Deposit-feeding mechanisms and resource partitioning in tropical holothurians

Aspidochirote holothurians found on tropical reef flats feed on particulate deposits which form a variety of substrata. The synaptid holothurian Opheodesoma grisea (Semper) feeds in a similar manner by scraping deposits from the surfaces of sea grasses. Distributional and gut content analyses showed that species partitioning is on the basis of substratum and particle size preference. Scanning electron microscopy revealed that the tentacles of aspidochirotes have a nodular surface while those of O. grisea have a tessellated surface structure. The twelve different species examined were shown to have different tentacular surface textures which bore an apparent relationship with the mean particle sizes selected by the different species. Light microscope studies of tentacle sections confirmed earlier observations on the extent of the water vascular system in aspidochirote and pinnate tentacles. From these observations a functional interpretation is proposed for tentacular operation and the means of particle selection in such holothurians.

Agricultural intensification and biodiversity partitioning in European landscapes comparing plants, carabids, and birds

Effects of agricultural intensification (AI) on biodiversity are often assessed on the plot scale, although processes determining diversity also operate on larger spatial scales. Here, we analyzed the diversity of vascular plants, carabid beetles, and birds in agricultural landscapes in cereal crop fields at the field (n = 1350), farm (n = 270), and European-region (n = 9) scale. We partitioned diversity into its additive components alpha, beta, and gamma, and assessed the relative contribution of beta diversity to total species richness at each spatial scale. AI was determined using pesticide and fertilizer inputs, as well as tillage operations and categorized into low, medium, and high levels. As AI was not significantly related to landscape complexity, we could disentangle potential AI effects on local vs. landscape community homogenization. AI negatively affected the species richness of plants and birds, but not carabid beetles, at all spatial scales. Hence, local AI was closely correlated to beta diversity on larger scales up to the farm and region level, and thereby was an indicator of farm-and region-wide biodiversity losses. At the scale of farms (12.83-20.52%) and regions (68.34-80.18%), beta diversity accounted for the major part of the total species richness for all three taxa, indicating great dissimilarity in environmental conditions on larger spatial scales. For plants, relative importance of alpha diversity decreased with AI, while relative importance of beta diversity on the farm scale increased with AI for carabids and birds. Hence, and in contrast to our expectations, AI does not necessarily homogenize local communities, presumably due to the heterogeneity of farming practices. In conclusion, a more detailed understanding of AI effects on diversity patterns of various taxa and at multiple spatial scales would contribute to more efficient agri-environmental schemes in agroecosystems.

Approximating the Set of Local Minima in Partial RNA Folding Landscapes

Motivation: We study a stochastic method for approximating the set of local minima in partial RNA folding landscapes associated with a bounded-distance neighbourhood of folding conformations. The conformations are limited to RNA secondary structures without pseudoknots. The method aims at exploring partial energy landscapes pL induced by folding simulations and their underlying neighbourhood relations. It combines an approximation of the number of local optima devised by Garnier and Kallel (2002) with a run-time estimation for identifying sets of local optima established by Reeves and Eremeev (2004).

Results: The method is tested on nine sequences of length between 50 nt and 400 nt, which allows us to compare the results with data generated by RNAsubopt and subsequent barrier tree calculations. On the nine sequences, the method captures on average 92% of local minima with settings designed for a target of 95%. The run-time of the heuristic can be estimated by O(n2D?ln?), where n is the sequence length, ? is the number of local minima in the partial landscape pL under consideration and D is the maximum number of steepest descent steps in attraction basins associated with pL.

A 50,000-year record of Late Pleistocene tropical vegetation and human impact in lowland Borneo.

There has been considerable uncertainty about the nature of Pleistocene environments colonised by the first modern humans in Island SE Asia, and about the vegetation of the Last Glacial Maximum (LGM) in the region. Here, the palynology from a series of exposures in the Great Cave of Niah, Sarawak, Malaysian Borneo, spanning a period from ca. 52,000 to 5000 BP is described. Vegetation during this period was climate-driven and often highly unstable. Interstadials are marked by lowland forest, sometimes rather dry and at times by mangroves. Stadials are indicated by taxa characteristic of open environments or, as at the LGM, by highly disturbed rather open forest. Stadials are also characterised by taxa now restricted to 1000-1600 m above sea level, suggesting temperature declines of ca 7-9 C relative to present, by comparison with modern lapse rates. The practice of biomass burning appears associated with the earliest human activity in the cave.

Imported and translated landscapes: Buenos Aires nineteenth-century waterfront parks

The study of urban and landscape history has recently questioned the peripheral condition of certain areas and re-examined them as valuable parts of an international network . In such a framework cities are not only recipients of foreign influences but active agents in their own urban transformations. Meanwhile, the regeneration of urban waterfronts appears increasingly in the spotlight globally , but the re-use of the waterfront as public space began more than a century ago.

Buenos Aires is an example of a ‘peripheral’ city, in which waterfront parks at the end of the nineteenth century were the product of international influences combined with local conditions, needs and expertise. Buenos Aires developed a continuous increase and diversity of leisure waterfront space, making it different from most European or ‘central’ cities. This paper will analyse the process of translation of landscape design on Buenos Aires’ waterfront while outlining the significance of waterfront parks to the city and its growing urban population.

Holocene environmental changes in northeast Thailand as reconstructed from a tropical wetland

Geochemical variables (TOC, C/N, TS, delta C-13) and diatom assemblages were analyzed in a lake sediment sequence from Nong (Lake) Han Kumphawapi in northeast Thailand to reconstruct regional climatic and environmental history during the Holocene. By around c. 10,000-9400 cal yr BP, a large shallow freshwater lake had formed in the Kumphawapi basin. Oxygenated bottom waters and a well-mixed water column were characteristic of this early lake stage, which was probably initiated by higher effective moisture and a stronger summer monsoon. Decreased run-off after c. 6700 cal yr BP favored increased aquatic productivity in the shallow lake. Multiple proxies indicate a marked lowering of the lake level around 5900 cal yr BP, the development of an extensive wetland around 5400 cal yr BP, and the subsequent transition to a peatland. The shift from shallow lake to wetland and later to a peatland is interpreted as a response to lower effective moisture. A hiatus at the transition from wetland to peatland suggests very low accumulation rates, which may result from very dry climatic conditions. A rise in groundwater and lake level around 3200 cal yr BP allowed the re-establishment of a wetland in the Kumphawapi basin. However, the sediments deposited between c. 3200 and 1600 cal yr BP provide evidence for at least two hiatuses at c. 2700-2500 cal yr BP, and at c. 1900-1600 cal yr BP, which would suggest surface dryness and consequently periods of low effective moisture. Around 1600 cal yr BP a new shallow lake became re-established in the basin. Although the underlying causes for this new lake phase remain unclear, we hypothesize that higher effective moisture was the main driving force. This shallow lake phase continued up to the present but was interrupted by higher nutrient fluxes to the lake around 1000-600 cal yr BP. Whether this was caused by intensified human impact in the catchment or, whether this signals a lowering of the lake level due to reduced effective moisture, needs to be corroborated by further studies in the region. The multi-proxy study of Kumphawapi's sediment core CP3A clearly shows that Kumphawapi is a sensitive archive for recording past shifts in effective moisture, and as such in the intensity of the Asian summer monsoon. Many more continental paleorecords, however, will be needed to fully understand the spatial and temporal patterns of past changes in Asian monsoon intensity and its ecosystem impacts. (C) 2012 Elsevier B.V. All rights reserved.

Temperature and water potential relations of tropical Trametes and other wood-decay fungi from the indigenous forests of Zimbabwe

Three isolates each, of nine different Trametes and five other wood inhabiting basidiomycetes, were collected from the indigenous forests of Zimbabwe, and the impact of temperature (20-60 degrees C), osmotic and matric potential (-0.5 to - 8.0 MPa), and their interactions on in vitro growth compared. Generally, there was no significant difference between growth of isolates of the same species in relation to temperature. Temperature relationships of the species studied correlated well with their geographic distributions. Species occurring in hot, dry regions tolerated a wide temperature range, with some showing unusually high thermotolerance (55 degrees, T. socotrana, T. cingulata and T. cervina). There were significant intra-strain differences for individual species in relation to solute potential on glycerol-modified media. Generally, growth of ail species was better on glycerol- and KCl-modified osmotic media than on a metrically-modified medium (PEG 8000) at 25, 30 and 37 degrees. The limits for growth on the osmotic media were significantly wider than matric medium, being - 4.5 to - 5.0 and - 2.5 to - 4.5 MPa, respectively. An Irpex sp. grew at lower water potentials than all other species, with good growth at - 7.0 MPa. This study suggests that the capacity of these fungi for effective growth over a range of temperatures, osmotic and matric potentials contributes to their rapid wood decay capacities in tropical climates.

Simplifying the representation of complex free-energy landscapes using sketch-map

A new scheme, sketch-map, for obtaining a low-dimensional representation of the region of phase space explored during an enhanced dynamics simulation is proposed. We show evidence, from an examination of the distribution of pairwise distances between frames, that some features of the free-energy surface are inherently high-dimensional. This makes dimensionality reduction problematic because the data does not satisfy the assumptions made in conventional manifold learning algorithms We therefore propose that when dimensionality reduction is performed on trajectory data one should think of the resultant embedding as a quickly sketched set of directions rather than a road map. In other words, the embedding tells one about the connectivity between states but does not provide the vectors that correspond to the slow degrees of freedom. This realization informs the development of sketch-map, which endeavors to reproduce the proximity information from the high-dimensionality description in a space of lower dimensionality even when a faithful embedding is not possible.