Copy number variation and transposable elements feature in recent, ongoing adaptation at the Cyp6g1 locus

The increased transcription of the Cyp6g1 gene of Drosophila melanogaster, and consequent resistance to insecticides such as DDT, is a widely cited example of adaptation mediated by cis-regulatory change. A fragment of an Accord transposable element inserted upstream of the Cyp6g1 gene is causally associated with resistance and has spread to high frequencies in populations around the world since the 1940s. Here we report the existence of a natural allelic series at this locus of D. melanogaster, involving copy number variation of Cyp6g1, and two additional transposable element insertions (a P and an HMS-Beagle). We provide evidence that this genetic variation underpins phenotypic variation, as the more derived the allele, the greater the level of DDT resistance. Tracking the spatial and temporal patterns of allele frequency changes indicates that the multiple steps of the allelic series are adaptive. Further, a DDT association study shows that the most resistant allele, Cyp6g1-[BP], is greatly enriched in the top 5% of the phenotypic distribution and accounts for ~16% of the underlying phenotypic variation in resistance to DDT. In contrast, copy number variation for another candidate resistance gene, Cyp12d1, is not associated with resistance. Thus the Cyp6g1 locus is a major contributor to DDT resistance in field populations, and evolution at this locus features multiple adaptive steps occurring in rapid succession.

Disturbance and the role of refuges in mediterranean climate streams

Refuges protect plant and animal populations from disturbance. Knowledge of refuges from disturbance in mediterranean climate rivers (med-rivers) has increased the last decade. We review disturbance processes and their relationship to refuges in streams in mediterranean climate regions (med-regions). Med-river fauna show high endemicity and their populations are often exposed to disturbance; hence the critical importance of refuges during (both seasonal and supraseasonal) disturbances. Disturbance pressures are increasing in med-regions, in particular from climatic change, salinisation, sedimentation, water extraction, hydropower generation, supraseasonal drought, and wildfire. Med-rivers show annual cycles of constrained precipitation and predictable seasonal drying, causing the biota to depend on seasonal refuges, in particular, those that are spatially predictable. This creates a spatial and temporal mosaic of inundation that determines habitat extent and refuge function. Refuges of sufficient size and duration to maintain populations, such as perennially flowing reaches, sustain biodiversity and may harbour relict populations, particularly during increasing aridification, where little other suitable habitat remains in landscapes. Therefore, disturbances that threaten perennial flows potentially cascade disproportionately to reduce regional scale biodiversity in med-regions. Conservation approaches for med-river systems need to conserve both refuges and refuge connectivity, reduce the impact of anthropogenic disturbances and sustain predictable, seasonal flow patterns.

A comparison of the seasonal movements of tiger sharks and green turtles provides insight into their predator-prey relationship

During the reproductive season, sea turtles use a restricted area in the vicinity of their nesting beaches, making them vulnerable to predation. At Raine Island (Australia), the highest density green turtle Chelonia mydas rookery in the world, tiger sharks Galeocerdo cuvier have been observed to feed on green turtles, and it has been suggested that they may specialise on such air-breathing prey. However there is little information with which to examine this hypothesis. We compared the spatial and temporal components of movement behaviour of these two potentially interacting species in order to provide insight into the predator-prey relationship. Specifically, we tested the hypothesis that tiger shark movements are more concentrated at Raine Island during the green turtle nesting season than outside the turtle nesting season when turtles are not concentrated at Raine Island. Turtles showed area-restricted search behaviour around Raine Island for ~3–4 months during the nesting period (November–February). This was followed by direct movement (transit) to putative foraging grounds mostly in the Torres Straight where they switched to area-restricted search mode again, and remained resident for the remainder of the deployment (53–304 days). In contrast, tiger sharks displayed high spatial and temporal variation in movement behaviour which was not closely linked to the movement behaviour of green turtles or recognised turtle foraging grounds. On average, tiger sharks were concentrated around Raine Island throughout the year. While information on diet is required to determine whether tiger sharks are turtle specialists our results support the hypothesis that they target this predictable and plentiful prey during turtle nesting season, but they might not focus on this less predictable food source outside the nesting season.

Limited population structure, genetic drift and bottlenecks characterise an endangered bird species in a dynamic, fire-prone ecosystem

Fire is a major disturbance process in many ecosystems world-wide, resulting in spatially and temporally dynamic landscapes. For populations occupying such environments, fire-induced landscape change is likely to influence population processes, and genetic patterns and structure among populations. The Mallee Emu-wren Stipiturus mallee is an endangered passerine whose global distribution is confined to fire-prone, semi-arid mallee shrublands in south-eastern Australia. This species, with poor capacity for dispersal, has undergone a precipitous reduction in distribution and numbers in recent decades. We used genetic analyses of 11 length-variable, nuclear loci to examine population structure and processes within this species, across its global range. Populations of the Mallee Emu-wren exhibited a low to moderate level of genetic diversity, and evidence of bottlenecks and genetic drift. Bayesian clustering methods revealed weak genetic population structure across the species' range. The direct effects of large fires, together with associated changes in the spatial and temporal patterns of suitable habitat, have the potential to cause population bottlenecks, serial local extinctions and subsequent recolonisation, all of which may interact to erode and homogenise genetic diversity in this species. Movement among temporally and spatially shifting habitat, appears to maintain long-term genetic connectivity. A plausible explanation for the observed genetic patterns is that, following extensive fires, recolonisation exceeds in-situ survival as the primary driver of population recovery in this species. These findings suggest that dynamic, fire-dominated landscapes can drive genetic homogenisation of populations of species with low-mobility and specialised habitat that otherwise would be expected to show strongly structured populations. Such effects must be considered when formulating management actions to conserve species in fire-prone systems.

Checked baggage: spatial negotiations in contemporary air travel

This paper examines the act of undertaking international air travel and analyses how it forces individuals to consider a range of ideas as a result of dislocation and attempts to re-align themselves within spatial, material and biological structures. In order to balance the shifts between spatial and material experiences, travellers employ imaginative and perceptive procedures, gaining knowledge through experience. At the intersection of participatory and spatial boundaries through the lens of multi-disciplinary literature, this paper explores how practices of individuals within international air travel provides alternative modes of thinking and navigating through personal, cultural and globalised public spaces.

Multitasking, working memory and remembering intentions

Multitasking refers to the performance of a range of tasks that have to be completed within a limited time period. it differs from dual task paradigms in that tasks are performed not in parallel, but by interleaving, switching from one to the other. it differs also from task switching paradigms in that the time scale is very much longer, multiple different tasks are involved, and most tasks have a clear end point. Multitasking has been studied extensively with particular sets of experts such as in aviation and in the military, and impairments of multitasking performance have been studied in patients with frontal lobe lesions. Much less is known as to how multitasking is achieved in healthy adults who have not had specific training in the necessary skills. This paper will provide a brief review of research on everyday multitasking, and summarise the results of some recent experiments on simulated everyday tasks chosen to require advance and on-line planning, retrospective memory, prospective memory, and visual, spatial and verbal short-term memory.

TMI for urban resilience : measuring and mapping long-term climate change effects on soil moisture

The effect of climate change on the shallow expansive foundation conditions of resident dwellings is costing several hundred billion dollars worldwide. The design and costs of constructing or repairing residential footings is greatly influenced by the degree of ground movement, which is driven by the magnitude of change in soil moisture. The impacts of climate change on urban infrastructure are expected to include accelerated degradation of materials and foundations of buildings and facilities, increased ground movement, changes in ground water affecting the chemical structure of foundations, and fatigue of structures from extreme storm events. Previous research found that residential houses that were built less than five years ago have suffered major cracks and other damage caused by slab movement after record rainfall. The Thornthwaite Moisture Index (TMI) categorises climate on the basis of rainfall, temperature, potential evapotranspiration and the water holding capacity of the soil. Originally TMI was mainly used to map soil moisture conditions for agriculture but soon became a method to predict pavement and foundation changes. Few researchers have developed TMI maps for Australia, but generally, their accuracy is low or unknown, and their use is limited. The aims of this paper are: (1) To produce accurate maps of TMI for the state of Victoria for 100 years (1913 to 2012) in 20 year periods using long-term historical climatic data and advanced spatial statistics methods in GIS, and (2) Analyse the spatial and temporal changes of TMI in Victoria. Preliminary results suggest that a better understanding of climate change through long-term TMI mapping can assist urban planning and guide construction regulations towards the development of cities which are more resilient.

Optimal sensor placement and measurement of wind for water quality studies in urban reservoirs

We collaborate with environmental scientists to study the hydrodynamics and water quality in an urban district, where the surface wind distribution is an essential input but undergoes high spatial and temporal variations due to the complex urban landform created by surrounding buildings. In this work, we study an optimal sensor placement scheme to measure the wind distribution over a large urban reservoir with a limited number of wind sensors. Unlike existing sensor placement solutions that assume Gaussian process of target phenomena, this study measures the wind which inherently exhibits strong non-Gaussian yearly distribution. By leveraging the local monsoon characteristics of wind, we segment a year into different monsoon seasons which follow a unique distribution respectively. We also use computational fluid dynamics to learn the spatial correlation of wind in the presence of surrounding buildings. The output of sensor placement is a set of the most informative locations to deploy the wind sensors, based on the readings of which we can accurately predict the wind over the entire reservoir surface in real time. 10 wind sensors are finally deployed around or on the water surface of an urban reservoir. The in-field measurement results of more than 3 months suggest that the proposed sensor placement and spatial prediction approach provides accurate wind measurement which outperforms the state-of-the-art Gaussian model based or interpolation based approaches.

Dynamics and spatio-temporal variability of environmental factors in Eastern Australia using functional principal component analysis

This paper introduces a new technique in ecology to analyze spatial and temporal variability in environmental variables. By using simple statistics, we explore the relations between abiotic and biotic variables that influence animal distributions. However, spatial and temporal variability in rainfall, a key variable in ecological studies, can cause difficulties to any basic model including time evolution. The study was of a landscape scale (three million square kilometers in eastern Australia), mainly over the period of 19982004. We simultaneously considered qualitative spatial (soil and habitat types) and quantitative temporal (rainfall) variables in a Geographical Information System environment. In addition to some techniques commonly used in ecology, we applied a new method, Functional Principal Component Analysis, which proved to be very suitable for this case, as it explained more than 97% of the total variance of the rainfall data, providing us with substitute variables that are easier to manage and are even able to explain rainfall patterns. The main variable came from a habitat classification that showed strong correlations with rainfall values and soil types. © 2010 World Scientific Publishing Company.

Conservation covenants on private land : issues with measuring and achieving biodiversity outcomes in Australia

Conservation covenants and easements have become essential tools to secure biodiversity outcomes on private land, and to assist in meeting international protection targets. In Australia, the number and spatial area of conservation covenants has grown significantly in the past decade. Yet there has been little research or detailed policy analysis of conservation covenanting in Australia. We sought to determine how conservation covenanting agencies were measuring the biodiversity conservation outcomes achieved on covenanted properties, and factors inhibiting or contributing to measuring these outcomes. In addition, we also investigated the drivers and constraints associated with actually delivering the biodiversity outcomes, drawing on detailed input from covenanting programs. Although all conservation covenanting programs had the broad aim of maintaining or improving biodiversity in their covenants in the long term, the specific stated objectives of conservation covenanting programs varied. Programs undertook monitoring and evaluation in different ways and at different spatial and temporal scales. Thus, it was difficult to determine the extent Australian conservation covenanting agencies were measuring the biodiversity conservation outcomes achieved on covenanted properties on a national scale. Lack of time available to covenantors to undertake management was one of the biggest impediments to achieving biodiversity conservation outcomes. A lack of financial resources and human capital to monitor, knowing what to monitor, inconsistent monitoring methodologies, a lack of benchmark data, and length of time to achieve outcomes were all considered potential barriers to monitoring the biodiversity conservation outcomes of conservation covenants.

Late Permian marine ecosystem collapse began in deeper waters: Evidence from brachiopod diversity and body size changes

Analysis of Permian-Triassic brachiopod diversity and body size changes from different water depths spanning the continental shelf to basinal facies in South China provides insights into the process of environmental deterioration. Comparison of the temporal changes of brachiopod diversity between deepwater and shallow-water facies demonstrates that deepwater brachiopods disappeared earlier than shallow-water brachiopods. This indicates that high environmental stress commenced first in deepwater settings and later extended to shallow waters. This environmental stress is attributed to major volcanic eruptions, which first led to formation of a stratified ocean and a chemocline in the outer shelf and deeper water environments, causing the disappearance of deep marine benthos including brachiopods. The chemocline then rapidly migrated upward and extended to shallow waters, causing widespread mass extinction of shallow marine benthos. We predict that the spatial and temporal patterns of earlier onset of disappearance/extinction and ecological crisis in deeper water ecosystems will be recorded during other episodes of rapid global warming.

Comparing kinematic changes between a finger-tapping task and unconstrained finger flexion-extension task in patients with Parkinson's disease.

Repetitive finger tapping is a well-established clinical test for the evaluation of parkinsonian bradykinesia, but few studies have investigated other finger movement modalities. We compared the kinematic changes (movement rate and amplitude) and response to levodopa during a conventional index finger-thumb-tapping task and an unconstrained index finger flexion-extension task performed at maximal voluntary rate (MVR) for 20 s in 11 individuals with levodopa-responsive Parkinson's disease (OFF and ON) and 10 healthy age-matched controls. Between-task comparisons showed that for all conditions, the initial movement rate was greater for the unconstrained flexion-extension task than the tapping task. Movement rate in the OFF state was slower than in controls for both tasks and normalized in the ON state. The movement amplitude was also reduced for both tasks in OFF and increased in the ON state but did not reach control levels. The rate and amplitude of movement declined significantly for both tasks under all conditions (OFF/ON and controls). The time course of rate decline was comparable for both tasks and was similar in OFF/ON and controls, whereas the tapping task was associated with a greater decline in MA, both in controls and ON, but not OFF. The findings indicate that both finger movement tasks show similar kinematic changes during a 20-s sustained MVR, but that movement amplitude is less well sustained during the tapping task than the unconstrained finger movement task. Both movement rate and amplitude improved with levodopa; however, movement rate was more levodopa responsive than amplitude.

Sensor placement and measurement of wind for water quality studies in urban reservoirs

We study the water quality in an urban district, where the surface wind distribution is an essential input but undergoes high spatial and temporal variations due to the impact of surrounding buildings. In this work, we develop an optimal sensor placement scheme to measure the wind distribution over a large urban reservoir using a limited number of wind sensors. Unlike existing solutions that assume Gaussian process of target phenomena, this study measures the wind that inherently exhibits strong non-Gaussian yearly distribution. By leveraging the local monsoon characteristics of wind, we segment a year into different monsoon seasons that follow a unique distribution respectively. We also use computational fluid dynamics to learn the spatial correlation of wind. The output of sensor placement is a set of the most informative locations to deploy the wind sensors, based on the readings of which we can accurately predict the wind over the entire reservoir in real time. Ten wind sensors are deployed. The in-field measurement results of more than 3 months suggest that the proposed sensor placement and spatial prediction scheme provides accurate wind measurement that outperforms the state-of-the-art Gaussian model based on interpolation-based approaches.

Sexual niche segregation and gender-specific individual specialisation in a highly dimorphic marine mammal

While sexual segregation is expected in highly dimorphic species, the local environment is a major factor driving the degree of resource partitioning within a population. Sexual and individual niche segregation was investigated in the Australian fur seal (Arctocephalus pusillus doriferus), which is a benthic foraging species restricted to the shallow continental shelf region of south-eastern Australia. Tracking data and the isotopic values of plasma, red blood cells and whiskers were combined to document spatial and dietary niche segregation throughout the year. Tracking data indicated that, in winter, males and females overlapped in their foraging habitat. All individuals stayed within central Bass Strait, relatively close (< 220 km) to the breeding colony. Accordingly, both genders exhibited similar plasma and red cell δ13C values. However, males exhibited greater δ13C intra-individual variation along the length of their whisker than females. This suggests that males exploited a greater diversity of foraging habitats throughout the year than their female counterparts, which are restricted in their foraging grounds by the need to regularly return to the breeding colony to suckle their pup. The degree of dietary sexual segregation was also surprisingly low, both sexes exhibiting a great overlap in their δ15N values. Yet, males displayed higher δ15N values than females, suggesting they fed upon a higher proportion of higher trophic level prey. Given that males and females exploit different resources (mainly foraging habitats), the degree of individual specialisation might differ between the sexes. Higher degrees of individual specialisation would be expected in males which exploit a greater range of resources. However, comparable levels of inter-individual variation in δ15N whisker values were found in the sampled males and females, and, surprisingly, all males exhibited similar seasonal and inter-annual variation in their δ13C whisker values, suggesting they all followed the same general dispersion pattern throughout the year.

Foraging strategies and reproductive success in two sympatric seabird species: influence of environmental variability

 This work focused on flexibility in foraging strategies in little penguins and short-tailed shearwaters, which represents an important mechanism enabling them to cope with highly dynamic ecosystems and provides a buffer against spatial and temporal changes in prey availability over the breeding period.