Statistics of RNA melting kinetics

We present and study the behavior of a simple kinetic model for the melting of RNA secondary structures, given that those structures are known. The model is then used as a map that. assigns structure dependent overall rate constants of melting (or refolding) to a sequence. This induces a landscape of reaction rates, or activation energies, over the space of sequences with fixed length. We study the distribution and the correlation structure of these activation energies. Correspondence to: P. Schuster     

Analysis of nitrogen saturation potential in Rocky Mountain tundra and forest: implications for aquatic systems

We employed grass and forest versions of the CENTURY model under a range of N deposition values (0.02–1.60 g N m^–2 y^–1) to explore the possibility that high observed lake and stream N was due to terrestrial N saturation of alpine tundra and subalpine forest in Loch Vale Watershed, Rocky Mountain National Park, Colorado. Model results suggest that N is limiting to subalpine forest productivity, but that excess leachate from alpine tundra is sufficient to account for the current observed stream N. Tundra leachate, combined with N leached from exposed rock surfaces, produce high N loads in aquatic ecosystems above treeline in the Colorado Front Range. A combination of terrestrial leaching, large N inputs from snowmelt, high watershed gradients, rapid hydrologic flushing and lake turnover times, and possibly other nutrient limitations of aquatic organisms constrain high elevation lakes and streams from assimilating even small increases in atmospheric N. CENTURY model simulations further suggest that, while increased N deposition will worsen the situation, nitrogen saturation is an ongoing phenomenon.     

Changes in carbon storage in temperate humic loamy soils after forest clearing and continuous corn cropping in France

Soil samples from forest and agricultural sites in three areas of southwest France were collected to determine the effect of forest conversion to continuous intensive corn cropping with no organic matter management on soil organic carbon (C) content. Soils were humic loamy soils and site characteristics that may affect soil C were as uniform as possible (slope, elevation, texture, soil type, vegetation). Three areas were selected, with adjacent sites of various ages of cultivation (3 to 35 yr), and paired control forest sites. The ploughed horizon (0-Dt cm) and the Dt-50 cm layer were collected at each agricultural site. In forest sites, each 10 cm layer was collected systematically down to 1 meter depth. Carbon concentrations were converted to total content to a given depth as the product of concentration, depth of sample and bulk density, and expressed in units of kg m^-2. For each site and each sampled layer, the mineral mass of soil was calculated, in order to base comparisons on the same soil mass rather than the same depth. The pattern of C accumulation in forest soils showed an exponential decrease with depth. Results suggested that soil organic carbon declined rapidly during the first years of cultivation, and at a slower rate thereafter. This pattern of decrease can be fitted by a bi-exponential model assuming that initial soil organic carbon can be separated into two parts, a very labile pool reduced during the first rapid decline and more refractory fractions oxidizing at a slower rate. Sampling to shallow depths (0-Dt cm) resulted in over-estimation of the rate of carbon release in proportion to the initial amount of C, and in under-estimation of the total loss of C with age. The results for the 0–50 cm horizon indicated that losses of total carbon average about 50% in these soils, ranging in initial carbon content from 19 to 32.5 kg m^-2. Carbon release to the atmosphere averaged 0.8 kg m^-2 yr^-1 to 50 cm depth during the first 10 years of cultivation. The results demonstrate that temperate soils may also be an important source of atmospheric carbon, when they are initially high in carbon content and then cultivated intensively with no organic matter management.     

Stomatal and environmental control of transpiration in a lowland tropical forest tree

Stomatal control of crown transpiration was studied in Anacardium excelsum, a large-leaved, emergent canopy species common in the moist forests of Central and northern South America. A construction crane equipped with a gondola was used to gain access to the uppermost level in the crown of a 35-m-tall individual. Stomatal conductance at the single leaf scale, and transpiration and total vapour phase conductance (stomatal and boundary layer) at the branch scale were measured simultaneously using the independent techniques of porometry and stem heat balance, respectively. This permitted the sensitivity of transpiration to a marginal change in stomatal conductance to be evaluated using a dimensionless coupling coefficient (1-ω) ranging from zero to 1, with 1 representing maximal stomatal control of transpiration. Average stomatal conductance varied from 0.09 mol m^?2 s^?1 during the dry season to 0.3 mol m^?2 s^?1 during the wet season. Since boundary layer conductance was relatively low (0.4 mol m^?2 s^?1), 1-ω ranged from 0.46 during the dry season to only 0.25 during the wet season. A pronounced stomatal response to humidity was observed, which strongly limited transpiration as evaporative demand increased. The stomatal response to humidity was apparent only when the leaf surface was used as the reference point for measurement of external vapour pressure. Average transpiration was predicted to be nearly the same during the dry and wet seasons despite a 1 kPa difference in the prevailing leaf-to-air vapour pressure difference. The patterns of stomatal behaviour and transpiration observed were consistent with recent proposals that stomatal responses to humidity are based on sensing the transpiration rate itself.     

The dynamics and retention of phosphorus in lentic and lotic patches of two river-lake systems

Two river-lake systems in a mosaic, lowland postglacial landscape (Masurian and Suwalskie Lakelands, northeastern Poland) of different length and flow were studied. The concentration of total and dissolved phosphorus (in water and in seston) and the retention of these two forms of P were analysed at several hydrological occasions in lakes of various morphometry and trophy, and in several stream fragments. The concentration and retention is equally highly variable in lake (lentic patches) and stream fragments (lotic patches) of the system. The polluted stream fragments at all occassions as well as the lakes in summer, are mainly exporting phoshorus. The patches which act as sources occur alternatively with patches which are P-sinks. This makes the whole system more or less balanced with respect to P movement in the landscape.     

Short-term photosynthesis measurements predict leaf carbon balance in tropical rain-forest canopy plants

Diel (24 h) courses of net CO₂ exchange of leaves were determined in eight species of tropical rainforest plants on Barro Colorado Island, Panama, during 1990 and 1991. The species included three canopy trees, one liana, two epiphytes and one hemiepiphyte. One of the species studied was growing in a rain-forest gap. Daily carbon gain varied considerably across species, leaf age, and season. The analysis of data for all plants from 64 complete day/night cycles revealed a linear relationship between the diurnal carbon gain and the maximum rate of net CO₂ uptake, A_max. Nocturnal net carbon loss was about 10% of diurnal carbon gain and was positively related to A_max. We conclude that short-term measurements of light-saturated photosynthesis, performed at periodic intervals throughout the season, allow the annual leaf carbon balance in these rain-forest plants to be predicted.     

Understorey vegetation moderates climate in open forests: The role of the skirt-forming grass tree Xanthorrhoea semiplana F.Muell

Microsites are created by abiotic and biotic features of the landscape and may provide essential habitats for the persistence of biota. Forest canopies and understorey plants may moderate wind and solar radiation to create microclimatic conditions that differ considerably from regional climates. Skirt-forming plants, where senescent leaves create hut-like cavities around the stem, create microsites that are sheltered from ambient conditions and extreme weather events, constituting potential refuges for wildlife. We investigate day and night temperatures and humidity for four locations (grass tree cavities, soil, 20 cm above-ground, 1 m above-ground) in a South Australian forest with relatively open canopy of stringybark eucalypts (Eucalyptus baxteri, E. obliqua) and an understorey of skirt-forming grass trees (Xanthorrhoea semiplana) at 5, 10, 20, and 40 m from the forest edge. We also measured the percentage of canopy and understorey covers. Generally, temperature and humidity differed significantly between more sheltered (grass tree cavities, soil) and open-air microsites, with the former being cooler during the day and warmer and more humid during the night. Furthermore, our results suggest that canopy cover tends to decrease, and understorey cover tends to increase, the temperature of microsites. Distance to the edge was not significantly related to temperature for any microsite, suggesting that the edge effect did not extend beyond 10 m from the edge. Overall, grass trees influenced microclimatic conditions by forming a dense understorey and providing cavities that are relatively insulated. The capacity of grass tree cavities to buffer external conditions increased linearly with ambient temperatures, by 0.46°C per degree increase in maximum and 0.25°C per degree decrease in minimum temperatures, potentially offsetting climate warming and enabling persistence of fauna within their thermal limits. These climate moderation properties will make grass trees increasingly important refuges as extreme weather events become more common under anthropogenic climate change.     

Defining null expectations for animal site fidelity

Site fidelity—the tendency to return to previously visited locations—is widespread across taxa. Returns may be driven by several mechanisms, including memory, habitat selection, or chance; however, pattern-based definitions group different generating mechanisms under the same label of ‘site fidelity’, often assuming memory as the main driver. We propose an operational definition of site fidelity as patterns of return that deviate from a null expectation derived from a memory-free movement model. First, using agent-based simulations, we show that without memory, intrinsic movement characteristics and extrinsic landscape characteristics are key determinants of return patterns and that even random movements may generate substantial probabilities of return. Second, we illustrate how to implement our framework empirically to establish ecologically meaningful, system-specific null expectations for site fidelity. Our approach provides a conceptual and operational framework to test hypotheses on site fidelity across systems and scales.