Comparison of methods for estimating the nucleotide substitution matrix

10.1186/1471-2105-9-511BMC Bioinformatics9-BBMI

The tragedy of the common? A comparative population genomic study of two bumblebee species

Within the theoretical framework of the small population paradigm, we investigated the population genomics and parasite load of two bumblebee species across the UK and Ireland. Bombus pratorum is widespread and common throughout its range while Bombus monticola is restricted to higher altitudes and shows a more fragmented distribution. Bombus monticola showed stronger population structuring, isolation-by-distance, and a deficit of heterozygotes in the most isolated population in the south of its range (Dartmoor). Heterozygosity and inbreeding coefficients (FIS) were comparable between both species, but the proportion of polymorphic sites was much greater in B. pratorum. Notably, both species have suffered significant declines in Ne over the last 100 generations and estimates and declines for both species were of similar orders of magnitude. No pattern of increased parasite prevalence in populations of lower heterozygosity was observed. Instead, ecological and demographic factors (age, latitude, date, habitat suitability) were the main drivers of parasite prevalence. Distinct patterns of selection were observed in both species in regions involved in regulation of transcription and neurotransmission and in particular pathways targeted by neonicotinoid insecticides. Our results highlight the pressing need for monitoring to include common as well as rare species. This should not focus solely on census population counts, but include estimates of Ne. We also highlight the need for further work to establish adaptive shifts in globally important pollinator communities

Micro-habitat distribution drives patch quality for sub-tropical rocky plateau amphibians in the northern Western Ghats, India.

The importance of patch quality for amphibians is frequently overlooked in distribution models. Here we demonstrate that it is highly important for the persistence of endemic and endangered amphibians found in the threatened and fragile ecosystems that are the rocky plateaus in Western Maharashtra, India. These plateaus are ferricretes of laterite and characterise the northern section of the Western Ghats/Sri Lanka Biodiversity Hotspot, the eighth most important global hotspot and one of the three most threatened by population growth. We present statistically supported habitat associations for endangered and data-deficient Indian amphibians, demonstrating significant relationships between individual species and their microhabitats. Data were collected during early monsoon across two seasons. Twenty-one amphibian taxa were identified from 14 lateritic plateaus between 67 and 1179m above sea level. Twelve of the study taxa had significant associations with microhabitats using a stepwise analysis of the AICc subroutine (distLM, Primer-e, v7). Generalist taxa were associated with increased numbers of microhabitat types. Non-significant associations are reported for the remaining 9 taxa. Microhabitat distribution was spatially structured and driven by climate and human activity. Woody plants were associated with 44% of high-elevation taxa. Of the 8 low-elevation taxa 63% related to water bodies and 60% of those were associated with pools. Rock size and abundance were important for 33% of high elevation specialists. Three of the 4 caecilians were associated with rocks in addition to soil and stream presence. We conclude the plateaus are individualistic patches whose habitat quality is defined by their microhabitats within climatic zones

Fabrication of photonic crystals in rare-earth doped chalcogenide glass films for enhanced upconversion

Gallium lanthanum oxysulfide (GLSO) is a promising host material for observing strong upconversion emission from trivalent rare-earth ions such as erbium (Er3+). Its attractive properties include high rare-earth solubility due to the lanthanum content of the glass former, a high refractive index (n = 2.2 at 550nm) for high radiative efficiency, and a low maximum phonon energy of approximately 425cm-1. Photonic crystals meanwhile can provide controlled light extraction, and may be capable of suppressing unwanted IR emission from lower lying metastable states. Here, we describe the fabrication of photonic crystals in annealed films of Er3+-doped GLSO deposited by RF sputtering. The most intense visible upconversion emission is observed in films annealed at 550°C, close to the bulk glass transition temperature. Hexagonal lattice photonic crystals are subsequently milled into the films using a focused ion beam (FIB). The milling parameters are optimized to produce the most vertical sidewall profile

A microscopic 2D lattice model of dimer granular compaction with friction

We study by Monte Carlo simulation the compaction dynamics of hard dimers in 2D under the action of gravity, subjected to vertical and horizontal shaking, considering also the case in which a friction force acts for horizontal displacements of the dimers. These forces are modeled by introducing effective probabilities for all kinds of moves of the particles. We analyze the dynamics for different values of the time $\tau$ during which the shaking is applied to the system and for different intensities of the forces. It turns out that the density evolution in time follows a stretched exponential behavior if $\tau$ is not very large, while a power law tail develops for larger values of $\tau$. Moreover, in the absence of friction, a critical value $\tau^*$ exists which signals the crossover between two different regimes: for $\tau < \tau^*$ the asymptotic density scales with a power law of $\tau$, while for $\tau > \tau^*$ it reaches logarithmically a maximal saturation value. Such behavior smears out when a finite friction force is present. In this situation the dynamics is slower and lower asymptotic densities are attained. In particular, for significant friction forces, the final density decreases linearly with the friction coefficient. We also compare the frictionless single tap dynamics to the sequential tapping dynamics, observing in the latter case an inverse logarithmic behavior of the density evolution, as found in the experiments.Comment: 10 pages, 15 figures, to be published in Phys. Rev.

Wetting films on chemically heterogeneous substrates

Based on a microscopic density functional theory we investigate the morphology of thin liquidlike wetting films adsorbed on substrates endowed with well-defined chemical heterogeneities. As paradigmatic cases we focus on a single chemical step and on a single stripe. In view of applications in microfluidics the accuracy of guiding liquids by chemical microchannels is discussed. Finally we give a general prescription of how to investigate theoretically the wetting properties of substrates with arbitrary chemical structures.Comment: 56 pages, RevTeX, 20 Figure

Vibration-induced "thermally activated" jamming transition in granular media

The quasi-static frequency response of a granular medium is measured by a forced torsion oscillator method, with forcing frequency $f_{p}$ in the range $10^{-4}$ Hz to 5 Hz, while weak vibrations at high-frequency $f_{s}$, in the range 50 Hz to 200 Hz, are generated by an external shaker. The intensity of vibration, $\Gamma$, is below the fluidization limit. A loss factor peak is observed in the oscillator response as a function of $\Gamma$ or $f_{p}$. In a plot of $\ln f_{p}$ against $1/\Gamma$, the position of the peak follows an Arrhenius-like behaviour over four orders of magnitude in $f_{p}$. The data can be described as a stochastic hopping process involving a probability factor $\exp(-\Gamma_{j}/\Gamma)$ with $\Gamma_{j}$ a $f_{s}$-dependent characteristic vibration intensity. A $f_{s}$-independent description is given by $\exp(-\tau_{j}/\tau)$, with $\tau_{j}$ an intrinsic characteristic time, and $\tau =\Gamma ^{n}/2\pi f_{s}$, n=0.5-0.6, an empirical control parameter with unit of time. $\tau$ is seen as the effective average time during which the perturbed grains can undergo structural rearrangement. The loss factor peak appears as a crossover in the dynamic behaviour of the vibrated granular system, which, at the time-scale $1/f_{p}$, is solid-like at low $\Gamma$, and the oscillator is jammed into the granular material, and is fluid-like at high $\Gamma$, where the oscillator can slide viscously.Comment: Final version to appear in PR

Toward a predictive understanding of earth’s microbiomes to address 21st century challenges

Microorganisms have shaped our planet and its inhabitants for over 3.5 billion years. Humankind has had a profound influence on the biosphere, manifested as global climate and land use changes, and extensive urbanization in response to a growing population. The challenges we face to supply food, energy, and clean water while maintaining and improving the health of our population and ecosystems are significant. Given the extensive influence of microorganisms across our biosphere, we propose that a coordinated, cross-disciplinary effort is required to understand, predict, and harness microbiome function. From the parallelization of gene function testing to precision manipulation of genes, communities, and model ecosystems and development of novel analytical and simulation approaches, we outline strategies to move microbiome research into an era of causality. These efforts will improve prediction of ecosystem response and enable the development of new, responsible, microbiome-based solutions to significant challenges of our time