Australian Institute of Marine Science

About: Australian Institute of Marine Science is a facility organization based out in Townsville, Queensland, Australia. It is known for research contribution in the topics: Coral reef & Reef. The organization has 1129 authors who have published 3593 publications receiving 221220 citations.

Classification and regression trees: a powerful yet simple technique for ecological data analysis

Abstract: Classification and regression trees are ideally suited for the analysis of com- plex ecological data. For such data, we require flexible and robust analytical methods, which can deal with nonlinear relationships, high-order interactions, and missing values. Despite such difficulties, the methods should be simple to understand and give easily interpretable results. Trees explain variation of a single response variable by repeatedly splitting the data into more homogeneous groups, using combinations of explanatory var- iables that may be categorical and/or numeric. Each group is characterized by a typical value of the response variable, the number of observations in the group, and the values of the explanatory variables that define it. The tree is represented graphically, and this aids exploration and understanding. Trees can be used for interactive exploration and for description and prediction of patterns and processes. Advantages of trees include: (1) the flexibility to handle a broad range of response types, including numeric, categorical, ratings, and survival data; (2) invariance to monotonic transformations of the explanatory variables; (3) ease and ro- bustness of construction; (4) ease of interpretation; and (5) the ability to handle missing values in both response and explanatory variables. Thus, trees complement or represent an alternative to many traditional statistical techniques, including multiple regression, analysis of variance, logistic regression, log-linear models, linear discriminant analysis, and survival models. We use classification and regression trees to analyze survey data from the Australian central Great Barrier Reef, comprising abundances of soft coral taxa (Cnidaria: Octocorallia) and physical and spatial environmental information. Regression tree analyses showed that dense aggregations, typically formed by three taxa, were restricted to distinct habitat types, each of which was defined by combinations of 3-4 environmental variables. The habitat definitions were consistent with known experimental findings on the nutrition of these taxa. When used separately, physical and spatial variables were similarly strong predictors of abundances and lost little in comparison with their joint use. The spatial variables are thus effective surrogates for the physical variables in this extensive reef complex, where infor- mation on the physical environment is often not available. Finally, we compare the use of regression trees and linear models for the analysis of these data and show how linear models fail to find patterns uncovered by the trees.

Global warming and recurrent mass bleaching of corals

Abstract: During 2015–2016, record temperatures triggered a pan-tropical episode of coral bleaching, the third global-scale event since mass bleaching was first documented in the 1980s. Here we examine how and why the severity of recurrent major bleaching events has varied at multiple scales, using aerial and underwater surveys of Australian reefs combined with satellite-derived sea surface temperatures. The distinctive geographic footprints of recurrent bleaching on the Great Barrier Reef in 1998, 2002 and 2016 were determined by the spatial pattern of sea temperatures in each year. Water quality and fishing pressure had minimal effect on the unprecedented bleaching in 2016, suggesting that local protection of reefs affords little or no resistance to extreme heat. Similarly, past exposure to bleaching in 1998 and 2002 did not lessen the severity of bleaching in 2016. Consequently, immediate global action to curb future warming is essential to secure a future for coral reefs.

Preparation of Genomic DNA from Bacteria

Abstract: Most protocols for the preparation of bacterial genomic DNA consist of lysis, followed by incubation with a nonspecific protease and a series of extractions prior to precipitation of the nucleic acids. Such procedures effectively remove contaminating proteins, but are not effective in removing exopolysaccharides which can interfere with the activity of enzymes such as restriction endonucleases and ligases. In this unit, however, the protease incubation is followed by a CTAB extraction whereby CTAB complexes both with polysaccharides and with residual protein, effectively removing both in the subsequent emulsification and extraction. This procedure is effective in producing digestible chromosomal DNA from a variety of gram-negative bacteria, all of which normally produce large amounts of polysaccharides. If large amounts of exceptionally clean DNA are required, the procedure can be scaled up and the DNA purified on a CsCl gradient, as described in the alternate protocol.

Present state and future of the world's mangrove forests

Abstract: SUMMARY Mangroves, the only woody halophytes living at the confluence of land and sea, have been heavily used traditionally for food, timber, fuel and medicine, and presently occupy about 181 000 km 2 of tropical and subtropical coastline. Over the past 50 years, approximately one-third of the world’s mangrove forests have been lost, but most data show very variable loss rates and there is considerable margin of error in most estimates. Mangroves are a valuable ecological and economic resource, being important nursery grounds and breeding sites for birds, fish, crustaceans, shellfish, reptiles and mammals; a renewable source of wood; accumulation sites for sediment, contaminants, carbon and nutrients; and offer protection against coastal erosion. The destruction of mangroves is usually positively related to human population density. Major reasons for destruction are urban development, aquaculture, mining and overexploitation for timber, fish, crustaceans and shellfish. Over the next 25 years, unrestricted clear felling, aquaculture, and overexploitation of fisheries will be the greatest threats, with lesser problems being alteration of hydrology, pollution and global warming. Loss of biodiversity is, and will continue to be, a severe problem as even pristine mangroves are species-poor compared with other tropical ecosystems. The future is not entirely bleak. The number of rehabilitation and restoration projects is increasing worldwide with some countries showing increases in mangrove area. The intensity of coastal aquaculture appears to have levelled off in some parts of the world. Some commercial projects and economic models indicate that mangroves can be used as a sustainable resource, especially for wood. The brightest note is that the rate of population growth is projected to slow during the next 50 years, with a gradual decline thereafter to the end of the century. Mangrove forests will continue to be exploited at current rates to 2025, unless they are seen as a valuable resource to be managed on a sustainable basis. After 2025, the future of mangroves will depend on technological and ecological advances