Mean growth rate when rare is not a reliable metric for persistence of species

The coexistence of many species within ecological communities poses a long‐standing theoretical puzzle. Modern coexistence theory (MCT) and related techniques explore this phenomenon by examining the chance of a species population growing from rarity in the presence of all other species. The mean growth rate when rare, , is used in MCT as a metric that measures persistence properties (like invasibility or time to extinction) of a population. Here we critique this reliance on and show that it fails to capture the effect of temporal random abundance variations on persistence properties. The problem becomes particularly severe when an increase in the amplitude of stochastic temporal environmental variations leads to an increase in , since at the same time it enhances random abundance fluctuations and the two effects are inherently intertwined. In this case, the chance of invasion and the mean extinction time of a population may even go down as increases.     

Conservation and divergence of axon guidance mechanisms.

Analysis of axon guidance mechanisms in vertebrates, Caenorhabditis elegans, and Drosophila melanogaster has led to the identification of several signaling pathways, many of which are strikingly conserved in function. Recent studies indicate that several axon guidance mechanisms are highly conserved in all animals, whereas others, though still conserved in a general sense, show strong evolutionary divergence at a detailed mechanistic level.     

Linking dispersal, immigration and scale in the neutral theory of biodiversity

In the classic spatially implicit formulation of Hubbell's neutral theory of biodiversity a local community receives immigrants from a metacommunity operating on a relatively slow timescale, and dispersal into the local community is governed by an immigration parameter m . A current problem with neutral theory is that m lacks a clear biological interpretation. Here, we derive analytical expressions that relate the immigration parameter m to the geometry of the plot defining the local community and the parameters of a dispersal kernel. Our results facilitate more rigorous and extensive tests of the neutral theory: we conduct a test of neutral theory by comparing estimates of m derived from fits to empirical species abundance distributions to those derived from dispersal kernels and find acceptable correspondence; and we generate a new prediction of neutral theory by investigating how the shapes of species abundance distributions change theoretically as the spatial scale of observation changes. We also discuss how our main analytical results can be used to assess the error in the mean-field approximations associated with spatially implicit formulations of neutral theory.     

A Statistical Comparison between Less and Common Applied Models to Estimate Geographical Distribution of Endangered Species (<Emphasis Type="Italic">Felis margarita</Emphasis>) in Central Iran

Species distribution in space is important in habitat conservation and biodiversity protection, so gaining knowledge about species range would be worthwhile to rescue endangered species and plan conservation policy. This study evaluates and compares the performance of an array of Species Distribution Models (SDMs), namely RF, SVM, MaxEnt, GLMNET, and MARS, in predicting rare sand cat distribution across a large unprotected sand dune area in central Iran. Due to absence of reliable data and difficulties in recording the species itself, the SDMs were challenged by limited data including 55 absence (background) and 40 presence points as well as nine climatic and geological parameters that influence on species distribution, including humidity, maximum, minimum and mean temperature, precipitation, amount of sunshine, ground water level, aspect, and DEM. Moreover, each model was replicated 20 times and the statistics including TSS, AUC, COR and Deviance were computed. Then, based on computed statistics, the model performances were evaluated by TUKEY and ANOVA. Finally, ensemble map was obtained by weighted approach using AUC. The results of this study showed that complex machine learning methods, like SVM, RF, and MaxEnt are more outperformed to predict the distribution of rare species.     

A comparison of two methods for measuring phosphate uptake by Monochrysis lutheri droop grown in continuous culture

Two methods for measuring phosphate uptake by phosphate-limited continuous cultures of Monochrysis lutheri Droop are found to yield comparable results. Data from both isotopic tracer (³³P) and disappearance experiments strongly support a Michaelis- Menten-type hyperbolic relationship between instantaneous uptake rate and ambient phosphate concentration. The data show no systematic linear trend in either the maximum uptake rate per cell or its associated half saturation constant with pre-conditioning steady state growth rate; a weak non-linear trend with pre-conditioning may, however, be present in the maximum uptake rate with an apparent maximum at intermediate growth rates.     

Combined monte carlo and molecular dynamics simulation of fully hydrated dioleyl and palmitoyl-oleyl phosphatidylcholine lipid bilayers

We have applied a new equilibration procedure for the atomic level simulation of a hydrated lipid bilayer to hydrated bilayers of dioleyl-phosphatidylcholine (DOPC) and palmitoyl-oleyl phosphatidylcholine (POPC). The procedure consists of alternating molecular dynamics trajectory calculations in a constant surface tension and temperature ensemble with configurational bias Monte Carlo moves to different regions of the configuration space of the bilayer in a constant volume and temperature ensemble. The procedure is applied to bilayers of 128 molecules of POPC with 4628 water molecules, and 128 molecules of DOPC with 4825 water molecules. Progress toward equilibration is almost three times as fast in central processing unit (CPU) time compared with a purely molecular dynamics (MD) simulation. Equilibration is complete, as judged by the lack of energy drift in 200-ps runs of continuous MD. After the equilibrium state was reached, as determined by agreement between the simulation volume per lipid molecule with experiment, continuous MD was run in an ensemble in which the lateral area was restrained to fluctuate about a mean value and a pressure of 1 atm applied normal to the bilayer surface. Three separate continuous MD runs, 200 ps in duration each, separated by 10,000 CBMC steps, were carried out for each system. Properties of the systems were calculated and averaged over the three separate runs. Results of the simulations are presented and compared with experimental data and with other recent simulations of POPC and DOPC. Analysis of the hydration environment in the headgroups supports a mechanism by which unsaturation contributes to reduced transition temperatures. In this view, the relatively horizontal orientation of the unsaturated bond increases the area per lipid, resulting in increased water penetration between the headgroups. As a result the headgroup-headgroup interactions are attenuated and shielded, and this contributes to the lowered transition temperature.