Two-step Brillouin zone sampling for efficient computation of electron dynamics in solids

We develop a numerical Brillouin-zone integration scheme for real-time propagation of electronic systems with time-dependent density functional theory. This scheme is based on the decomposition of a large simulation into a set of small independent simulations. The performance of the decomposition scheme is examined in both linear and nonlinear regimes by computing the linear optical properties of bulk silicon and high-order harmonic generation. The decomposition of a large simulation into a set of independent simulations can improve the efficiency of parallel computation by reducing communication and synchronization overhead and enhancing the portability of simulations across a relatively small cluster machine.

Enhancement of wavefront measurement sensitivity in a zonal wavefront sensor without curtailing the sensing speed

In this paper we propose a zonal wavefront sensing scheme that facilitates wavefront measurement with enhanced sensitivity at the standard video rate. We achieve this enhanced sensitivity by implementing a sequential display of binary holograms described over each zone sampling the incident wavefront with the help of a ferroelectric liquid crystal spatial light modulator. By keeping the number of active zones as 24 and using a camera with an imaging frame rate equal to the binary hologram display rate of the spatial light modulator, we are able to reach the sensing frame rate of 60 Hz. In addition to enhancement in sensitivity, the proposed scheme facilitates zone wise tuning of binary holograms and eliminates the possibility of any crosstalk between adjacent zones. We perform a proof-of-principle experiment that validates the proposed zonal wavefront sensing scheme and demonstrates its advantages.

eDNA Captures Microhabitat Partitioning in a Kelp Forest Ecosystem

Environmental DNA (eDNA) metabarcoding is an increasingly important tool for surveying biodiversity in marine ecosystems. However, the scale of temporal and spatial variability in eDNA signatures, and how this variation may impact eDNA-based marine biodiversity assessments, remains uncertain. To address this question, we systematically examined variation in vertebrate eDNA signatures across depth (0 m to 10 m) and horizontal space (nearshore and surf zone) over three successive days in a Southern California kelp forest. Across a broad range of marine vertebrates (teleosts, elasmobranchs, birds, and mammals), results showed significant variation in species richness and community assemblages across 4-5 m depth, reflecting microhabitat depth preferences of common Southern California nearshore rocky reef taxa. We also found significant differences in community assemblages between nearshore and surf zone sampling stations at the same depth, and across three sampling days. Patterns of microhabitat partitioning in eDNA signatures across space and time were largely consistent with known habitat preferences and species behavior. Results highlight the sensitivity of eDNA in capturing fine-scale vertical, horizontal, and temporal variation in marine vertebrate communities, demonstrating the ability of eDNA to capture a highly localized snapshot of marine biodiversity in dynamic coastal environments.

A “feet digging” swash zone sampling method for the sandy beach bivalve Donax deltoides (Bivalvia: Donacidae)

ABSTRACTA “feet digging” method for sampling the sandy beach bivalve Donax deltoides was evaluated by comparison to quadrat-based results from eleven beaches in subtropical eastern Australia. The method was developed from a recreational fishing technique that involves twisting one’s feet into the thixotropic sand to dislodge buried clams which are then recovered by hand. Several plots are sampled across the swash zone in one five-minute sampling unit and the process is replicated at several locations along the beach. Mean feet digging clam counts were proportional to mean transect linear clam densities (r = 0.98). Clam length-frequency distributions from feet digging were similar to those from quadrat sampling except that feet digging was not effective for clams < 16 mm. Feet digging counts are sensitive to both across shore (tidal) and alongshore variation in clam abundance and were less precise than those from quadrat-based methods (CV 1.2× larger). However, feet digging is fast and the method should be useful for low cost surveys of Donax deltoides and similar “surf clams”.

Genes, geology and germs: gut microbiota across a primate hybrid zone are explained by site soil properties, not host species

Gut microbiota in geographically isolated host populations are often distinct. These differences have been attributed to between-population differences in host behaviours, environments, genetics and geographical distance. However, which factors are most important remains unknown. Here, we fill this gap for baboons by leveraging information on 13 environmental variables from 14 baboon populations spanning a natural hybrid zone. Sampling across a hybrid zone allowed us to additionally test whether phylosymbiosis (codiversification between hosts and their microbiota) is detectable in admixed, closely related primates. We found little evidence of genetic effects: none of host genetic ancestry, host genetic relatedness nor genetic distance between host populations were strong predictors of baboon gut microbiota. Instead, gut microbiota were best explained by the baboons' environments, especially the soil's geologic history and exchangeable sodium. Indeed, soil effects were 15 times stronger than those of host–population F ST, perhaps because soil predicts which foods are present, or because baboons are terrestrial and consume soil microbes incidentally with their food. Our results support an emerging picture in which environmental variation is the dominant predictor of host-associated microbiomes. We are the first to show that such effects overshadow host species identity among members of the same primate genus.

Importance of biogenic substrates for the stone crab Menippe nodifrons Stimpson, 1859 (Brachyura: Eriphioidea)

In order to better understand the ecology of the different growth phases of the stone crab, Menippe nodifrons, and provide information for conservation of the natural stocks, this study describes the utilization of different biogenic substrates by this species in the intertidal zone. Sampling was carried out by hand at Ubatuba, State of São Paulo, Brazil. Crabs were captured among rocks or in association with three different biogenic substrates: Phragmatopoma lapidosa, Sargassum cymosum and Schizoporella unicornis. In the laboratory, the substrates were sorted and scanned for specimens of M. nodifrons, which were separated and measured at their maximum carapace width (CW), and classified as juvenile or adult specimens. Sex ratio and size distribution of crabs were analyzed for each of the substrate types. A total of 686 specimens of M. nodifrons were obtained during the sampling, ranging in size between 2.4 and 82.5 mm CW. Different mean sizes were recorded in the different substrates (P < 0.05). The high prevalence of juveniles in the samples suggests that these microhabitats are fundamental for the juvenile development of M. nodifrons, as they provide refuge, protection and probably food for juveniles.