivity between Australia and New Guinea/Wallacea during the Miocene and Pliocene need to be revised. The antiquity of several endemic New Guinean clades strongly suggests a substantially older period of connection stretching back to the Middle Miocene, and implies that New Guinea was colonized by multiple clades almost immediately after its principal formation.

KRAB zinc-finger proteins localise to novel KAP1-containing foci that are adjacent to PML nuclear bodies

The KRAB-zinc finger proteins (KRAB-ZFPs) represent a very large, but poorly understood, family of transcriptional regulators in mammals. They are thought to repress transcription via their interaction with KRAB-associated protein 1 (KAP1), which then assembles a complex of chromatin modifiers to lay down histone marks that are associated with inactive chromatin. Studies of KRAB-ZFP/KAP1-mediated gene silencing, using reporter constructs and ectopically expressed proteins, have shown colocalisation of both KAP1 and repressed reporter target genes to domains of constitutive heterochromatin in the nucleus. However, we show here that although KAP1 does indeed become recruited to pericentric heterochromatin during differentiation of mouse embryonic stem (ES) cells, endogenous KRAB-ZFPs do not. Rather, KRAB-ZFPs and KAP1 relocalise to novel nucleoplasmic foci that we have termed KRAB- and KAP1-associated (KAKA) foci. HP1s can also concentrate in these foci and there is a close spatial relationship between KAKA nuclear foci and PML nuclear bodies. Finally, we reveal differential requirements for the recruitment of KAP1 to pericentric heterochromatin and KAKA foci, and suggest that KAKA foci may contain sumoylated KAP1 - the form of the protein that is active in transcriptional repression.

A convolutional neural network for automatic analysis of aerial imagery

This paper introduces a new method to automate the detection of marine species in aerial imagery using a Machine Learning approach. Our proposed system has at its core, a convolutional neural network. We compare this trainable classifier to a handcrafted classifier based on color features, entropy and shape analysis. Experiments demonstrate that the convolutional neural network outperforms the handcrafted solution. We also introduce a negative training example-selection method for situations where the original training set consists of a collection of labeled images in which the objects of interest (positive examples) have been marked by a bounding box. We show that picking random rectangles from the background is not necessarily the best way to generate useful negative examples with respect to learning.

Levels and trends of PBDEs and HBCDs in the global environment : status at the end of 2012

In this paper, we have compiled and reviewed the most recent literature, published from January2010 to December 2012, relating to the human exposure, environmental distribution, behaviour, fate and concentration time trends of polybrominated diphenyl ether (PBDE) and hexabromocyclododecane (HBCD) flame retardants, in order to establish their current trends and priorities for future study. Due to the large volume of literature included, we have provided full detail of the reviewed studies as Electronic Supplementary Information and here summarise the most relevant findings. Decreasing time trends for penta-mix PBDE congeners were seen for soils in northern Europe, sewage sludge in Sweden and the USA, carp from a US river, trout from three of the Great Lakes and in Arctic and UK marine mammals and many birds, but increasing time trends continue in Arctic polar bears and some birds at high trophic levels in northern Europe. This is a result of the time delay inherent in long-range atmospheric transport processes. In general, concentrations of BDE209 (the major component of the deca-mix PBDE product) are continuing to increase. Of major concern is the possible/likely debromination of the large reservoir of BDE209 in soils and sediments worldwide, to yield lower brominated congeners which are both more mobile and more toxic, and we have compiled the most recent evidence for the occurrence of this degradation process. Numerous studies reported here reinforce the importance o f this future concern. Time trends for HBCDs are mixed, with both increases and decreases evident in different matrices and locations and, notably, with increasing occurrence in birds of prey.

An organization of visual and auditory fear conditioning in the lateral amygdala

Pavlovian fear conditioning is an evolutionary conserved and extensively studied form of associative learning and memory. In mammals, the lateral amygdala (LA) is an essential locus for Pavlovian fear learning and memory. Despite significant progress unraveling the cellular mechanisms responsible for fear conditioning, very little is known about the anatomical organization of neurons encoding fear conditioning in the LA. One key question is how fear conditioning to different sensory stimuli is organized in LA neuronal ensembles. Here we show that Pavlovian fear conditioning, formed through either the auditory or visual sensory modality, activates a similar density of LA neurons expressing a learning-induced phosphorylated extracellular signal-regulated kinase (p-ERK1/2). While the size of the neuron population specific to either memory was similar, the anatomical distribution differed. Several discrete sites in the LA contained a small but significant number of p-ERK1/2-expressing neurons specific to either sensory modality. The sites were anatomically localized to different levels of the longitudinal plane and were independent of both memory strength and the relative size of the activated neuronal population, suggesting some portion of the memory trace for auditory and visually cued fear conditioning is allocated differently in the LA. Presenting the visual stimulus by itself did not activate the same p-ERK1/2 neuron density or pattern, confirming the novelty of light alone cannot account for the specific pattern of activated neurons after visual fear conditioning. Together, these findings reveal an anatomical distribution of visual and auditory fear conditioning at the level of neuronal ensembles in the LA.

Evolution of New Zealand insects : summary and prospectus for future research

Knowledge on the evolution of the New Zealand insect fauna is reviewed and outstanding questions are highlighted. The New Zealand insect fauna is a composite of old and recent lineages and many spectacular examples of evolutionary processes are evident, including species radiations, hybridisation and unusual adaptations. We discuss the origins and evolution of four prominent communities within the insect fauna: terrestrial lowland insects, alpine insects, aquatic insects and insect communities from offshore islands. Within each of these communities, significant lineages are discussed, and in particular the crucial adaptations that enable these lineages to thrive and diversify. Glacial history has had a dramatic impact on the New Zealand insects, and the effects on different lineages are discussed. The New Zealand insects are unique, yet many are threatened with extinction, and efforts to preserve the fauna are reviewed. Despite the accumulating knowledge, major gaps still exist and these are outlined, as are opportunities to address key questions. The review concludes with a synthesis and a discussion of how systematics, new technologies and integrative approaches have the promise to improve dramatically our understanding of New Zealand insect evolution.

Combustion analysis of microalgae methyl ester in a common rail direct injection diesel engine

In this study, the biodiesel properties and effects of blends of oil methyl ester petroleum diesel on a CI direct injection diesel engine is investigated. Blends were obtained from the marine dinoflagellate Crypthecodinium cohnii and waste cooking oil. The experiment was conducted using a four-cylinder, turbo-charged common rail direct injection diesel engine at four loads (25%, 50%, 75% and 100%). Three blends (10%, 20% and 50%) of microalgae oil methyl ester and a 20% blend of waste cooking oil methyl ester were compared to petroleum diesel. To establish suitability of the fuels for a CI engine, the effects of the three microalgae fuel blends at different engine loads were assessed by measuring engine performance, i.e. mean effective pressure (IMEP), brake mean effective pressure (BMEP), in cylinder pressure, maximum pressure rise rate, brake-specific fuel consumption (BSFC), brake thermal efficiency (BTE), heat release rate and gaseous emissions (NO, NOx,and unburned hydrocarbons (UHC)). Results were then compared to engine performance characteristics for operation with a 20% waste cooking oil/petroleum diesel blend and petroleum diesel. In addition, physical and chemical properties of the fuels were measured. Use of microalgae methyl ester reduced the instantaneous cylinder pressure and engine output torque, when compared to that of petroleum diesel, by a maximum of 4.5% at 50% blend at full throttle. The lower calorific value of the microalgae oil methyl ester blends increased the BSFC, which ultimately reduced the BTE by up to 4% at higher loads. Minor reductions of IMEP and BMEP were recorded for both the microalgae and the waste cooking oil methyl ester blends at low loads, with a maximum of 7% reduction at 75% load compared to petroleum diesel. Furthermore, compared to petroleum diesel, gaseous emissions of NO and NOx, increased for operations with biodiesel blends. At full load, NO and NOx emissions increased by 22% when 50% microalgae blends were used. Petroleum diesel and a 20% blend of waste cooking oil methyl ester had emissions of UHC that were similar, but those of microalgae oil methyl ester/petroleum diesel blends were reduced by at least 50% for all blends and engine conditions. The tested microalgae methyl esters contain some long-chain, polyunsaturated fatty acid methyl esters (FAMEs) (C22:5 and C22:6) not commonly found in terrestrial-crop-derived biodiesels yet all fuel properties were satisfied or were very close to the ASTM 6751-12 and EN14214 standards. Therefore, Crypthecodinium cohnii- derived microalgae biodiesel/petroleum blends of up to 50% are projected to meet all fuel property standards and, engine performance and emission results from this study clearly show its suitability for regular use in diesel engines.

Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide

Aboveground–belowground interactions exert critical controls on the composition and function of terrestrial ecosystems, yet the fundamental relationships between plant diversity and soil microbial diversity remain elusive. Theory predicts predominantly positive associations but tests within single sites have shown variable relationships, and associations between plant and microbial diversity across broad spatial scales remain largely unexplored. We compared the diversity of plant, bacterial, archaeal and fungal communities in one hundred and forty-five 1 m2 plots across 25 temperate grassland sites from four continents. Across sites, the plant alpha diversity patterns were poorly related to those observed for any soil microbial group. However, plant beta diversity (compositional dissimilarity between sites) was significantly correlated with the beta diversity of bacterial and fungal communities, even after controlling for environmental factors. Thus, across a global range of temperate grasslands, plant diversity can predict patterns in the composition of soil microbial communities, but not patterns in alpha diversity.

Is lek breeding rare in bats?

Bats (Mammalia: Chiroptera) are among the most successful mammals and likely display the widest range of mating systems within the Class. One mating system that is underrepresented in the Chiroptera is lek breeding, which is characterized by aggregations of sexually displaying males that are visited by receptive females who appraise male displays and actively choose mates, yet receive no direct benefits such as assistance in parenting. Leks are thought to form when males can defend neither resources nor females, making it more economical to establish small breeding territories and self-advertise through sexual displays. Lekking is rare in mammals, and it has been suggested that a lack in the mobility required by females to economically seek out aggregations of sexually displaying males may explain this rarity. Bats, like birds, do not suffer reduced mobility and yet out of over a thousand described species, only one has been confirmed to breed in leks. We examine the rarity of lekking in bats by providing an overview on the current state of knowledge of their mating systems and discuss the ecological and social determinants for the observed trends, contrasted with the prerequisites of lek-breeding behaviour. We use the breeding behaviour of New Zealand's lesser short-tailed bat Mystacina tuberculata, which is believed to be a lek breeder, as a case study for the examination of potential lekking behaviour in bats, and highlight the importance of such research for the development of effective conservation strategies.

The presence of ultrasonic harmonics in the calls of the rifleman (Acanthisitta chloris)

Ultrasonic vocalisations (frequencies > 20 kHz) have been extensively studied in the context of echolocation by bats and other mammals (Sales & Pye 1974; Wilson & Hare 2004). Ultrasonic calls have also been recorded from birds, including the blue-throated hummingbird ( Lampornis clemenciae ) (Pytte et al. 2004), where it was first thought that individuals made use of high pitch calls to avoid masking by background noise in a visually obscured environment. Similarly, city-dwelling great tits ( Parus major ) use song with a higher minimum frequency (although not ultrasonic) compared to woodland birds to communicate with conspecifics to avoid the predominantly low-frequency background noise in the city (Slabbekorn & Peet 2003). The theory that birds use ultrasound to avoid noise masking was discarded when it was discovered that there was no corresponding auditory brainstem response (i.e. sensory perception) to the ultrasonic calls in the hummingbirds producing those calls.

Kiwi Forego Vision in the Guidance of Their Nocturnal Activities

Background In vision, there is a trade-off between sensitivity and resolution, and any eye which maximises information gain at low light levels needs to be large. This imposes exacting constraints upon vision in nocturnal flying birds. Eyes are essentially heavy, fluid-filled chambers, and in flying birds their increased size is countered by selection for both reduced body mass and the distribution of mass towards the body core. Freed from these mass constraints, it would be predicted that in flightless birds nocturnality should favour the evolution of large eyes and reliance upon visual cues for the guidance of activity. Methodology/Principal Findings We show that in Kiwi (Apterygidae), flightlessness and nocturnality have, in fact, resulted in the opposite outcome. Kiwi show minimal reliance upon vision indicated by eye structure, visual field topography, and brain structures, and increased reliance upon tactile and olfactory information. Conclusions/Significance This lack of reliance upon vision and increased reliance upon tactile and olfactory information in Kiwi is markedly similar to the situation in nocturnal mammals that exploit the forest floor. That Kiwi and mammals evolved to exploit these habitats quite independently provides evidence for convergent evolution in their sensory capacities that are tuned to a common set of perceptual challenges found in forest floor habitats at night and which cannot be met by the vertebrate visual system. We propose that the Kiwi visual system has undergone adaptive regressive evolution driven by the trade-off between the relatively low rate of gain of visual information that is possible at low light levels, and the metabolic costs of extracting that information.

The conservation status of New Zealand bats, 2009

The New Zealand Threat Classification System (NZTCS) is a national system used to assess the risk of extinction faced by New Zealand plants, animals and fungi. The system is specifically designed to be relevant to New Zealand's unusual ecological and geographic conditions. We undertook a re-evaluation of the status of seven bat taxa based on our knowledge of New Zealand bats using revised NZTCS criteria. Five taxa were listed as Threatened or At Risk: one as Nationally Critical (long-tailed bat Chalinolobus tuberculatus ‘South Island’), one as Nationally Endangered (southern lesser short-tailed bat Mystacina tuberculata tuberculata), two as Nationally Vulnerable (long-tailed bat ‘North Island’ and northern lesser short-tailed bat M. t. aupourica) and one as Declining (central lesser short-tailed bat M. t. rhyacobia). One taxon was assessed as Data Deficient (greater short-tailed bat M. robusta) and one (little red flying fox Pteropus scapulatus) as Vagrant. We suspect declines result primarily from predation and competition from introduced mammals, habitat degradation, and disturbance.

Landform characterization using geophysics—Recent advances, applications, and emerging tools

This paper presents an overview of the strengths and limitations of existing and emerging geophysical tools for landform studies. The objectives are to discuss recent technical developments and to provide a review of relevant recent literature, with a focus on propagating field methods with terrestrial applications. For various methods in this category, including ground-penetrating radar (GPR), electrical resistivity (ER), seismics, and electromagnetic (EM) induction, the technical backgrounds are introduced, followed by section on novel developments relevant to landform characterization. For several decades, GPR has been popular for characterization of the shallow subsurface and in particular sedimentary systems. Novel developments in GPR include the use of multi-offset systems to improve signal-to-noise ratios and data collection efficiency, amongst others, and the increased use of 3D data. Multi-electrode ER systems have become popular in recent years as they allow for relatively fast and detailed mapping. Novel developments include time-lapse monitoring of dynamic processes as well as the use of capacitively-coupled systems for fast, non-invasive surveys. EM induction methods are especially popular for fast mapping of spatial variation, but can also be used to obtain information on the vertical variation in subsurface electrical conductivity. In recent years several examples of the use of plane wave EM for characterization of landforms have been published. Seismic methods for landform characterization include seismic reflection and refraction techniques and the use of surface waves. A recent development is the use of passive sensing approaches. The use of multiple geophysical methods, which can benefit from the sensitivity to different subsurface parameters, is becoming more common. Strategies for coupled and joint inversion of complementary datasets will, once more widely available, benefit the geophysical study of landforms.Three cases studies are presented on the use of electrical and GPR methods for characterization of landforms in the range of meters to 100. s of meters in dimension. In a study of polygonal patterned ground in the Saginaw Lowlands, Michigan, USA, electrical resistivity tomography was used to characterize differences in subsurface texture and water content associated with polygon-swale topography. Also, a sand-filled thermokarst feature was identified using electrical resistivity data. The second example is on the use of constant spread traversing (CST) for characterization of large-scale glaciotectonic deformation in the Ludington Ridge, Michigan. Multiple CST surveys parallel to an ~. 60. m high cliff, where broad (~. 100. m) synclines and narrow clay-rich anticlines are visible, illustrated that at least one of the narrow structures extended inland. A third case study discusses internal structures of an eolian dune on a coastal spit in New Zealand. Both 35 and 200. MHz GPR data, which clearly identified a paleosol and internal sedimentary structures of the dune, were used to improve understanding of the development of the dune, which may shed light on paleo-wind directions.