A steepest descent calculation of RNA pseudoknots

We enumerate possible topologies of pseudoknots in single-stranded RNA molecules. We use a steepest-descent approximation in the large N matrix field theory, and a Feynman diagram formalism to describe the resulting pseudoknot structure

Another tool in the toolbox? Using fire and grazing to promote bird diversity in highly fragmented landscapes

The grasslands of central North America have experienced drastic reductions in extent, removal of historic disturbance patterns, and homogenization of remaining fragments. This has resulted in steep declines for a broad swath of grassland biodiversity. Recent work in relatively extensive grasslands has demonstrated that mimicking historic disturbance patterns using a fire‐grazing interaction can increase the abundance and diversity of grassland birds through increased habitat heterogeneity. We examined the efficacy of this management strategy for promoting avian diversity in highly fragmented landscapes, which represent the bulk of remaining grassland bird habitats in the tallgrass prairie region. We quantified the population density of obligate and facultative grassland bird species along transects in 13 experimental research pastures in the Grand River Grasslands of Iowa and Missouri (USA), divided among three treatments: 1) spatially discrete fires and free access by cattle (“patch‐burn grazed”), 2) free access by cattle and a single complete burn (“grazed‐and‐burned”), and 3) a single complete burn with no cattle (“burned‐only”). We expected that patch‐burn grazing would produce a bird community that overlapped that of the grazed‐and‐burned and burned‐only treatments, because it would provide habitat for species associated with both. However, an analysis of similarity (ANOSIM) showed that community structure on pastures managed using patch‐burn grazing instead diverged significantly from both of the other treatments. Differences in community structure were most highly correlated with visual obstruction and wooded edge density in the landscape, suggesting bird communities are differentiated not only by their structural habitat requirements, but also by the varying degrees of sensitivity to landscape fragmentation of their component species. The future success of this management scheme for fragmented grasslands hinges on if, after an optimal stocking rate is identified, adequate habitat can be maintained for a diverse bird community, or whether fragmentation will perpetually limit the efficacy of this method in these landscapes.Peer reviewedNatural Resource Ecology and Managemen

Analysis of Abrupt Transitions in Ecological Systems

The occurrence and causes of abrupt transitions, thresholds, or regime shifts between ecosystem states are of great concern and the likelihood of such transitions is increasing for many ecological systems. General understanding of abrupt transitions has been advanced by theory, but hindered by the lack of a common, accessible, and data-driven approach to characterizing them. We apply such an approach to 30–60 years of data on environmental drivers, biological responses, and associated evidence from pelagic ocean, coastal benthic, polar marine, and semi-arid grassland ecosystems. Our analyses revealed one case in which the response (krill abundance) linearly tracked abrupt changes in the driver (Pacific Decadal Oscillation), but abrupt transitions detected in the three other cases (sea cucumber abundance, penguin abundance, and black grama grass production) exhibited hysteretic relationships with drivers (wave intensity, sea-ice duration, and amounts of monsoonal rainfall, respectively) through a variety of response mechanisms. The use of a common approach across these case studies illustrates that: the utility of leading indicators is often limited and can depend on the abruptness of a transition relative to the lifespan of responsive organisms and observation intervals; information on spatiotemporal context is useful for comparing transitions; and ancillary information from associated experiments and observations aids interpretation of response-driver relationships. The understanding of abrupt transitions offered by this approach provides information that can be used to manage state changes and underscores the utility of long-term observations in multiple sentinel sites across a variety of ecosystems.Organismic and Evolutionary Biolog

Effects of tidal-forcing variations on tidal properties along a narrow convergent estuary

A 1D analytical framework is implemented in a narrow convergent estuary that is 78 km in length (the Guadiana, Southern Iberia) to evaluate the tidal dynamics along the channel, including the effects of neap-spring amplitude variations at the mouth. The close match between the observations (damping from the mouth to ∼ 30 km, shoaling upstream) and outputs from semi-closed channel solutions indicates that the M2 tide is reflected at the estuary head. The model is used to determine the contribution of reflection to the dynamics of the propagating wave. This contribution is mainly confined to the upper one third of the estuary. The relatively constant mean wave height along the channel (< 10% variations) partly results from reflection effects that also modify significantly the wave celerity and the phase difference between tidal velocity and elevation (contradicting the definition of an “ideal” estuary). Furthermore, from the mouth to ∼ 50 km, the variable friction experienced by the incident wave at neap and spring tides produces wave shoaling and damping, respectively. As a result, the wave celerity is largest at neap tide along this lower reach, although the mean water level is highest in spring. Overall, the presented analytical framework is useful for describing the main tidal properties along estuaries considering various forcings (amplitude, period) at the estuary mouth and the proposed method could be applicable to other estuaries with small tidal amplitude to depth ratio and negligible river discharge.info:eu-repo/semantics/publishedVersio