Genetic composition of the Ascension Island green turtle rookery based on mitochondrial DNA : implications for sampling and diversity

In species of conservation concern it is often difficult to be certain that population diversity and structure have been adequately characterised by genetic sampling. Since practical and financial constraints tend to be associated with increasing sample sizes in many conservation genetic studies, it is important to consider the potential for sampling error and bias due to inadequate samples or spatio-temporal structure within populations. We analysed sequence data from the mitochondrial DNA control region in a large sample (n = 245) of green sea turtles Chelonia mydas collected at the globally important rookery of Ascension Island, South Atlantic. We examined genetic diversity and structure among 10 sampling sites, 4 beach clusters and 4 nesting seasons, and evaluated the genetic composition of Ascension against other Atlantic nesting populations, including the well-studied rookery at Tortuguero (Costa Rica). Finally, we used rarefaction and GENESAMP analyses to assess the ability of different sample sizes to provide acceptable genetic representations of a population, using Ascension and Tortuguero as models. On Ascension, we found 13 haplotypes, of which only 3 had been previously observed in the rookery, and 5 previously undescribed. We detected no differentiation among beach clusters or sampling seasons, and only weak differentiation among the 3 primary nesting sites. The increased sample size for Ascension provided higher resolution and statistical power in describing genetic structure among all other known Atlantic rookeries. Our extrapolations showed that a maximum of 18 and 6 haplotypes are expected to occur in Ascension and Tortuguero, respectively, and that current sample sizes are sufficient to describe most of the variation. We recommend using rarefaction and GENESAMP analyses on a rookery-by-rookery basis to evaluate whether a sample set adequately describes mitochondrial DNA diversity, thus strengthening subsequent phylogeographic and mixed stock analyses, and management recommendations for conservation.

Nonnegative Blind Source Separation by Sparse Component Analysis Based on Determinant Measure

The problem of nonnegative blind source separation (NBSS) is addressed in this paper, where both the sources and the mixing matrix are nonnegative. Because many real-world signals are sparse, we deal with NBSS by sparse component analysis. First, a determinant-based sparseness measure, named D-measure, is introduced to gauge the temporal and spatial sparseness of signals. Based on this measure, a new NBSS model is derived, and an iterative sparseness maximization (ISM) approach is proposed to solve this model. In the ISM approach, the NBSS problem can be cast into row-to-row optimizations with respect to the unmixing matrix, and then the quadratic programming (QP) technique is used to optimize each row. Furthermore, we analyze the source identifiability and the computational complexity of the proposed ISM-QP method. The new method requires relatively weak conditions on the sources and the mixing matrix, has high computational efficiency, and is easy to implement. Simulation results demonstrate the effectiveness of our method.

Temporal allocation of foraging effort in female Australian fur seals (Arctocephalus pusillus doriferus)

Across an individual's life, foraging decisions will be affected by multiple intrinsic and extrinsic drivers that act at differing timescales. This study aimed to assess how female Australian fur seals allocated foraging effort and the behavioural changes used to achieve this at three temporal scales: within a day, across a foraging trip and across the final six months of the lactation period. Foraging effort peaked during daylight hours (57% of time diving) with lulls in activity just prior to and after daylight. Dive duration reduced across the day (196 s to 168 s) but this was compensated for by an increase in the vertical travel rate (1500–1600 m•h−1) and a reduction in postdive duration (111–90 s). This suggests physiological constraints (digestive costs) or prey availability may be limiting mean dive durations as a day progresses. During short trips (<2.9 d), effort remained steady at 55% of time diving, whereas, on long trips (>2.9 d) effort increased up to 2–3 d and then decreased. Dive duration decreased at the same rate in short and long trips, respectively, before stabilising (long trips) between 4–5 d. Suggesting that the same processes (digestive costs or prey availability) working at the daily scale may also be present across a trip. Across the lactation period, foraging effort, dive duration and vertical travel rate increased until August, before beginning to decrease. This suggests that as the nutritional demands of the suckling pup and developing foetus increase, female effort increases to accommodate this, providing insight into the potential constraints of maternal investment in this species

Australia’s strategic culture: constraints and opportunities in security policymaking

 This article draws on fourth generation strategic culture debates to show the gap between the rhetoric of Australian defence and the more modest reality. Our analysis shows that these limits derive from tensions between national strategic culture and organizational strategic subcultures. There are serious debates in the nation regarding the preferred course of the Australian military and security policy. This article frames these debates by examining the ‘keepers’ of Australia's national strategic culture, the existence of several competing strategic subcultures, and the importance of norm entrepreneurs in changing defence and national security thinking. Strategic subcultures foster compartmentalization, constraints, and bureaucratic silos that narrow national conceptions of security threats and opportunities, and impinge on the formation of coherent foreign and defence policy in relation to the Asia-Pacific region. This analysis shows that a distinct national strategic culture and organizational strategic subcultures endure beyond individual governments, placing potential limits on Australia's interface with other Asia-Pacific strategic cultures in the future.

Differential temporal expression of milk miRNA during the lactation cycle of the marsupial tammar wallaby (Macropus eugenii)

Lactation is a key aspect of mammalian evolution for adaptation of various reproductive strategies along different mammalian lineages. Marsupials, such as tammar wallaby, adopted a short gestation and a relatively long lactation cycle, the newborn is immature at birth and significant development occurs postnatally during lactation. Continuous changes of tammar milk composition may contribute to development and immune protection of pouch young. Here, in order to address the putative contribution of newly identified secretory milk miRNA in these processes, high throughput sequencing of miRNAs collected from tammar milk at different time points of lactation was conducted. A comparative analysis was performed to find distribution of miRNA in milk and blood serum of lactating wallaby.

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.

Phylogenetic analysis of beak and feather disease virus across a host ring-species complex

Pathogens have been hypothesized to play a major role in host diversity and speciation. Susceptibility of hybrid hosts to pathogens is thought to be a common phenomenon that could promote host population divergence and subsequently speciation. However, few studies have tested for pathogen infection across animal hybrid zones while testing for codivergence of the pathogens in the hybridizing host complex. Over 8 y, we studied natural infection by a rapidly evolving single-strand DNA virus, beak and feather diseases virus (BFDV), which infects parrots, exploiting a host-ring species complex (Platycercus elegans) in Australia. We found that host subspecies and their hybrids varied strikingly in both BFDV prevalence and load: both hybrid and phenotypically intermediate subspecies had lower prevalence and load compared with parental subspecies, while controlling for host age, sex, longitude and latitude, as well as temporal effects. We sequenced viral isolates throughout the range, which revealed patterns of genomic variation analogous to Mayr's ring-species hypothesis, to our knowledge for the first time in any host-pathogen system. Viral phylogeny, geographic location, intraspecific host density, and parrot community diversity and composition did not explain the differences in BFDV prevalence or load between subpopulations. Overall, our analyses suggest that functional host responses to infection, or force of infection, differ between subspecies and hybrids. Our findings highlight the role of host hybridization and clines in altering host-pathogen interactions, dynamics that can have important implications for models of speciation with gene flow, and offer insights into how pathogens may adapt to diverging host populations.

Pan-atlantic analysis of the overlap of a highly migratory species, the leatherback turtle, with pelagic longline fisheries

Large oceanic migrants play important roles in ecosystems, yet many species are of conservation concern as a result of anthropogenic threats, of which incidental capture by fisheries is frequently identified. The last large populations of the leatherback turtle, Dermochelys coriacea, occur in the Atlantic Ocean, but interactions with industrial fisheries could jeopardize recent positive population trends, making bycatch mitigation a priority. Here, we perform the first pan-Atlantic analysis of spatio-temporal distribution of the leatherback turtle and ascertain overlap with longline fishing effort. Data suggest that the Atlantic probably consists of two regional management units: northern and southern (the latter including turtles breeding in South Africa). Although turtles and fisheries show highly diverse distributions, we highlight nine areas of high susceptibility to potential bycatch (four in the northern Atlantic and five in the southern/equatorial Atlantic) that are worthy of further targeted investigation and mitigation. These are reinforced by reports of leatherback bycatch at eight of these sites. International collaborative efforts are needed, especially from nations hosting regions where susceptibility to bycatch is likely to be high within their exclusive economic zone (northern Atlantic: Cape Verde, Gambia, Guinea Bissau, Mauritania, Senegal, Spain, USA and Western Sahara; southern Atlantic: Angola, Brazil, Namibia and UK) and from nations fishing in these high-susceptibility areas, including those located in international waters.

Monitoring and analysis of respiratory patterns using microwave doppler radar

 Noncontact detection characteristic of Doppler radar provides an unobtrusive means of respiration detection and monitoring. This avoids additional preparations, such as physical sensor attachment or special clothing, which can be useful for certain healthcare applications. Furthermore, robustness of Doppler radar against environmental factors, such as light, ambient temperature, interference from other signals occupying the same bandwidth, fading effects, reduce environmental constraints and strengthens the possibility of employing Doppler radar in long-term respiration detection, and monitoring applications such as sleep studies. This paper presents an evaluation in the of use of microwave Doppler radar for capturing different dynamics of breathing patterns in addition to the respiration rate. Although finding the respiration rate is essential, identifying abnormal breathing patterns in real-time could be used to gain further insights into respiratory disorders and refine diagnostic procedures. Several known breathing disorders were professionally role played and captured in a real-time laboratory environment using a noncontact Doppler radar to evaluate the feasibility of this noncontact form of measurement in capturing breathing patterns under different conditions associated with certain breathing disorders. In addition to that, inhalation and exhalation flow patterns under different breathing scenarios were investigated to further support the feasibility of Doppler radar to accurately estimate the tidal volume. The results obtained for both experiments were compared with the gold standard measurement schemes, such as respiration belt and spirometry readings, yielding significant correlations with the Doppler radar-based information. In summary, Doppler radar is highlighted as an alternative approach not only for determining respiration rates, but also for identifying breathing patterns and tidal volumes as a preferred nonwearable alternative to the conventional - ontact sensing methods.

Influence of prolonged bed-rest on spectral and temporal electromyographic motor control characteristics of the superficial lumbo-pelvic musculature

Little is known about the motor control of the lumbo-pelvic musculature in microgravity and its simulation (bed-rest). Analysis of spectral and temporal electromyographic variables can provide information on motor control relevant for normal function. This study examined the effect of 56-days of bed-rest with 1-year follow-up in 10 male subjects on the median frequency and the activation timing in surface electromyographic recordings from five superficial lumbo-pelvic muscles during a repetitive knee movement task. Trunk fat mass (from whole body-composition measurements) and movement accuracy as possible explanatory factors were included. Increased median frequency was observed in the lumbar erector spinae starting late in bed-rest, but this was not seen in its synergist, the thoracic erector spinae (p<.0001). These changes persisted up to 1-year after bed-rest and were independent of changes in body-composition or movement accuracy. Analysis suggested decreases of median frequency (p<.0001) in the abdominal and gluteal muscles to result from increased (p<.01) trunk fat levels during and after bed-rest. No changes in lumbo-pelvic muscle activation timing were seen. The results suggest that bed-rest particularly affects the shorter lumbar erector spinae and that the temporal sequencing of superficial lumbo-pelvic muscle activation is relatively robust.

Climate-related spatial and temporal variation in bill morphology over the past century in Australian parrots

Aim: Allen's rule posits that the appendages of endothermic organisms will be larger in warmer climates to allow for dumping of heat loads. Given a link between appendage size and climate, we tested the prediction that climate change has driven the evolution of larger bills in birds, resulting in measurable changes over the recent past. Location: Australia. Methods: We explored geographical and temporal variation in bill surface area of five Australian parrot species to determine whether individuals from warmer climates have larger bills, and whether there have been increases in bill surface area over time, consistent with climatic warming. Measurements were obtained from museum specimens dating from 1871 to 2008. These data were then related to geographical location, collection date and locality-specific climate data, in order to construct and compare models of spatio-temporal and climate-related variation in bill morphology. Results: There have been increases in bill surface area in mulga parrots (Psephotus varius), gang-gang cockatoos (Callocephalon fimbriatum), red-rumped parrots (Psephotus haematonotus) and male crimson rosellas (Platycercus elegans), equating to a c. 4-10% increase in bill surface area since 1871. Average maximum summer temperature in the 5 years prior to specimen collection also positively predicted bill surface area in mulga parrots, red-rumped parrots and crimson rosellas, consistent with Allen's rule. With the exception of red-rumped parrots, however, models with geographical location and year of collection were still better predictors of bill surface area than local climate at the date of collection. Main conclusions: Our analysis provides evidence that four species of parrot have exhibited adaptive change in bills over the past century potentially mitigating the thermal stress caused by climatic warming. Although consistent with the predicted effects of climate change, the temporal patterns we observe may have additional causes, however, such as changes in primary productivity, habitat or food availability.

Small-variance asymptotics for bayesian nonparametric models with constraints

The users often have additional knowledge when Bayesian nonparametric models (BNP) are employed, e.g. for clustering there may be prior knowledge that some of the data instances should be in the same cluster (must-link constraint) or in different clusters (cannot-link constraint), and similarly for topic modeling some words should be grouped together or separately because of an underlying semantic. This can be achieved by imposing appropriate sampling probabilities based on such constraints. However, the traditional inference technique of BNP models via Gibbs sampling is time consuming and is not scalable for large data. Variational approximations are faster but many times they do not offer good solutions. Addressing this we present a small-variance asymptotic analysis of the MAP estimates of BNP models with constraints. We derive the objective function for Dirichlet process mixture model with constraints and devise a simple and efficient K-means type algorithm. We further extend the small-variance analysis to hierarchical BNP models with constraints and devise a similar simple objective function. Experiments on synthetic and real data sets demonstrate the efficiency and effectiveness of our algorithms.

Detection and analysis of human respiration using microwave Doppler radar

 Non-contact detection characteristic of Doppler radar provides an unobtrusive means of respiration detection and monitoring. This avoids additional preparations such as physical sensor attachment or special clothing. Furthermore, robustness of Doppler radar against environmental factors reduce environmental constraints and strengthens the possibility of employing Doppler radar as a practical biomedical devices in the future particularly in long term monitoring applications such as in sleep studies.

Systematic approach to the quantitative voltammetric analysis of the Fe III /Fe II component of the [α 2 -Fe(OH 2 )P 2 W 17 O 61 ] 7-/8- reduction process in buffered and unbuffered aqueous media

The one-electron reduction of [α2-FeIII(OH2)P2W17O61]7- at a glassy carbon electrode was investigated using cyclic and rotating-disk-electrode voltammetry in buffered and unbuffered aqueous solutions over the pH range 3.45−7.50 with an ionic strength of approximately 0.6 M maintained. The behavior is well-described by a square-scheme mechanism P + e- ↔ Q (E10/ = −0.275 V, k10/ = 0.008 cm s-1, and α1 = 1/2), PH+ + e- ↔ QH+ (E20/ = −0.036 V, k20/ = 0.014 cm s-1, and α2 = 1/2), PH+ ↔ P + H+ (KP = 3.02 × 10-6 M), and QH+ ↔ Q + H+ (KQ = 2.35 × 10-10 M), where P, Q, PH+, and QH+ correspond to [α2-FeIII(OH)P2W17O61]8-, [α2-FeII(OH)P2W17O61]9-, [α2-FeIII(OH2)P2W17O61]7-, and [α2-FeII(OH2)P2W17O61]8-, respectively; E10‘ and E20‘ are the formal potentials, k10‘ and k20‘ are the formal (standard) rate constants, and KP and KQ are the acid dissociation constants for the relevant reactions. The analysis for the buffered media is based on the approach of Laviron who demonstrated that a square scheme with fully reversible protonations, reversible or quasi reversible electron transfers with the assumption that α1 = α2, can be well-described by the behavior of a simple redox couple, ox + e- ↔ red, whose formal potential, Eapp0‘, and standard rate constant, kapp0‘, are straightforwardly derived functions of pH, as are the values of E10‘, k10‘, E20‘, k20‘, and KP (only three of the four thermodynamic parameters in a square scheme can be specified). It was assumed that αapp = 1/2, and the simulation program DigiSim was used to determine the values of Eapp0‘ and kapp0‘, which are required to describe the cyclic voltammograms obtained in buffered media in the pH range from 3.45 to 7.52 (buffer-related reactions which effect general acid−base catalysis are included in the simulations). DigiSim simulations of cyclic voltammograms obtained in unbuffered media yielded the values of E10‘ and k10‘; KQ was then directly computed from thermodynamic constraints. These simulations included additional reactions between the redox species and H2O. The value of the diffusion coefficient of the [α2-FeIII(OH2)P2W17O61]7-, 2.92 × 10-6 cm2 s-1, was determined using DigiSim simulations of voltammograms at a rotating disk electrode in buffered and unbuffered media at pH 3.45. The diffusion coefficients of all redox species were assumed to be identical. When the pH is greater than 6, instability of P (i.e., [α2-FeIII(OH)P2W17O61]8-) led to the loss of the reactant and precluded lengthy experimentation.

Overcoming data scarcity of Twitter: using tweets as bootstrap with application to autism-related topic content analysis

Notwithstanding recent work which has demonstrated the potential of using Twitter messages for content-specific data mining and analysis, the depth of such analysis is inherently limited by the scarcity of data imposed by the 140 character tweet limit. In this paper we describe a novel approach for targeted knowledge exploration which uses tweet content analysis as a preliminary step. This step is used to bootstrap more sophisticated data collection from directly related but much richer content sources. In particular we demonstrate that valuable information can be collected by following URLs included in tweets. We automatically extract content from the corresponding web pages and treating each web page as a document linked to the original tweet show how a temporal topic model based on a hierarchical Dirichlet process can be used to track the evolution of a complex topic structure of a Twitter community. Using autism-related tweets we demonstrate that our method is capable of capturing a much more meaningful picture of information exchange than user-chosen hashtags.