Sampling phylogenetic tree space with the generalized Gibbs sampler

The generalized Gibbs sampler (GGS) is a recently developed Markov chain Monte Carlo (MCMC) technique that enables Gibbs-like sampling of state spaces that lack a convenient representation in terms of a fixed coordinate system. This paper describes a new sampler, called the tree sampler, which uses the GGS to sample from a state space consisting of phylogenetic trees. The tree sampler is useful for a wide range of phylogenetic applications, including Bayesian, maximum likelihood, and maximum parsimony methods. A fast new algorithm to search for a maximum parsimony phylogeny is presented, using the tree sampler in the context of simulated annealing. The mathematics underlying the algorithm is explained and its time complexity is analyzed. The method is tested on two large data sets consisting of 123 sequences and 500 sequences, respectively. The new algorithm is shown to compare very favorably in terms of speed and accuracy to the program DNAPARS from the PHYLIP package.

Women and children during Aldermaston Peace march 1965

Women and children with placards and banners during Aldermaston Peace march 1965. The march covered the distance between Ipswich and Brisbane, Australia, walked in relays covering approximately two miles each. Most relay sections were sponsored by one or more individual organisations.

Women wearing peace aprons during Peace march in Brisbane, Australia 1963

Women wearing peace aprons during Peace march in Brisbane, Australia 1963. Cars can be seen in the background.

Women and men during the 1963 Peace March, Brisbane, Australia

Women and men during Peace march in Brisbane, Australia 1963. Car can be seen in the background. Two men one with drum follow the women, one of which has a banner Women strike for peace say U.A.W. The Union of Australian Women is a national organisation that was formed in 1950. Its aim is to work for the status and wellbeing of women across the world. It has been involved in a wide variety of campaigns that concern women. The Union of Australian Women networks with other women's community and union groups on such issues.

Compiling a GIS database of tree farms on Leyte Island

As part of ACIAR project ASEM/2003/052, Improving Financial Returns to Smallholder Tree Farmers in the Philippines, plantations of timber trees in Leyte Island, the Philippines were located using a systematic survey of the island. The survey was undertaken in order to compile a database of plantations which could be used to guide the planning of project activities. In addition to recording a range of qualitative and quantitative information for each plantation, the survey spatially referenced each site using a Global Positioning System (GPS) to electronic maps of the island which were held in a Geographical Information System (GIS). Microsoft Excel and Mapsource® software were used as the software links between GPS coordinates and the GIS. Mapping of farm positions was complicated by different datums being used for maps of Leyte Island and this caused GPS positions to be displaced from equivalent positions on the map. Photos of the sites were hyperlinked to their map positions in the GIS in order to assist staff to recall site characteristics.

Women with umbrellas during Peace march on Sunday April 5th 1964, Brisbane.

Two women with umbrellas outside a cemetery during Peace march, Sunday April 5th Brisbane, Australia, 1964.

Members of the Union of Australian Women with banner during Hiroshima Day 1964, Brisbane

Members of the Union of Australian Women with banner during Hiroshima Day 1964, Brisbane, Australia. The Union of Australian Women is a national organisation that was formed in 1950. Its aim is to work for the status and wellbeing of women across the world. It has been involved in a wide variety of campaigns that concern women. The Union of Australian Women networks with other women's community and union groups on such issues.

The effect of water fluoridation on the bone mineral density of young women [Saskatoon study]

Introduction: Osteogenic effects of therapeutic fluoride have been reported; however, the impact of exposure to low level water fluoridation on bone density is not clear. We investigated the effect of long-term exposure to fluoridated water from growth to young adulthood on bone mineral density (BMD). Methods: BMD was measured in 24 healthy women from Regina (fluoride 0.1 mg/L) and 33 from Saskatoon (fluoride 1.0 mg/L), with no differences between groups for height, weight, lifestyle or dietary factors. Results: Saskatoon women had significantly higher mean BMD at total anterior-posterior lumbar spine (APS) and estimated volumetric L3 (VLS), with no difference at total body (TB) or proximal femur (PF). Conclusion: Exposure to water fluoridation during the growing years may have a power impact on axial spine bone density in young women.

Food habits of young and middle-aged women living outside the capital cities of Australia

Young (18-22 years) and middle-aged (45-49 years) women living in urban and rural areas of New South Wales completed a brief food frequency questionnaire as part of a wider health survey. Urban women in both age groups consumed meat less frequently than women in rural areas; and women in the less populated rural areas were more likely to eat green and yellow vegetables and least likely to eat dried beans. There were few other geographic differences in food habits. Middle-aged women consumed reduced-fat milk, fruit, vegetables, fish, biscuits and cakes significantly more frequently, and rice, pasta, full-cream milk, fried food and take-away food less frequently than younger women. Smokers in both age groups consumed fresh fruit, vegetables and breakfast cereals significantly less frequently than non-smokers, and women with low levels of habitual physical activity consumed fresh fruit and cereals less frequently than more active women. The findings suggest that strategies aimed at changing eating behaviours should be age-group-specific and targeted specifically to smokers and less active women.