Dynamic Niche Clustering: a fuzzy variable radius niching technique for multimodal optimisation in GAs

This paper describes the recent developments and improvements made to the variable radius niching technique called Dynamic Niche Clustering (DNC). DNC is fitness sharing based technique that employs a separate population of overlapping fuzzy niches with independent radii which operate in the decoded parameter space, and are maintained alongside the normal GA population. We describe a speedup process that can be applied to the initial generation which greatly reduces the complexity of the initial stages. A split operator is also introduced that is designed to counteract the excessive growth of niches, and it is shown that this improves the overall robustness of the technique. Finally, the effect of local elitism is documented and compared to the performance of the basic DNC technique on a selection of 2D test functions. The paper is concluded with a view to future work to be undertaken on the technique.

A variable radius niching technique for speciation in genetic algorithms

In this paper, a continuation of a variable radius niche technique called Dynamic Niche Clustering developed by (Gan & Warwick, 1999) is presented. The technique employs a separate dynamic population of overlapping niches that coexists alongside the normal population. An empirical analysis of the updated methodology on a large group of standard optimisation test-bed functions is also given. The technique is shown to perform almost as well as standard fitness sharing with regards to stability and the accuracy of peak identification, but it outperforms standard fitness sharing with regards to time complexity. It is also shown that the technique is capable of forming niches of varying size depending on the characteristics of the underlying peak that the niche is populating.

Population structure of the migratory fish Prochilodus lineatus (Characiformes) from rio Grande basin (Brazil), an area fragmented by dams

1. Prochilodus lineatus (Prochilodontidae, Characiformes) is a migratory species of great economic importance both in fisheries and aquaculture that is found throughout the Jacui, Paraiba do Sul, Parana, Paraguay and Uruguay river basins in South America. Earlier population studies of P. lineatus in the rio Grande basin (Parana basin) indicated the existence of a single population; however, the range of this species has been fragmented by the construction of several dams. Such dams modified the environmental conditions and could have constrained the reproductive migration of P. lineatus, possibly leading to changes in the population genetic structure. 2. In order to evaluate how genetic diversity is allocated in the rio Grande basin, 141 specimens of P. lineatus from eight collection sites were analysed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) with 15 restriction enzymes. 3. Forty-six haplotypes were detected, and 70% of them are restricted. The mean genetic variability indexes (h = 0.7721 and pi = 1.6%) were similar to those found in natural populations with a large effective size. Fst and Exact Test values indicated a lack of structuring among the samples, and the model of isolation by distance was tested and rejected. 4. The haplotype network indicated that this population of P. lineatus has been maintained as a single variable stock with some differences in the genetic composition (haplotypes) between samples. Indications of population expansion were detected, and this finding was supported by neutrality tests and mismatch distribution analyses. 5. The present study focused on regions between dams to serve as a parameter for further evaluations of genetic variability and the putative impact of dams and repopulation programmes in natural populations of P. lineatus. Copyright (C) 2011 John Wiley & Sons, Ltd.

Exploring the extent and nature of the diversity of the doctoral population in Australia : A profile of the respondents to a 2005 national survey

Although there is general agreement that diversity is a feature of doctoral education in Australia, there are various forms and levels of diversity, many of which are not captured by analyses that rely on categories for analysing the doctoral education population that are those commonly used in education at the undergraduate level, such as sex, age, mode of study, type of enrolment, citizenship, and Broad Field of Study, etc. These categories primarily reflect concerns to do with funding and issues of participation and equity. Our analysis of data from a national survey of doctoral candidates carried out in 2005 as part of a Linkage Grant project “Reconceptualising the doctoral experience’, suggests that not all of these categories are relevant to critical concerns for doctoral education. Nor do analyses at a macro-level represent the particularity of the doctoral experience. They can mask the reality of a highly variable student population, and one that is not necessarily represented accurately or helpfully by ascribing group identities.

Urban living and obesity : is it independent of its population and lifestyle characteristics?

OBJECTIVES: Living in an urban area influences obesity. However, little is known about whether this relationship is truly independent of, or merely mediated through, the demographic, socio-economic and lifestyle characteristics of urban populations. We aimed to identify and quantify the magnitude of this relationship in a Sri Lankan population.

METHODS: Cross-sectional study of adults aged 20-64 years representing the urban (n = 770) and rural (n = 630) populations, in the district of Colombo in 2004. Obesity was measured as a continuous variable using body mass index (BMI). Demographic, socio-economic and lifestyle factors were assessed. Gender-specific multivariable regression models were developed to quantify the independent effect of urban/ rural living and other variables on increased BMI.

RESULTS: The BMI (mean; 95% confidence interval) differed significantly between urban (men: 23.3; 22.8-23.8; women: 24.2; 23.7-24.7) and rural (men: 22.3; 21.9-22.7; women: 23.2; 22.7-23.7) sectors (P < 0.01). The observed association remained stable independently of all other variables in the regression models among both men (coefficient = 0.64) and women (coefficient = 0.95). These coefficients equated to 2.2 kg weight for the average man and 1.7 kg for the average woman. Other independent associations of BMI were with income (coefficient = 1.74), marital status (1.48), meal size (1.53) and religion (1.20) among men, and with age (0.87), marital status (2.25) and physical activity (0.96) among women.

CONCLUSIONS: Urban living is associated with obesity independently of most other demographic, socio-economic and lifestyle characteristics of the population. Targeting urban populations may be useful for consideration when developing strategies to reduce the prevalence of obesity.

Population dynamics of the infaunal bivalve, Soletellina alba

The population dynamics of the infaunal bivalve Soletellina alba was investigated at three sites situated within close proximity to the mouth of the Hopkins River estuary. The initial study design was planned to examine the importance of winter flooding to the persistence of this bivalve mollusc within the Hopkins estuary, since mass mortalities have been observed during previous years coincident with periods of winter flooding. Unfortunately, the climatic conditions experienced during this study were atypical compared to the long-term average, so detailed sampling was limited to two, unanticipated, non-flood years rather than two, highly anticipated, flood years. This hampered my ability to conduct complete tests of the importance of winter flooding. Patterns of river discharge and the frequency and duration of mouth opening and closing differed greatly from that expected. Unexpectedly, periods of mouth closure were not always associated with periods of minimal river discharge; low salinities were another unexpected result during an extended period of mouth closure during 1998. As expected, salinities varied considerably with increasing water depth when the estuary mouth was open. Mouth closure lead to salinities becoming more uniform between water depths but hypoxic and anoxic conditions became evident via stratification in the water column at 1 m below the Australian Height Datum (AHD). Other than trends associated with increased water depth, significant variation was not evident between measurements of salinity taken from three sites within close proximity of the estuary mouth (approximately 500 m), or during changes in tide. The most pertinent anomaly was the absence of winter flooding. The distribution and abundance of juvenile and adult S. alba was variable across all Dates, Sites and Channel elevations (i.e. water depths) sampled during this study. An experimental test comparing the recruitment of juveniles at different channel elevations and in sediments of varying particle size was conducted during an exceptionally successful period of recruitment during 1999. The results of these tests showed that recruitment was greatest at the shallowest channel elevation used, and there was little evidence that sediment particle size influenced recruitment. In contrast to 1999, recruitment during 1997 or 1998 was extremely poor. Growth rates were monitored using tagged individuals held in caged and uncaged plots, which revealed that growth was highly variable among individuals, but not between Sites. These tests also revealed that growth was negligible during the colder, winter months, and that the fastest growing individuals were capable of growing 0.2 mm/day. Mixed results were obtained for tests of potential cage artifacts and the influence of handling. Caging and differing amounts of handling did not appear to influence growth, but there was evidence that cages and handling influenced bivalve condition and number of mortalities. These direct tests appeared to be the most appropriate method for determining growth rates of this species, since attempts to analyse length-frequency data were made difficult by the apparent convergence of cohorts, and shell aging is difficult due to the thin, fragile nature of the shell. As expected, mass mortalities were observed during the flood of 1996, but not during the two non-flood years of 1997 and 1998. There were, however, some considerable declines in abundances at some channel elevations during the two non-flood years. However, these declines were attributable to the complete disappearance of individuals, rather than the sudden presence of numerous, recently dead individuals that typify observed declines during winter flooding. The complete disappearance of individuals suggest that S. alba may be capable of post-settlement emigration, or that they were consumed by an unknown predator. Salinity tolerance tests showed that bivalves exposed to low salinities (≤6 ppt), exhibited poorer condition and took longer to re-burrow into sediments than those exposed to greater salinities (≥14 ppt), while death of bivalves exposed to salinities ≤1 ppt occurred after 8 days of exposure. These tests provide evidence that low salinities are probably the principal cause of mass mortalities during winter flooding, although the interaction between salinity, temperature and turbidity also deserve consideration. The results of this study indicate that certain aspects of winter flooding, especially salinity, are responsible for the mass mortalities of S. alba rather than the result of a short-lived life history. I hypothesise that the survival of very young juveniles (between 0.5 and 1 mm shell length) and rapid growth rates are important features of the life history of S. alba that explain its successful persistence within the Hopkins River estuary. The rapid rates of growth suggest that it may be possible for juveniles that survive winter flooding to grow, reach sexual maturity, and reproduce before the onset of the next flood event. Unfortunately, the increased survivorship of juveniles during periods of winter flooding was not demonstrated by this study because of the absence of winter flooding and also relatively poor recruitment. It is highly likely that this species is capable of completing it entire life cycle within the estuary since the absence of other nearby populations, together with periods of mouth closure, are likely to greatly limit the potential contribution made by larvae entering from the surrounding marine environment. This study has added considerably to our knowledge of how infauna cope with life in the intermittently closing estuaries that typify semi-arid coastlines in the Southern Hemisphere.

Critical appraisal of health literacy indices revealed variable underlying constructs, narrow content and psychometric weaknesses

Objective
Health literacy refers to an individual's ability to seek, understand, and use health information. A range of indices exist that purport to measure health literacy across individuals and populations. This study aimed to review the development and content of existing indices and to critically appraise their properties.

Study Design and Setting
Using standardized search terms, published generic health literacy indices (1990–2008) were identified. Using a methodological framework, each was evaluated for purpose, validity (face, content, construct), reliability, responsiveness, feasibility, and generalizability.

Results
Nineteen instruments were evaluated. Three measurement approaches were identified: direct testing of individual abilities, self-report of abilities, and population-based proxy measures. Composition of underlying constructs and content varied widely across instruments, and none appeared to fully measure a person's ability to seek, understand, and use health information. The content was focused primarily on reading comprehension and numeracy; scoring categories were poorly defined and may not be mutually exclusive, and few indices had been assessed for reliability.

Conclusion
Health literacy is not consistently measured, making it difficult to interpret and compare health literacy at individual and population levels. Empirical evidence demonstrating validity and reliability of existing indices is required, and more comprehensive health literacy instruments need to be developed.

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.

Movement patterns for a critically endangered species, the Leatherback Turtle (Dermochelys coriacea), linked to foraging success and population status

Foraging success for pelagic vertebrates may be revealed by horizontal and vertical movement patterns. We show markedly different patterns for leatherback turtles in the North Atlantic versus Eastern Pacific, which feed on gelatinous zooplankton that are only occasionally found in high densities. In the Atlantic, travel speed was characterized by two modes, indicative of high foraging success at low speeds (<15 km d−1) and transit at high speeds (20–45 km d−1). Only a single mode was evident in the Pacific, which occurred at speeds of 21 km d−1 indicative of transit. The mean dive depth was more variable in relation to latitude but closer to the mean annual depth of the thermocline and nutricline for North Atlantic than Eastern Pacific turtles. The most parsimonious explanation for these findings is that Eastern Pacific turtles rarely achieve high foraging success. This is the first support for foraging behaviour differences between populations of this critically endangered species and suggests that longer periods searching for prey may be hindering population recovery in the Pacific while aiding population maintenance in the Atlantic.

Ecosystem relevance of variable jellyfish biomass in the Irish Sea between years, regions and water types

Monitoring the abundance and distribution of taxa is essential to assess their contribution to ecosystem processes. For marine taxa that are difficult to study or have long been perceived of little ecological importance, quantitative information is often lacking. This is the case for jellyfish (medusae and other gelatinous plankton). In the present work, 4 years of scyphomedusae by-catch data from the 2007-2010 Irish Sea juvenile gadoid fish survey were analysed with three main objectives: (1) to provide quantitative and spatially-explicit species-specific biomass data, for a region known to have an increasing trend in jellyfish abundance; (2) to investigate whether year-to-year changes in catch-biomass are due to changes in the numbers or in the size of medusa (assessed as the mean mass per individual), and (3) to determine whether inter-annual variation patterns are consistent between species and water masses. Scyphomedusae were present in 97% of samples (N=306). Their overall annual median catch-biomass ranged from 0.19 to 0.92gm-3 (or 8.6 to 42.4gm-2). Aurelia aurita and Cyanea spp. (Cyanea lamarckii and Cyanea capillata) made up 77.7% and 21.5% of the total catch-biomass respectively, but species contributions varied greatly between sub-regions and years. No consistent pattern was detected between the distribution and inter-annual variations of the two genera, and contrasting inter-annual patterns emerged when considering abundance either as biomass or as density. Significantly, A.aurita medusae were heavier in stratified than in mixed waters, which we hypothesize may be linked to differences in timing and yield of primary and secondary productions between water masses. These results show the vulnerability of time-series from bycatch datasets to phenological changes and highlight the importance of taking species- and population-specific distribution patterns into account when integrating jellyfish into ecosystem models.

Using occupancy as a state variable for monitoring the critically endangered Alaotran gentle lemur Hapalemur alaotrensis

Although monitoring is an essential tool for biodiversity conservation, monitoring programmes are often poorly designed and thus unlikely to produce results that are meaningful for management. Monitoring is especially challenging when dealing with rare and elusive species in areas where conservation resources are particularly limited. In such cases, monitoring techniques aimed at estimating occupancy represent an attractive alternative to traditional methods concerned with estimating population size, as the collection of detection/non-detection data is in general less costly and easier to implement. In this study, we evaluated the use of occupancy as a state variable for the monitoring of the Alaotran gentle lemur Hapalemur alaotrensis, a Critically Endangered primate exclusively inhabiting the dense marshes around Lake Alaotra in Madagascar. We used a likelihood-based modelling approach that explicitly accounts for detectability. This showed that the probability of detection of H. alaotrensis was extremely low and depended on site characteristics that can vary in space and time, confirming the need to account for imperfect detection when monitoring this species. We used our models to explore factors affecting the probability of occupancy and detection to identify management implications, and also developed recommendations for the ongoing monitoring of this species. The method applied in this study provides an efficient tool for the monitoring of an elusive species and has the potential to provide a flexible sampling framework for local community based monitoring initiatives.

Avian influenza infection dynamics under variable climatic conditions, viral prevalence is rainfall driven in waterfowl from temperate, south-east Australia

Understanding Avian Influenza Virus (AIV) infection dynamics in wildlife is crucial because of possible virus spill over to livestock and humans. Studies from the northern hemisphere have suggested several ecological and environmental drivers of AIV prevalence in wild birds. To determine if the same drivers apply in the southern hemisphere, where more irregular environmental conditions prevail, we investigated AIV prevalence in ducks in relation to biotic and abiotic factors in south-eastern Australia. We sampled duck faeces for AIV and tested for an effect of bird numbers, rainfall anomaly, temperature anomaly and long-term ENSO (El-Ni&ntilde;o Southern Oscillation) patterns on AIV prevalence. We demonstrate a positive long term effect of ENSO-related rainfall on AIV prevalence. We also found a more immediate response to rainfall where AIV prevalence was positively related to rainfall in the preceding 3-7 months. Additionally, for one duck species we found a positive relationship between their numbers and AIV prevalence, while prevalence was negatively or not affected by duck numbers in the remaining four species studied. In Australia largely non-seasonal rainfall patterns determine breeding opportunities and thereby influence bird numbers. Based on our findings we suggest that rainfall influences age structures within populations, producing an influx of immunologically naïve juveniles within the population, which may subsequently affect AIV infection dynamics. Our study suggests that drivers of AIV dynamics in the northern hemisphere do not have the same influence at our south-east Australian field site in the southern hemisphere due to more erratic climatological conditions.

Mammographic screening: measurement of the cost in a population based programme in Victoria, Australia

STUDY OBJECTIVES: To estimate the cost per woman participating in a mammographic screening programme, and to describe methods for measuring costs. DESIGN: Expenditure, resource usage, and throughput were monitored over a 12 month period. Unit costs for each phase of the screening process were estimated and linked with the probabilities of each screening outcome to obtain the cost per woman screened and the cost per breast cancer detected. SETTING: A pilot, population based Australian programme offering free two-view mammographic screening. PARTICIPANTS: A total of 5986 women aged 50-69 years who lived in the target area, were listed on the electoral roll, had no previous breast cancer, and attended the programme. RESULTS: Unit costs for recruitment, screening, and recall mammography were $17.54, $60.04, and $175.54, respectively. The costs of clinical assessment for women with subsequent clear, benign, malignant (palpable), and malignant (impalpable) diagnoses were $173.71, $527.29, $436.62, and $567.22, respectively. The cost per woman screened was $117.70, and the cost per breast cancer detected was $11,550. CONCLUSIONS: The cost per woman screened is a key variable in assessment of the cost effectiveness of mammographic screening, and is likely to vary between health care settings. Its measurement is justified if decisions about health care services are to be based on cost effectiveness criteria.

Distinctively variable sequence-based nuclear DNA markers for multilocus phylogeography of the soybean- and rice-infecting fungal pathogen Rhizoctonia solani AG-1 IA

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A comparison of statistical methods for genomic selection in a mice population

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)