Image Fusion Applied to Satellite Imagery for the Improved Mapping and Monitoring of Coral Reefs: a Proposal

NASA Astrophysics Data System (ADS)

Gholoum, M.; Bruce, D.; Hazeam, S. Al

2012-07-01

A coral reef ecosystem, one of the most complex marine environmental systems on the planet, is defined as biologically diverse and immense. It plays an important role in maintaining a vast biological diversity for future generations and functions as an essential spawning, nursery, breeding and feeding ground for many kinds of marine species. In addition, coral reef ecosystems provide valuable benefits such as fisheries, ecological goods and services and recreational activities to many communities. However, this valuable resource is highly threatened by a number of environmental changes and anthropogenic impacts that can lead to reduced coral growth and production, mass coral mortality and loss of coral diversity. With the growth of these threats on coral reef ecosystems, there is a strong management need for mapping and monitoring of coral reef ecosystems. Remote sensing technology can be a valuable tool for mapping and monitoring of these ecosystems. However, the diversity and complexity of coral reef ecosystems, the resolution capabilities of satellite sensors and the low reflectivity of shallow water increases the difficulties to identify and classify its features. This paper reviews the methods used in mapping and monitoring coral reef ecosystems. In addition, this paper proposes improved methods for mapping and monitoring coral reef ecosystems based on image fusion techniques. This image fusion techniques will be applied to satellite images exhibiting high spatial and low to medium spectral resolution with images exhibiting low spatial and high spectral resolution. Furthermore, a new method will be developed to fuse hyperspectral imagery with multispectral imagery. The fused image will have a large number of spectral bands and it will have all pairs of corresponding spatial objects. This will potentially help to accurately classify the image data. Accuracy assessment use ground truth will be performed for the selected methods to determine the quality of the information derived from image classification. The research will be applied to the Kuwait's southern coral reefs: Kubbar and Um Al-Maradim.

The History of Electromagnetic Induction Techniques in Soil Survey

NASA Astrophysics Data System (ADS)

Brevik, Eric C.; Doolittle, Jim

2014-05-01

Electromagnetic induction (EMI) has been used to characterize the spatial variability of soil properties since the late 1970s. Initially used to assess soil salinity, the use of EMI in soil studies has expanded to include: mapping soil types; characterizing soil water content and flow patterns; assessing variations in soil texture, compaction, organic matter content, and pH; and determining the depth to subsurface horizons, stratigraphic layers or bedrock, among other uses. In all cases the soil property being investigated must influence soil apparent electrical conductivity (ECa) either directly or indirectly for EMI techniques to be effective. An increasing number and diversity of EMI sensors have been developed in response to users' needs and the availability of allied technologies, which have greatly improved the functionality of these tools. EMI investigations provide several benefits for soil studies. The large amount of georeferenced data that can be rapidly and inexpensively collected with EMI provides more complete characterization of the spatial variations in soil properties than traditional sampling techniques. In addition, compared to traditional soil survey methods, EMI can more effectively characterize diffuse soil boundaries and identify included areas of dissimilar soils within mapped soil units, giving soil scientists greater confidence when collecting spatial soil information. EMI techniques do have limitations; results are site-specific and can vary depending on the complex interactions among multiple and variable soil properties. Despite this, EMI techniques are increasingly being used to investigate the spatial variability of soil properties at field and landscape scales.

Quantitative phase imaging of biological cells using spatially low and temporally high coherent light source.

PubMed

Ahmad, Azeem; Dubey, Vishesh; Singh, Gyanendra; Singh, Veena; Mehta, Dalip Singh

2016-04-01

In this Letter, we demonstrate quantitative phase imaging of biological samples, such as human red blood cells (RBCs) and onion cells using narrow temporal frequency and wide angular frequency spectrum light source. This type of light source was synthesized by the combined effect of spatial, angular, and temporal diversity of speckle reduction technique. The importance of using low spatial and high temporal coherence light source over the broad band and narrow band light source is that it does not require any dispersion compensation mechanism for biological samples. Further, it avoids the formation of speckle or spurious fringes which arises while using narrow band light source.

Environmental Assessment and Monitoring with ICAMS (Image Characterization and Modeling System) Using Multiscale Remote-Sensing Data

NASA Technical Reports Server (NTRS)

Lam, N.; Qiu, H.-I.; Quattrochi, Dale A.; Zhao, Wei

1997-01-01

With the rapid increase in spatial data, especially in the NASA-EOS (Earth Observing System) era, it is necessary to develop efficient and innovative tools to handle and analyze these data so that environmental conditions can be assessed and monitored. A main difficulty facing geographers and environmental scientists in environmental assessment and measurement is that spatial analytical tools are not easily accessible. We have recently developed a remote sensing/GIS software module called Image Characterization and Modeling System (ICAMS) to provide specialized spatial analytical tools for the measurement and characterization of satellite and other forms of spatial data. ICAMS runs on both the Intergraph-MGE and Arc/info UNIX and Windows-NT platforms. The main techniques in ICAMS include fractal measurement methods, variogram analysis, spatial autocorrelation statistics, textural measures, aggregation techniques, normalized difference vegetation index (NDVI), and delineation of land/water and vegetated/non-vegetated boundaries. In this paper, we demonstrate the main applications of ICAMS on the Intergraph-MGE platform using Landsat Thematic Mapper images from the city of Lake Charles, Louisiana. While the utilities of ICAMS' spatial measurement methods (e.g., fractal indices) in assessing environmental conditions remain to be researched, making the software available to a wider scientific community can permit the techniques in ICAMS to be evaluated and used for a diversity of applications. The findings from these various studies should lead to improved algorithms and more reliable models for environmental assessment and monitoring.

A six-year grazing exclusion changed plant species diversity of a Stipa breviflora desert steppe community, northern China.

PubMed

Wang, Xing; Yang, Xinguo; Wang, Lei; Chen, Lin; Song, Naiping; Gu, Junlong; Xue, Yi

2018-01-01

Excluding grazers is one of most efficient ways to restore degraded grasslands in desert-steppe communities, but may negatively affect the recovery of plant species diversity. However, diversity differences between grazed and fenced grasslands in desert-steppe are poorly known. In a Stipa breviflora desert steppe community in Northern China, we established six plots to examine spatial patterns of plant species diversity under grazed and fenced conditions, respectively. We addressed three aspects of species diversity: (1) The logistic, exponential and power models were used to describe the species-area curve (SAR). Species richness, abundance and Shannon diversity values change differently with increasing sampling areas inside and outside of the fence. The best fitted model for SAR was the logistic model. Excluding grazers had a significant impact on the shape of SAR. (2) Variograms was applied to examine the spatial characteristics of plant species diversity. We found strong spatial autocorrelations in the diversity variables both inside and outside the fence. After grazing exclusion, the spatial heterogeneity decreased in species richness, increased in abundance and did not change in Shannon diversity. (3) We used variance partitioning to determine the relative contributions of spatial and environmental factors to plant species diversity patterns. Environmental factors explained the largest proportion of variation in species diversity, while spatial factors contributed little. Our results suggest that grazing enclosures decreased species diversity patterns and the spatial pattern of the S. breviflora desert steppe community was predictable.

A six-year grazing exclusion changed plant species diversity of a Stipa breviflora desert steppe community, northern China

PubMed Central

Wang, Xing; Yang, Xinguo; Wang, Lei; Chen, Lin; Gu, Junlong; Xue, Yi

2018-01-01

Excluding grazers is one of most efficient ways to restore degraded grasslands in desert-steppe communities, but may negatively affect the recovery of plant species diversity. However, diversity differences between grazed and fenced grasslands in desert-steppe are poorly known. In a Stipa breviflora desert steppe community in Northern China, we established six plots to examine spatial patterns of plant species diversity under grazed and fenced conditions, respectively. We addressed three aspects of species diversity: (1) The logistic, exponential and power models were used to describe the species-area curve (SAR). Species richness, abundance and Shannon diversity values change differently with increasing sampling areas inside and outside of the fence. The best fitted model for SAR was the logistic model. Excluding grazers had a significant impact on the shape of SAR. (2) Variograms was applied to examine the spatial characteristics of plant species diversity. We found strong spatial autocorrelations in the diversity variables both inside and outside the fence. After grazing exclusion, the spatial heterogeneity decreased in species richness, increased in abundance and did not change in Shannon diversity. (3) We used variance partitioning to determine the relative contributions of spatial and environmental factors to plant species diversity patterns. Environmental factors explained the largest proportion of variation in species diversity, while spatial factors contributed little. Our results suggest that grazing enclosures decreased species diversity patterns and the spatial pattern of the S. breviflora desert steppe community was predictable. PMID:29456890

Comparison of Bayesian clustering and edge detection methods for inferring boundaries in landscape genetics

USGS Publications Warehouse

Safner, T.; Miller, M.P.; McRae, B.H.; Fortin, M.-J.; Manel, S.

2011-01-01

Recently, techniques available for identifying clusters of individuals or boundaries between clusters using genetic data from natural populations have expanded rapidly. Consequently, there is a need to evaluate these different techniques. We used spatially-explicit simulation models to compare three spatial Bayesian clustering programs and two edge detection methods. Spatially-structured populations were simulated where a continuous population was subdivided by barriers. We evaluated the ability of each method to correctly identify boundary locations while varying: (i) time after divergence, (ii) strength of isolation by distance, (iii) level of genetic diversity, and (iv) amount of gene flow across barriers. To further evaluate the methods' effectiveness to detect genetic clusters in natural populations, we used previously published data on North American pumas and a European shrub. Our results show that with simulated and empirical data, the Bayesian spatial clustering algorithms outperformed direct edge detection methods. All methods incorrectly detected boundaries in the presence of strong patterns of isolation by distance. Based on this finding, we support the application of Bayesian spatial clustering algorithms for boundary detection in empirical datasets, with necessary tests for the influence of isolation by distance. ?? 2011 by the authors; licensee MDPI, Basel, Switzerland.

Two sampling methods yield distinct microbial signatures in the nasopharynges of asthmatic children.

PubMed

Pérez-Losada, Marcos; Crandall, Keith A; Freishtat, Robert J

2016-06-16

The nasopharynx is a reservoir for pathogens associated with respiratory illnesses, such as asthma. Next-generation sequencing (NGS) has been used to characterize the nasopharyngeal microbiome during health and disease. Most studies so far have surveyed the nasopharynx as a whole; however, less is known about spatial variation (biogeography) in nasal microenvironments and how sampling techniques may capture that microbial diversity. We used targeted 16S rRNA MiSeq sequencing and two different sampling strategies [nasal washes (NW) and nasal brushes (NB)] to characterize the nasopharyngeal microbiota in 30 asthmatic children. Nasal brushing is more abrasive than nasal washing and targeted the inner portion of the inferior turbinate. This region is expected to be different from other nasal microenvironments. Nasal washing is not spatially specific. Our 30 × 2 nasal microbiomes generated 1,474,497 sequences, from which we identified an average of 157 and 186 OTUs per sample in the NW and NB groups, respectively. Microbiotas from NB showed significantly higher alpha-diversity than microbiotas from NW. Similarly, both nasal microbiotas were distinct from each other (PCoA) and significantly differed in their community composition and abundance in at least 9 genera (effective size ≥1 %). Nasopharyngeal microenvironments in asthmatic children contain microbiotas with different diversity and structure. Nasal washes and brushes capture that diversity differently. Future microbial studies of the nasopharynx need to be aware of potential spatial variation (biogeography).

Spatial Analysis in Determining Physical Factors of Pedestrian Space Livability, Case Study: Pedestrian Space on Jalan Kemasan, Yogyakarta

NASA Astrophysics Data System (ADS)

Fauzi, A. F.; Aditianata, A.

2018-02-01

The existence of street as a place to perform various human activities becomes an important issue nowadays. In the last few decades, cars and motorcycles dominate streets in various cities in the world. On the other hand, human activity on the street is the determinant of the city livability. Previous research has pointed out that if there is lots of human activity in the street, then the city will be interesting. Otherwise, if the street has no activity, then the city will be boring. Learning from that statement, now various cities in the world are developing the concept of livable streets. Livable streets shown by diversity of human activities conducted in the streets’ pedestrian space. In Yogyakarta, one of the streets shown diversity of human activities is Jalan Kemasan. This study attempts to determine the physical factors of pedestrian space affecting the livability in Jalan Kemasan Yogyakarta through spatial analysis. Spatial analysis was performed by overlay technique between liveable point (activity diversity) distribution map and variable distribution map. Those physical pedestrian space research variable included element of shading, street vendors, building setback, seat location, divider between street and pedestrian way, and mixed use building function. More diverse the activity of one variable, then those variable are more affected then others. Overlay result then strengthened by field observation to qualitatively ensure the deduction. In the end, this research will provide valuable input for street and pedestrian space planning that is comfortable for human activities.

Geomorphology Drives Amphibian Beta Diversity in Atlantic Forest Lowlands of Southeastern Brazil

PubMed Central

Luiz, Amom Mendes; Leão-Pires, Thiago Augusto; Sawaya, Ricardo J.

2016-01-01

Beta diversity patterns are the outcome of multiple processes operating at different scales. Amphibian assemblages seem to be affected by contemporary climate and dispersal-based processes. However, historical processes involved in present patterns of beta diversity remain poorly understood. We assess and disentangle geomorphological, climatic and spatial drivers of amphibian beta diversity in coastal lowlands of the Atlantic Forest, southeastern Brazil. We tested the hypothesis that geomorphological factors are more important in structuring anuran beta diversity than climatic and spatial factors. We obtained species composition via field survey (N = 766 individuals), museum specimens (N = 9,730) and literature records (N = 4,763). Sampling area was divided in four spatially explicit geomorphological units, representing historical predictors. Climatic descriptors were represented by the first two axis of a Principal Component Analysis. Spatial predictors in different spatial scales were described by Moran Eigenvector Maps. Redundancy Analysis was implemented to partition the explained variation of species composition by geomorphological, climatic and spatial predictors. Moreover, spatial autocorrelation analyses were used to test neutral theory predictions. Beta diversity was spatially structured in broader scales. Shared fraction between climatic and geomorphological variables was an important predictor of species composition (13%), as well as broad scale spatial predictors (13%). However, geomorphological variables alone were the most important predictor of beta diversity (42%). Historical factors related to geomorphology must have played a crucial role in structuring amphibian beta diversity. The complex relationships between geomorphological history and climatic gradients generated by the Serra do Mar Precambrian basements were also important. We highlight the importance of combining spatially explicit historical and contemporary predictors for understanding and disentangling major drivers of beta diversity patterns. PMID:27171522

Geomorphology Drives Amphibian Beta Diversity in Atlantic Forest Lowlands of Southeastern Brazil.

PubMed

Luiz, Amom Mendes; Leão-Pires, Thiago Augusto; Sawaya, Ricardo J

2016-01-01

Beta diversity patterns are the outcome of multiple processes operating at different scales. Amphibian assemblages seem to be affected by contemporary climate and dispersal-based processes. However, historical processes involved in present patterns of beta diversity remain poorly understood. We assess and disentangle geomorphological, climatic and spatial drivers of amphibian beta diversity in coastal lowlands of the Atlantic Forest, southeastern Brazil. We tested the hypothesis that geomorphological factors are more important in structuring anuran beta diversity than climatic and spatial factors. We obtained species composition via field survey (N = 766 individuals), museum specimens (N = 9,730) and literature records (N = 4,763). Sampling area was divided in four spatially explicit geomorphological units, representing historical predictors. Climatic descriptors were represented by the first two axis of a Principal Component Analysis. Spatial predictors in different spatial scales were described by Moran Eigenvector Maps. Redundancy Analysis was implemented to partition the explained variation of species composition by geomorphological, climatic and spatial predictors. Moreover, spatial autocorrelation analyses were used to test neutral theory predictions. Beta diversity was spatially structured in broader scales. Shared fraction between climatic and geomorphological variables was an important predictor of species composition (13%), as well as broad scale spatial predictors (13%). However, geomorphological variables alone were the most important predictor of beta diversity (42%). Historical factors related to geomorphology must have played a crucial role in structuring amphibian beta diversity. The complex relationships between geomorphological history and climatic gradients generated by the Serra do Mar Precambrian basements were also important. We highlight the importance of combining spatially explicit historical and contemporary predictors for understanding and disentangling major drivers of beta diversity patterns.

Wildlife tradeoffs based on landscape models of habitat

USGS Publications Warehouse

Loehle, C.; Mitchell, M.S.

2000-01-01

It is becoming increasingly clear that the spatial structure of landscapes affects the habitat choices and abundance of wildlife. In contrast to wildlife management based on preservation of critical habitat features such as nest sites on a beach or mast trees, it has not been obvious how to incorporate spatial structure into management plans. We present techniques to accomplish this goal. We used multiscale logistic regression models developed previously for neotropical migrant bird species habitat use in South Carolina (USA) as a basis for these techniques. Based on these models we used a spatial optimization technique to generate optimal maps (probability of occurrence, P = 1.0) for each of seven species. To emulate management of a forest for maximum species diversity, we defined the objective function of the algorithm as the sum of probabilities over the seven species, resulting in a complex map that allowed all seven species to coexist. The map that allowed for coexistence is not obvious, must be computed algorithmically, and would be difficult to realize using rules of thumb for habitat management. To assess how management of a forest for a single species of interest might affect other species, we analyzed tradeoffs by gradually increasing the weighting on a single species in the objective function over a series of simulations. We found that as habitat was increasingly modified to favor that species, the probability of presence for two of the other species was driven to zero. This shows that whereas it is not possible to simultaneously maximize the likelihood of presence for multiple species with divergent habitat preferences, compromise solutions are possible at less than maximal likelihood in many cases. Our approach suggests that efficiency of habitat management for species diversity can by maximized for even small landscapes by incorporating spatial context. The methods we present are suitable for wildlife management, endangered species conservation, and nature reserve design.

Turbulence mitigation scheme based on spatial diversity in orbital-angular-momentum multiplexed system

NASA Astrophysics Data System (ADS)

Zou, Li; Wang, Le; Zhao, Shengmei

2017-10-01

Atmospheric turbulence (AT) induced crosstalk can significantly impair the performance of free-space optical (FSO) communication link using orbital angular momentum (OAM) multiplexing. In this paper, we propose a spatial diversity (SD) turbulence mitigation scheme in an OAM-multiplexed FSO communication link. First, we present a SD mitigation model for the OAM-multiplexed FSO communication link under AT. Then we present a SD combining technique based on equal gain to enhance AT tolerance of the OAM-multiplexed FSO communication link. The numerical results show that performance of the OAM-multiplexed communication link has greatly improved by the proposed scheme. When the turbulence strength Cn2 is 5 × 10-15m - 2 / 3, the transmission distance is 1000 m and the channel signal-to-noise ratio (SNR) is 20 dB, the bit-error-rate (BER) performance of four spatial multiplexed OAM modes lm = + 1 , + 2 , + 3 , + 4 are 3 fold increase in comparison with those results without the proposed scheme. The proposed scheme is a promising direction for compensating the interference caused by AT in the OAM-multiplexed FSO communication link.

Spatial assessment of Geo-environmental data by the integration of Remote Sensing and GIS techniques for Sitakund Region, Eastern foldbelt, Bangladesh.

NASA Astrophysics Data System (ADS)

Gazi, M. Y.; Rahman, M.; Islam, M. A.; Kabir, S. M. M.

2016-12-01

Techniques of remote sensing and geographic information systems (GIS) have been applied for the analysis and interpretation of the Geo-environmental assessment to Sitakund area, located within the administrative boundaries of the Chittagong district, Bangladesh. Landsat ETM+ image with a ground resolution of 30-meter and Digital Elevation Model (DEM) has been adopted in this study in order to produce a set of thematic maps. The diversity of the terrain characteristics had a major role in the diversity of recipes and types of soils that are based on the geological structure, also helped to diversity in land cover and use in the region. The geological situation has affected on the general landscape of the study area. The problem of research lies in the possibility of the estimating the techniques of remote sensing and geographic information systems in the evaluation of the natural data for the study area spatially as well as determine the appropriate in grades for the appearance of the ground and in line with the reality of the region. Software for remote sensing and geographic information systems were adopted in the analysis, classification and interpretation of the prepared thematic maps in order to get to the building of the Geo-environmental assessment map of the study area. Low risk geo-environmental land mostly covered area of Quaternary deposits especially with area of slope wash deposits carried by streams. Medium and high risk geo-environmental land distributed with area of other formation with the study area, mostly the high risk shows area of folds and faults. The study has assessed the suitability of lands for agricultural purpose and settlements in less vulnerable areas within this region.

beta-diversity and species accumulation in antarctic coastal benthos: influence of habitat, distance and productivity on ecological connectivity.

PubMed

Thrush, Simon F; Hewitt, Judi E; Cummings, Vonda J; Norkko, Alf; Chiantore, Mariachiara

2010-07-30

High Antarctic coastal marine environments are comparatively pristine with strong environmental gradients, which make them important places to investigate biodiversity relationships. Defining how different environmental features contribute to shifts in beta-diversity is especially important as these shifts reflect both spatio-temporal variations in species richness and the degree of ecological separation between local and regional species pools. We used complementary techniques (species accumulation models, multivariate variance partitioning and generalized linear models) to assess how the roles of productivity, bio-physical habitat heterogeneity and connectivity change with spatial scales from metres to 100's of km. Our results demonstrated that the relative importance of specific processes influencing species accumulation and beta-diversity changed with increasing spatial scale, and that patterns were never driven by only one factor. Bio-physical habitat heterogeneity had a strong influence on beta-diversity at scales <290 km, while the effects of productivity were low and significant only at scales >40 km. Our analysis supports the emphasis on the analysis of diversity relationships across multiple spatial scales and highlights the unequal connectivity of individual sites to the regional species pool. This has important implications for resilience to habitat loss and community homogenisation, especially for Antarctic benthic communities where rates of recovery from disturbance are slow, there is a high ratio of poor-dispersing and brooding species, and high biogenic habitat heterogeneity and spatio-temporal variability in primary production make the system vulnerable to disturbance. Consequently, large areas need to be included within marine protected areas for effective management and conservation of these special ecosystems in the face of increasing anthropogenic disturbance.

Fine-resolution imaging of solar features using Phase-Diverse Speckle

NASA Technical Reports Server (NTRS)

Paxman, Richard G.

1995-01-01

Phase-diverse speckle (PDS) is a novel imaging technique intended to overcome the degrading effects of atmospheric turbulence on fine-resolution imaging. As its name suggests, PDS is a blend of phase-diversity and speckle-imaging concepts. PDS reconstructions on solar data were validated by simulation, by demonstrating internal consistency of PDS estimates, and by comparing PDS reconstructions with those produced from well accepted speckle-imaging processing. Several sources of error in data collected with the Swedish Vacuum Solar Telescope (SVST) were simulated: CCD noise, quantization error, image misalignment, and defocus error, as well as atmospheric turbulence model error. The simulations demonstrate that fine-resolution information can be reliably recovered out to at least 70% of the diffraction limit without significant introduction of image artifacts. Additional confidence in the SVST restoration is obtained by comparing its spatial power spectrum with previously-published power spectra derived from both space-based images and earth-based images corrected with traditional speckle-imaging techniques; the shape of the spectrum is found to match well the previous measurements. In addition, the imagery is found to be consistent with, but slightly sharper than, imagery reconstructed with accepted speckle-imaging techniques.

Area-based tests for association between spatial patterns

NASA Astrophysics Data System (ADS)

Maruca, Susan L.; Jacquez, Geoffrey M.

Edge effects pervade natural systems, and the processes that determine spatial heterogeneity (e.g. physical, geochemical, biological, ecological factors) occur on diverse spatial scales. Hence, tests for association between spatial patterns should be unbiased by edge effects and be based on null spatial models that incorporate the spatial heterogeneity characteristic of real-world systems. This paper develops probabilistic pattern association tests that are appropriate when edge effects are present, polygon size is heterogeneous, and the number of polygons varies from one classification to another. The tests are based on the amount of overlap between polygons in each of two partitions. Unweighted and area-weighted versions of the statistics are developed and verified using scenarios representing both polygon overlap and avoidance at different spatial scales and for different distributions of polygon sizes. These statistics were applied to Soda Butte Creek, Wyoming, to determine whether stream microhabitats, such as riffles, pools and glides, can be identified remotely using high spatial resolution hyperspectral imagery. These new ``spatially explicit'' techniques provide information and insights that cannot be obtained from the spectral information alone.

Spatial landscape model to characterize biological diversity using R statistical computing environment.

PubMed

Singh, Hariom; Garg, R D; Karnatak, Harish C; Roy, Arijit

2018-01-15

Due to urbanization and population growth, the degradation of natural forests and associated biodiversity are now widely recognized as a global environmental concern. Hence, there is an urgent need for rapid assessment and monitoring of biodiversity on priority using state-of-art tools and technologies. The main purpose of this research article is to develop and implement a new methodological approach to characterize biological diversity using spatial model developed during the study viz. Spatial Biodiversity Model (SBM). The developed model is scale, resolution and location independent solution for spatial biodiversity richness modelling. The platform-independent computation model is based on parallel computation. The biodiversity model based on open-source software has been implemented on R statistical computing platform. It provides information on high disturbance and high biological richness areas through different landscape indices and site specific information (e.g. forest fragmentation (FR), disturbance index (DI) etc.). The model has been developed based on the case study of Indian landscape; however it can be implemented in any part of the world. As a case study, SBM has been tested for Uttarakhand state in India. Inputs for landscape ecology are derived through multi-criteria decision making (MCDM) techniques in an interactive command line environment. MCDM with sensitivity analysis in spatial domain has been carried out to illustrate the model stability and robustness. Furthermore, spatial regression analysis has been made for the validation of the output. Copyright © 2017 Elsevier Ltd. All rights reserved.

Modeling the Spatial and Temporal Variation of Monthly and Seasonal Precipitation on the Nevada Test Site and Vicinity, 1960-2006

USGS Publications Warehouse

Blainey, Joan B.; Webb, Robert H.; Magirl, Christopher S.

2007-01-01

The Nevada Test Site (NTS), located in the climatic transition zone between the Mojave and Great Basin Deserts, has a network of precipitation gages that is unusually dense for this region. This network measures monthly and seasonal variation in a landscape with diverse topography. Precipitation data from 125 climate stations on or near the NTS were used to spatially interpolate precipitation for each month during the period of 1960 through 2006 at high spatial resolution (30 m). The data were collected at climate stations using manual and/or automated techniques. The spatial interpolation method, applied to monthly accumulations of precipitation, is based on a distance-weighted multivariate regression between the amount of precipitation and the station location and elevation. This report summarizes the temporal and spatial characteristics of the available precipitation records for the period 1960 to 2006, examines the temporal and spatial variability of precipitation during the period of record, and discusses some extremes in seasonal precipitation on the NTS.

On the capacity of MIMO-OFDM based diversity and spatial multiplexing in Radio-over-Fiber system

NASA Astrophysics Data System (ADS)

El Yahyaoui, Moussa; El Moussati, Ali; El Zein, Ghaïs

2017-11-01

This paper proposes a realistic and global simulation to predict the behavior of a Radio over Fiber (RoF) system before its realization. In this work we consider a 2 × 2 Multiple-Input Multiple-Output (MIMO) Orthogonal Frequency Division Multiplexing (OFDM) RoF system at 60 GHz. This system is based on Spatial Diversity (SD) which increases reliability (decreases probability of error) and Spatial Multiplexing (SMX) which increases data rate, but not necessarily reliability. The 60 GHz MIMO channel model employed in this work based on a lot of measured data and statistical analysis named Triple-S and Valenzuela (TSV) model. To the authors best knowledge; it is the first time that this type of TSV channel model has been employed for 60 GHz MIMO-RoF system. We have evaluated and compared the performance of this system according to the diversity technique, modulation schemes, and channel coding rate for Line-Of-Sight (LOS) desktop environment. The SMX coded is proposed as an intermediate system to improve the Signal to Noise Ratio (SNR) and the data rate. The resulting 2 × 2 MIMO-OFDM SMX system achieves a higher data rate up to 70 Gb/s with 64QAM and Forward Error Correction (FEC) limit of 10-3 over 25-km fiber transmission followed by 3-m wireless transmission using 7 GHz bandwidth of millimeter wave band.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taddese, Biniyam Tesfaye; Antonsen, Thomas M.; Ott, Edward

Classical analogs of the quantum mechanical concepts of the Loschmidt Echo and quantum fidelity are developed with the goal of detecting small perturbations in a closed wave chaotic region. Sensing techniques that employ a one-recording-channel time-reversal-mirror, which in turn relies on time reversal invariance and spatial reciprocity of the classical wave equation, are introduced. In analogy with quantum fidelity, we employ scattering fidelity techniques which work by comparing response signals of the scattering region, by means of cross correlation and mutual information of signals. The performance of the sensing techniques is compared for various perturbations induced experimentally in an acousticmore » resonant cavity. The acoustic signals are parametrically processed to mitigate the effect of dissipation and to vary the spatial diversity of the sensing schemes. In addition to static boundary condition perturbations at specified locations, perturbations to the medium of wave propagation are shown to be detectable, opening up various real world sensing applications in which a false negative cannot be tolerated.« less

Congruence between morphological and molecular markers inferred from the analysis of the intra-morphotype genetic diversity and the spatial structure of Oxalis tuberosa Mol.

PubMed

Pissard, Audrey; Arbizu, Carlos; Ghislain, Marc; Faux, Anne-Michèle; Paulet, Sébastien; Bertin, Pierre

2008-01-01

Oxalis tuberosa is an important crop cultivated in the highest Andean zones. A germplasm collection is maintained ex situ by CIP, which has developed a morphological markers system to classify the accessions into morphotypes, i.e. groups of morphologically identical accessions. However, their genetic uniformity is currently unknown. The ISSR technique was used in two experiments to determine the relationships between both morphological and molecular markers systems. The intra-morphotype genetic diversity, the spatial structures of the diversity and the congruence between both markers systems were determined. In the first experience, 44 accessions representing five morphotypes, clearly distinct from each other, were analyzed. At the molecular level, the accessions exactly clustered according to their morphotypes. However, a genetic variability was observed inside each morphotype. In the second experiment, 34 accessions gradually differing from each other on morphological base were analyzed. The morphological clustering showed no geographical structure. On the opposite, the molecular analysis showed that the genetic structure was slightly related to the collection site. The correlation between both markers systems was weak but significant. The lack of perfect congruence between morphological and molecular data suggests that the morphological system may be useful for the morphotypes management but is not appropriate to study the genetic structure of the oca. The spatial structure of the genetic diversity can be related to the evolution of the species and the discordance between the morphological and molecular structures may result from similar selection pressures at different places leading to similar forms with a different genetic background.

[Spatial distribution and scale effect of species diversity of secondary forests in montane region of eastern Liaoning Province, China.

PubMed

Deng, Li Ping; Bai, Xue Jiao; Qin, Sheng Jin; Wei, Ya Wei; Zhou, Yong Bin; Li, Lu Lu; Niu, Sha Sha; Han, Mei Na

2016-07-01

With secondary forest in the montane region of eastern Liaoning Province as research object, this paper analyzed the spatial distribution and scale effect of Gleason richness index, Simpson dominance index, Shannon diversity index and Pielou evenness index in a 4 hm 2 plot. The results showed that spatial distributions of the four diversity indices showed higher spatial heterogeneity. Variance of the four diversity indices varied with increasing scale. Coefficients of variation of the four diversity indices decreased with increasing scale. The four diversity indices of the tree layer were higher than those of the shrub layer, and the variation tendency varied with increasing scale. The results indicated that sampling scale should be taken into account when studying species diversity in the montane region of eastern Liaoning Province.

Performance analysis of fiber-based free-space optical communications with coherent detection spatial diversity.

PubMed

Li, Kangning; Ma, Jing; Tan, Liying; Yu, Siyuan; Zhai, Chao

2016-06-10

The performances of fiber-based free-space optical (FSO) communications over gamma-gamma distributed turbulence are studied for multiple aperture receiver systems. The equal gain combining (EGC) technique is considered as a practical scheme to mitigate the atmospheric turbulence. Bit error rate (BER) performances for binary-phase-shift-keying-modulated coherent detection fiber-based free-space optical communications are derived and analyzed for EGC diversity receptions through an approximation method. To show the net diversity gain of a multiple aperture receiver system, BER performances of EGC are compared with a single monolithic aperture receiver system with the same total aperture area (same average total incident optical power on the aperture surface) for fiber-based free-space optical communications. The analytical results are verified by Monte Carlo simulations. System performances are also compared for EGC diversity coherent FSO communications with or without considering fiber-coupling efficiencies.

Show Me: Diversity and Isolation Indicators of Spatial Segregation within and across Missouri's School Districts

ERIC Educational Resources Information Center

Tate, William F.; Hogrebe, Mark C.

2018-01-01

Our study examines patterns of spatial segregation using diversity and isolation indicators within and across Missouri school districts. Evaluating segregation from a critical spatial perspective emphasizes the importance of place when evaluating the quality of educational opportunity for diverse student populations. The methodology involves the…

Impact factors identification of spatial heterogeneity of herbaceous plant diversity on five southern islands of Miaodao Archipelago in North China

NASA Astrophysics Data System (ADS)

Chi, Yuan; Shi, Honghua; Wang, Xiaoli; Qin, Xuebo; Zheng, Wei; Peng, Shitao

2016-09-01

Herbaceous plants are widely distributed on islands and where they exhibit spatial heterogeneity. Accurately identifying the impact factors that drive spatial heterogeneity can reveal typical island biodiversity patterns. Five southern islands in the Miaodao Archipelago, North China were studied herein. The spatial distribution of herbaceous plant diversity on these islands was analyzed, and the impact factors and their degree of impact on spatial heterogeneity were identified using CCA ordination and ANOVA. The results reveal 114 herbaceous plant species, belonging to 94 genera from 34 families in the 50 plots sampled. The total species numbers on different islands were significantly positively correlated with island area, and the average α diversity was correlated with human activities, while the β diversity among islands was more affected by island area than mutual distances. Spatial heterogeneity within islands indicated that the diversities were generally high in areas with higher altitude, slope, total nitrogen, total carbon, and canopy density, and lower moisture content, pH, total phosphorus, total potassium, and aspect. Among the environmental factors, pH, canopy density, total K, total P, moisture content, altitude, and slope had significant gross effects, but only canopy density exhibited a significant net effect. Terrain affected diversity by restricting plantation, plantation in turn influenced soil properties and the two together affected diversity. Therefore, plantation was ultimately the fundamental driving factor for spatial heterogeneity in herbaceous plant diversity on the five islands.

Multiple Spatial Coherence Resonances and Spatial Patterns in a Noise-Driven Heterogeneous Neuronal Network

NASA Astrophysics Data System (ADS)

Li, Yu-Ye; Ding, Xue-Li

2014-12-01

Heterogeneity of the neurons and noise are inevitable in the real neuronal network. In this paper, Gaussian white noise induced spatial patterns including spiral waves and multiple spatial coherence resonances are studied in a network composed of Morris—Lecar neurons with heterogeneity characterized by parameter diversity. The relationship between the resonances and the transitions between ordered spiral waves and disordered spatial patterns are achieved. When parameter diversity is introduced, the maxima of multiple resonances increases first, and then decreases as diversity strength increases, which implies that the coherence degrees induced by noise are enhanced at an intermediate diversity strength. The synchronization degree of spatial patterns including ordered spiral waves and disordered patterns is identified to be a very low level. The results suggest that the nervous system can profit from both heterogeneity and noise, and the multiple spatial coherence resonances are achieved via the emergency of spiral waves instead of synchronization patterns.

Probing plasmons in three dimensions by combining complementary spectroscopies in a scanning transmission electron microscope

DOE PAGES

Hachtel, Jordan A.; Marvinney, Claire; Mouti, Anas; ...

2016-03-02

The nanoscale optical response of surface plasmons in three-dimensional metallic nanostructures plays an important role in many nanotechnology applications, where precise spatial and spectral characteristics of plasmonic elements control device performance. Electron energy loss spectroscopy (EELS) and cathodoluminescence (CL) within a scanning transmission electron microscope have proven to be valuable tools for studying plasmonics at the nanoscale. Each technique has been used separately, producing three-dimensional reconstructions through tomography, often aided by simulations for complete characterization. Here we demonstrate that the complementary nature of the two techniques, namely that EELS probes beam-induced electronic excitations while CL probes radiative decay, allows usmore » to directly obtain a spatially- and spectrally-resolved picture of the plasmonic characteristics of nanostructures in three dimensions. Furthermore, the approach enables nanoparticle-by-nanoparticle plasmonic analysis in three dimensions to aid in the design of diverse nanoplasmonic applications.« less

A Brief History of the use of Electromagnetic Induction Techniques in Soil Survey

NASA Astrophysics Data System (ADS)

Brevik, Eric C.; Doolittle, James

2017-04-01

Electromagnetic induction (EMI) has been used to characterize the spatial variability of soil properties since the late 1970s. Initially used to assess soil salinity, the use of EMI in soil studies has expanded to include: mapping soil types; characterizing soil water content and flow patterns; assessing variations in soil texture, compaction, organic matter content, and pH; and determining the depth to subsurface horizons, stratigraphic layers or bedrock, among other uses. In all cases the soil property being investigated must influence soil apparent electrical conductivity (ECa) either directly or indirectly for EMI techniques to be effective. An increasing number and diversity of EMI sensors have been developed in response to users' needs and the availability of allied technologies, which have greatly improved the functionality of these tools and increased the amount and types of data that can be gathered with a single pass. EMI investigations provide several benefits for soil studies. The large amount of georeferenced data that can be rapidly and inexpensively collected with EMI provides more complete characterization of the spatial variations in soil properties than traditional sampling techniques. In addition, compared to traditional soil survey methods, EMI can more effectively characterize diffuse soil boundaries and identify included areas of dissimilar soils within mapped soil units, giving soil scientists greater confidence when collecting spatial soil information. EMI techniques do have limitations; results are site-specific and can vary depending on the complex interactions among multiple and variable soil properties. Despite this, EMI techniques are increasingly being used to investigate the spatial variability of soil properties at field and landscape scales. The future should witness a greater use of multiple-frequency and multiple-coil EMI sensors and integration with other sensors to assess the spatial variability of soil properties. Data analysis will be improved with advanced processing and presentation systems and more sophisticated geostatistical modeling algorithms will be developed and used to interpolate EMI data, improve the resolution of subsurface features, and assess soil properties.

Visible light high-resolution imaging system for large aperture telescope by liquid crystal adaptive optics with phase diversity technique.

PubMed

Xu, Zihao; Yang, Chengliang; Zhang, Peiguang; Zhang, Xingyun; Cao, Zhaoliang; Mu, Quanquan; Sun, Qiang; Xuan, Li

2017-08-30

There are more than eight large aperture telescopes (larger than eight meters) equipped with adaptive optics system in the world until now. Due to the limitations such as the difficulties of increasing actuator number of deformable mirror, most of them work in the infrared waveband. A novel two-step high-resolution optical imaging approach is proposed by applying phase diversity (PD) technique to the open-loop liquid crystal adaptive optics system (LC AOS) for visible light high-resolution adaptive imaging. Considering the traditional PD is not suitable for LC AOS, the novel PD strategy is proposed which can reduce the wavefront estimating error caused by non-modulated light generated by liquid crystal spatial light modulator (LC SLM) and make the residual distortions after open-loop correction to be smaller. Moreover, the LC SLM can introduce any aberration which realizes the free selection of phase diversity. The estimating errors are greatly reduced in both simulations and experiments. The resolution of the reconstructed image is greatly improved on both subjective visual effect and the highest discernible space resolution. Such technique can be widely used in large aperture telescopes for astronomical observations such as terrestrial planets, quasars and also can be used in other applications related to wavefront correction.

What Is the Role of Land-Use Compositions and Spatial Configurations in Sediment Yield from Mountainous Watershed?

NASA Astrophysics Data System (ADS)

Shi, Z. H.

2014-12-01

There are strong ties between land use and sediment yield in watersheds. Many studies have used multivariate regression techniques to explore the response of sediment yield to land-use compositions and spatial configurations in watersheds. However, one issue with the use of conventional statistical methods to address relationships between land-use compositions and spatial configurations and sediment yield is multicollinearity. This paper examines the combined effects of land-use compositions and land-use spatial configurations of the watershed on the specific sediment yield of the Upper Du River watershed (8,973 km2) in China using the Soil and Water Assessment Tool (SWAT) and partial least-squares regression (PLSR). The land-use compositions and spatial configurations of the watershed were calculated at the sub-watershed scale. The sediment yields from sub-watershed were evaluated using SWAT model. The first-order factors were identified by calculating the variable importance for the projection (VIP). The results revealed that the land-use compositions exerted the largest effects on the specific sediment yield and explained 61.2% of the variation in the specific sediment yield. Land-use spatial configurations were also found to have a large effect on the specific sediment yield and explained 21.7% of the observed variation in the specific sediment yield. The following are the dominant first-order factors of the specific sediment yield at the sub-watershed scale: the areal percentages of agriculture and forest, patch density, value of the Shannon's diversity index, contagion. The VIP values suggested that the Shannon's diversity index and contagion are important factors for sediment delivery.

Metacommunity composition of web-spiders in a fragmented neotropical forest: relative importance of environmental and spatial effects.

PubMed

Baldissera, Ronei; Rodrigues, Everton N L; Hartz, Sandra M

2012-01-01

The distribution of beta diversity is shaped by factors linked to environmental and spatial control. The relative importance of both processes in structuring spider metacommunities has not yet been investigated in the Atlantic Forest. The variance explained by purely environmental, spatially structured environmental, and purely spatial components was compared for a metacommunity of web spiders. The study was carried out in 16 patches of Atlantic Forest in southern Brazil. Field work was done in one landscape mosaic representing a slight gradient of urbanization. Environmental variables encompassed plot- and patch-level measurements and a climatic matrix, while principal coordinates of neighbor matrices (PCNMs) acted as spatial variables. A forward selection procedure was carried out to select environmental and spatial variables influencing web-spider beta diversity. Variation partitioning was used to estimate the contribution of pure environmental and pure spatial effects and their shared influence on beta-diversity patterns, and to estimate the relative importance of selected environmental variables. Three environmental variables (bush density, land use in the surroundings of patches, and shape of patches) and two spatial variables were selected by forward selection procedures. Variation partitioning revealed that 15% of the variation of beta diversity was explained by a combination of environmental and PCNM variables. Most of this variation (12%) corresponded to pure environmental and spatially environmental structure. The data indicated that (1) spatial legacy was not important in explaining the web-spider beta diversity; (2) environmental predictors explained a significant portion of the variation in web-spider composition; (3) one-third of environmental variation was due to a spatial structure that jointly explains variation in species distributions. We were able to detect important factors related to matrix management influencing the web-spider beta-diversity patterns, which are probably linked to historical deforestation events.

Stair-Step Pattern of Soil Bacterial Diversity Mainly Driven by pH and Vegetation Types Along the Elevational Gradients of Gongga Mountain, China

PubMed Central

Li, Jiabao; Shen, Zehao; Li, Chaonan; Kou, Yongping; Wang, Yansu; Tu, Bo; Zhang, Shiheng; Li, Xiangzhen

2018-01-01

Ecological understandings of soil bacterial community succession and assembly mechanism along elevational gradients in mountains remain not well understood. Here, by employing the high-throughput sequencing technique, we systematically examined soil bacterial diversity patterns, the driving factors, and community assembly mechanisms along the elevational gradients of 1800–4100 m on Gongga Mountain in China. Soil bacterial diversity showed an extraordinary stair-step pattern along the elevational gradients. There was an abrupt decrease of bacterial diversity between 2600 and 2800 m, while no significant change at either lower (1800–2600 m) or higher (2800–4100 m) elevations, which coincided with the variation in soil pH. In addition, the community structure differed significantly between the lower and higher elevations, which could be primarily attributed to shifts in soil pH and vegetation types. Although there was no direct effect of MAP and MAT on bacterial community structure, our partial least squares path modeling analysis indicated that bacterial communities were indirectly influenced by climate via the effect on vegetation and the derived effect on soil properties. As for bacterial community assembly mechanisms, the null model analysis suggested that environmental filtering played an overwhelming role in the assembly of bacterial communities in this region. In addition, variation partition analysis indicated that, at lower elevations, environmental attributes explained much larger fraction of the β-deviation than spatial attributes, while spatial attributes increased their contributions at higher elevations. Our results highlight the importance of environmental filtering, as well as elevation-related spatial attributes in structuring soil bacterial communities in mountain ecosystems. PMID:29636740

Performance analysis of decode-and-forward dual-hop optical spatial modulation with diversity combiner over atmospheric turbulence

NASA Astrophysics Data System (ADS)

Odeyemi, Kehinde O.; Owolawi, Pius A.; Srivastava, Viranjay M.

2017-11-01

Dual-hops transmission is a growing interest technique that can be used to mitigate against atmospheric turbulence along the Free Space Optical (FSO) communication links. This paper analyzes the performance of Decode-and-Forward (DF) dual-hops FSO systems in-conjunction with spatial modulation and diversity combiners over a Gamma-Gamma atmospheric turbulence channel using heterodyne detection. Maximum Ratio Combiner (MRC), Equal Gain Combiner (EGC) and Selection Combiner (SC) are considered at the relay and destination as mitigation tools to improve the system error performance. Power series expansion of modified Bessel function is used to derive the closed form expression for the end-to-end Average Pairwise Error Probability (APEP) expressions for each of the combiners under study and a tight upper bound on the Average Bit Error Rate (ABER) per hop is given. Thus, the overall end-to-end ABER for the dual-hops FSO system is then evaluated. The numerical results depicted that dual-hops transmission systems outperformed the direct link systems. Moreover, the impact of having the same and different combiners at the relay and destination are also presented. The results also confirm that the combination of dual hops transmission with spatial modulation and diversity combiner significantly improves the systems error rate with the MRC combiner offering an optimal performance with respect to variation in atmospheric turbulence, change in links average received SNR and link range of the system.

Patterns of orchid bee species diversity and turnover among forested plateaus of central Amazonia

PubMed Central

Machado, Carolina de Barros; Galetti, Pedro Manoel; Oliveira, Marcio; Dirzo, Rodolfo; Fernandes, Geraldo Wilson

2017-01-01

The knowledge of spatial pattern and geographic beta-diversity is of great importance for biodiversity conservation and interpreting ecological information. Tropical forests, especially the Amazon Rainforest, are well known for their high species richness and low similarity in species composition between sites, both at local and regional scales. We aimed to determine the effect and relative importance of area, isolation and climate on species richness and turnover in orchid bee assemblages among plateaus in central Brazilian Amazonia. Variance partitioning techniques were applied to assess the relative effects of spatial and environmental variables on bee species richness, phylogeny and composition. We hypothesized that greater abundance and richness of orchid bees would be found on larger plateaus, with a set of core species occurring on all of them. We also hypothesized that smaller plateaus would possess lower phylogenetic diversity. We found 55 bee species distributed along the nine sampling sites (plateaus) with 17 of them being singletons. There was a significant decrease in species richness with decreasing size of plateaus, and a significant decrease in the similarity in species composition with greater distance and climatic variation among sampling sites. Phylogenetic diversity varied among the sampling sites but was directly related to species richness. Although not significantly related to plateau area, smaller or larger PDFaith were observed in the smallest and the largest plateaus, respectively. PMID:28410432

Patterns of orchid bee species diversity and turnover among forested plateaus of central Amazonia.

PubMed

Antonini, Yasmine; Machado, Carolina de Barros; Galetti, Pedro Manoel; Oliveira, Marcio; Dirzo, Rodolfo; Fernandes, Geraldo Wilson

2017-01-01

The knowledge of spatial pattern and geographic beta-diversity is of great importance for biodiversity conservation and interpreting ecological information. Tropical forests, especially the Amazon Rainforest, are well known for their high species richness and low similarity in species composition between sites, both at local and regional scales. We aimed to determine the effect and relative importance of area, isolation and climate on species richness and turnover in orchid bee assemblages among plateaus in central Brazilian Amazonia. Variance partitioning techniques were applied to assess the relative effects of spatial and environmental variables on bee species richness, phylogeny and composition. We hypothesized that greater abundance and richness of orchid bees would be found on larger plateaus, with a set of core species occurring on all of them. We also hypothesized that smaller plateaus would possess lower phylogenetic diversity. We found 55 bee species distributed along the nine sampling sites (plateaus) with 17 of them being singletons. There was a significant decrease in species richness with decreasing size of plateaus, and a significant decrease in the similarity in species composition with greater distance and climatic variation among sampling sites. Phylogenetic diversity varied among the sampling sites but was directly related to species richness. Although not significantly related to plateau area, smaller or larger PDFaith were observed in the smallest and the largest plateaus, respectively.

Demonstration/Validation of Incremental Sampling at Two Diverse Military Ranges and Development of an Incremental Sampling Tool

DTIC Science & Technology

2010-06-01

Sampling (MIS)? • Technique of combining many increments of soil from a number of points within exposure area • Developed by Enviro Stat (Trademarked...Demonstrating a reliable soil sampling strategy to accurately characterize contaminant concentrations in spatially extreme and heterogeneous...into a set of decision (exposure) units • One or several discrete or small- scale composite soil samples collected to represent each decision unit

Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities.

PubMed

Parks, Donovan H; Beiko, Robert G

2013-01-01

High-throughput sequencing techniques have made large-scale spatial and temporal surveys of microbial communities routine. Gaining insight into microbial diversity requires methods for effectively analyzing and visualizing these extensive data sets. Phylogenetic β-diversity measures address this challenge by allowing the relationship between large numbers of environmental samples to be explored using standard multivariate analysis techniques. Despite the success and widespread use of phylogenetic β-diversity measures, an extensive comparative analysis of these measures has not been performed. Here, we compare 39 measures of phylogenetic β diversity in order to establish the relative similarity of these measures along with key properties and performance characteristics. While many measures are highly correlated, those commonly used within microbial ecology were found to be distinct from those popular within classical ecology, and from the recently recommended Gower and Canberra measures. Many of the measures are surprisingly robust to different rootings of the gene tree, the choice of similarity threshold used to define operational taxonomic units, and the presence of outlying basal lineages. Measures differ considerably in their sensitivity to rare organisms, and the effectiveness of measures can vary substantially under alternative models of differentiation. Consequently, the depth of sequencing required to reveal underlying patterns of relationships between environmental samples depends on the selected measure. Our results demonstrate that using complementary measures of phylogenetic β diversity can further our understanding of how communities are phylogenetically differentiated. Open-source software implementing the phylogenetic β-diversity measures evaluated in this manuscript is available at http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity.

Diversity of rare and abundant bacteria in surface waters of the Southern Adriatic Sea.

PubMed

Quero, Grazia Marina; Luna, Gian Marco

2014-10-01

Bacteria are fundamental players in the functioning of the ocean, yet relatively little is known about the diversity of bacterioplankton assemblages and the factors shaping their spatial distribution. We investigated the diversity and community composition of bacterioplankton in surface waters of the Southern Adriatic sub-basin (SAd) in the Mediterranean Sea, across an environmental gradient from coastal to offshore stations. Bacterioplankton diversity was investigated using a whole-assemblage genetic fingerprinting technique (Automated Ribosomal Intergenic Spacer Analysis, ARISA) coupled with 16S rDNA amplicon pyrosequencing. The main physico-chemical variables showed clear differences between coastal and offshore stations, with the latter displaying generally higher temperature, salinity and oxygen content. Bacterioplankton richness was higher in coastal than offshore waters. Bacterial community composition (BCC) differed significantly between coastal and offshore waters, and appeared to be influenced by temperature (explaining up to 30% of variance) and by the trophic state. Pyrosequencing evidenced dominance of Alphaproteobacteria (SAR11 cluster), uncultured Gammaproteobacteria (Rhodobacteraceae) and Cyanobacteria (Synechococcus). Members of the Bacteroidetes phylum were also abundant, and accounted for 25% in the station characterized by the higher organic carbon availability. Bacterioplankton assemblages included a few dominant taxa and a very large proportion (85%) of rare (<0.1%) bacteria, the vast majority of which was unique to each sampling station. The first detailed census of bacterioplankton taxa in the SAd sub-basin, performed using next generation sequencing, indicates that assemblages are highly heterogeneous, spatially structured according to the environmental conditions, and comprise a large number of rare taxa. The high turnover diversity, particularly evident at the level of the rare taxa, suggests to direct future investigations toward larger spatial or temporal scales, to better understand the role of bacterioplankton in the ecosystem functioning and the biogeochemistry of the basin. Copyright © 2014 Elsevier B.V. All rights reserved.

Process, pattern and scale: hydrogeomorphology and plant diversity in forested wetlands across multiple spatial scales

NASA Astrophysics Data System (ADS)

Alexander, L.; Hupp, C. R.; Forman, R. T.

2002-12-01

Many geodisturbances occur across large spatial scales, spanning entire landscapes and creating ecological phenomena in their wake. Ecological study at large scales poses special problems: (1) large-scale studies require large-scale resources, and (2) sampling is not always feasible at the appropriate scale, and researchers rely on data collected at smaller scales to interpret patterns across broad regions. A criticism of landscape ecology is that findings at small spatial scales are "scaled up" and applied indiscriminately across larger spatial scales. In this research, landscape scaling is addressed through process-pattern relationships between hydrogeomorphic processes and patterns of plant diversity in forested wetlands. The research addresses: (1) whether patterns and relationships between hydrogeomorphic, vegetation, and spatial variables can transcend scale; and (2) whether data collected at small spatial scales can be used to describe patterns and relationships across larger spatial scales. Field measurements of hydrologic, geomorphic, spatial, and vegetation data were collected or calculated for 15- 1-ha sites on forested floodplains of six (6) Chesapeake Bay Coastal Plain streams over a total area of about 20,000 km2. Hydroperiod (day/yr), floodplain surface elevation range (m), discharge (m3/s), stream power (kg-m/s2), sediment deposition (mm/yr), relative position downstream and other variables were used in multivariate analyses to explain differences in species richness, tree diversity (Shannon-Wiener Diversity Index H'), and plant community composition at four spatial scales. Data collected at the plot (400-m2) and site- (c. 1-ha) scales are applied to and tested at the river watershed and regional spatial scales. Results indicate that plant species richness and tree diversity (Shannon-Wiener diversity index H') can be described by hydrogeomorphic conditions at all scales, but are best described at the site scale. Data collected at plot and site scales are tested for spatial heterogeneity across the Chesapeake Bay Coastal Plain using a geostatistical variogram, and multiple regression analysis is used to relate plant diversity, spatial, and hydrogeomorphic variables across Coastal Plain regions and hydrologic regimes. Results indicate that relationships between hydrogeomorphic processes and patterns of plant diversity at finer scales can proxy relationships at coarser scales in some, not all, cases. Findings also suggest that data collected at small scales can be used to describe trends across broader scales under limited conditions.

Research Techniques Made Simple: Emerging Methods to Elucidate Protein Interactions through Spatial Proximity.

PubMed

Che, Yonglu; Khavari, Paul A

2017-12-01

Interactions between proteins are essential for fundamental cellular processes, and the diversity of such interactions enables the vast variety of functions essential for life. A persistent goal in biological research is to develop assays that can faithfully capture different types of protein interactions to allow their study. A major step forward in this direction came with a family of methods that delineates spatial proximity of proteins as an indirect measure of protein-protein interaction. A variety of enzyme- and DNA ligation-based methods measure protein co-localization in space, capturing novel interactions that were previously too transient or low affinity to be identified. Here we review some of the methods that have been successfully used to measure spatially proximal protein-protein interactions. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

MALDI-MS and NanoSIMS imaging techniques to study cnidarian-dinoflagellate symbioses.

PubMed

Kopp, C; Wisztorski, M; Revel, J; Mehiri, M; Dani, V; Capron, L; Carette, D; Fournier, I; Massi, L; Mouajjah, D; Pagnotta, S; Priouzeau, F; Salzet, M; Meibom, A; Sabourault, C

2015-04-01

Cnidarian-dinoflagellate photosynthetic symbioses are fundamental to biologically diverse and productive coral reef ecosystems. The hallmark of this symbiotic relationship is the ability of dinoflagellate symbionts to supply their cnidarian host with a wide range of nutrients. Many aspects of this association nevertheless remain poorly characterized, including the exact identity of the transferred metabolic compounds, the mechanisms that control their exchange across the host-symbiont interface, and the precise subcellular fate of the translocated materials in cnidarian tissues. This lack of knowledge is mainly attributed to difficulties in investigating such metabolic interactions both in situ, i.e. on intact symbiotic associations, and at high spatial resolution. To address these issues, we illustrate the application of two in situ and high spatial resolution molecular and ion imaging techniques-matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) and the nano-scale secondary-ion mass spectrometry (NanoSIMS) ion microprobe. These imaging techniques provide important new opportunities for the detailed investigation of many aspects of cnidarian-dinoflagellate associations, including the dynamics of cellular interactions. Copyright © 2014 Elsevier GmbH. All rights reserved.

Toward seamless hydrologic predictions across spatial scales

NASA Astrophysics Data System (ADS)

Samaniego, Luis; Kumar, Rohini; Thober, Stephan; Rakovec, Oldrich; Zink, Matthias; Wanders, Niko; Eisner, Stephanie; Müller Schmied, Hannes; Sutanudjaja, Edwin H.; Warrach-Sagi, Kirsten; Attinger, Sabine

2017-09-01

Land surface and hydrologic models (LSMs/HMs) are used at diverse spatial resolutions ranging from catchment-scale (1-10 km) to global-scale (over 50 km) applications. Applying the same model structure at different spatial scales requires that the model estimates similar fluxes independent of the chosen resolution, i.e., fulfills a flux-matching condition across scales. An analysis of state-of-the-art LSMs and HMs reveals that most do not have consistent hydrologic parameter fields. Multiple experiments with the mHM, Noah-MP, PCR-GLOBWB, and WaterGAP models demonstrate the pitfalls of deficient parameterization practices currently used in most operational models, which are insufficient to satisfy the flux-matching condition. These examples demonstrate that J. Dooge's 1982 statement on the unsolved problem of parameterization in these models remains true. Based on a review of existing parameter regionalization techniques, we postulate that the multiscale parameter regionalization (MPR) technique offers a practical and robust method that provides consistent (seamless) parameter and flux fields across scales. Herein, we develop a general model protocol to describe how MPR can be applied to a particular model and present an example application using the PCR-GLOBWB model. Finally, we discuss potential advantages and limitations of MPR in obtaining the seamless prediction of hydrological fluxes and states across spatial scales.

A comparative analysis reveals weak relationships between ecological factors and beta diversity of stream insect metacommunities at two spatial levels.

PubMed

Heino, Jani; Melo, Adriano S; Bini, Luis Mauricio; Altermatt, Florian; Al-Shami, Salman A; Angeler, David G; Bonada, Núria; Brand, Cecilia; Callisto, Marcos; Cottenie, Karl; Dangles, Olivier; Dudgeon, David; Encalada, Andrea; Göthe, Emma; Grönroos, Mira; Hamada, Neusa; Jacobsen, Dean; Landeiro, Victor L; Ligeiro, Raphael; Martins, Renato T; Miserendino, María Laura; Md Rawi, Che Salmah; Rodrigues, Marciel E; Roque, Fabio de Oliveira; Sandin, Leonard; Schmera, Denes; Sgarbi, Luciano F; Simaika, John P; Siqueira, Tadeu; Thompson, Ross M; Townsend, Colin R

2015-03-01

The hypotheses that beta diversity should increase with decreasing latitude and increase with spatial extent of a region have rarely been tested based on a comparative analysis of multiple datasets, and no such study has focused on stream insects. We first assessed how well variability in beta diversity of stream insect metacommunities is predicted by insect group, latitude, spatial extent, altitudinal range, and dataset properties across multiple drainage basins throughout the world. Second, we assessed the relative roles of environmental and spatial factors in driving variation in assemblage composition within each drainage basin. Our analyses were based on a dataset of 95 stream insect metacommunities from 31 drainage basins distributed around the world. We used dissimilarity-based indices to quantify beta diversity for each metacommunity and, subsequently, regressed beta diversity on insect group, latitude, spatial extent, altitudinal range, and dataset properties (e.g., number of sites and percentage of presences). Within each metacommunity, we used a combination of spatial eigenfunction analyses and partial redundancy analysis to partition variation in assemblage structure into environmental, shared, spatial, and unexplained fractions. We found that dataset properties were more important predictors of beta diversity than ecological and geographical factors across multiple drainage basins. In the within-basin analyses, environmental and spatial variables were generally poor predictors of variation in assemblage composition. Our results revealed deviation from general biodiversity patterns because beta diversity did not show the expected decreasing trend with latitude. Our results also call for reconsideration of just how predictable stream assemblages are along ecological gradients, with implications for environmental assessment and conservation decisions. Our findings may also be applicable to other dynamic systems where predictability is low.

Modeling α- and β-diversity in a tropical forest from remotely sensed and spatial data

NASA Astrophysics Data System (ADS)

Hernández-Stefanoni, J. Luis; Gallardo-Cruz, J. Alberto; Meave, Jorge A.; Rocchini, Duccio; Bello-Pineda, Javier; López-Martínez, J. Omar

2012-10-01

Comprehensive information on species distribution and species composition patterns of plant communities is required for effective conservation and management of biodiversity. Remote sensing offers an inexpensive means of attaining complete spatial coverage for large areas, at regular time intervals, and can therefore be extremely useful for estimating both species richness and spatial variation of species composition (α- and β-diversity). An essential step to map such attributes is to identify and understand their main drivers. We used remotely sensed data as a surrogate of plant productivity and habitat structure variables for explaining α- and β-diversity, and evaluated the relative roles of productivity-habitat structure and spatial variables in explaining observed patterns of α- and β-diversity by using a Principal Coordinates of Neighbor Matrices analysis. We also examined the relationship between remotely sensed and field data, in order to map α- and β-diversity at the landscape-level in the Yucatan Peninsula, using a regression kriging procedure. These two procedures integrate the relationship of species richness and spatial species turnover both with remotely sensed data and spatial structure. The empirical models so obtained can be used to predict species richness and variation in species composition, and they can be regarded as valuable tools not only for identifying areas with high local species richness (α-diversity), but also areas with high species turnover (β-diversity). Ultimately, information obtained in this way can help maximize the number of species preserved in a landscape.

Biodiversity and ecosystem stability across scales in metacommunities

PubMed Central

Wang, Shaopeng; Loreau, Michel

2016-01-01

Although diversity-stability relationships have been extensively studied in local ecosystems, the global biodiversity crisis calls for an improved understanding of these relationships in a spatial context. Here we use a dynamical model of competitive metacommunities to study the relationships between species diversity and ecosystem variability across scales. We derive analytic relationships under a limiting case; these results are extended to more general cases with numerical simulations. Our model shows that, while alpha diversity decreases local ecosystem variability, beta diversity generally contributes to increasing spatial asynchrony among local ecosystems. Consequently, both alpha and beta diversity provide stabilizing effects for regional ecosystems, through local and spatial insurance effects, respectively. We further show that at the regional scale, the stabilizing effect of biodiversity increases as spatial environmental correlation increases. Our findings have important implications for understanding the interactive effects of global environmental changes (e.g. environmental homogenization) and biodiversity loss on ecosystem sustainability at large scales. PMID:26918536

Standing variation in spatially growing populations

NASA Astrophysics Data System (ADS)

Fusco, Diana; Gralka, Matti; Kayser, Jona; Hallatschek, Oskar

Patterns of genetic diversity not only reflect the evolutionary history of a species but they can also determine the evolutionary response to environmental change. For instance, the standing genetic diversity of a microbial population can be key to rescue in the face of an antibiotic attack. While genetic diversity is in general shaped by both demography and evolution, very little is understood when both factors matter, as e.g. for biofilms with pronounced spatial organization. Here, we quantitatively explore patterns of genetic diversity by using microbial colonies and well-mixed test tube populations as antipodal model systems with extreme and very little spatial structure, respectively. We find that Eden model simulations and KPZ theory can remarkably reproduce the genetic diversity in microbial colonies obtained via population sequencing. The excellent agreement allows to draw conclusions on the resilience of spatially-organized populations and to uncover new strategies to contain antibiotic resistance.

Virus evolution and transmission in an ever more connected world

PubMed Central

Pybus, Oliver G.; Tatem, Andrew J.; Lemey, Philippe

2015-01-01

The frequency and global impact of infectious disease outbreaks, particularly those caused by emerging viruses, demonstrate the need for a better understanding of how spatial ecology and pathogen evolution jointly shape epidemic dynamics. Advances in computational techniques and the increasing availability of genetic and geospatial data are helping to address this problem, particularly when both information sources are combined. Here, we review research at the intersection of evolutionary biology, human geography and epidemiology that is working towards an integrated view of spatial incidence, host mobility and viral genetic diversity. We first discuss how empirical studies have combined viral spatial and genetic data, focusing particularly on the contribution of evolutionary analyses to epidemiology and disease control. Second, we explore the interplay between virus evolution and global dispersal in more depth for two pathogens: human influenza A virus and chikungunya virus. We discuss the opportunities for future research arising from new analyses of human transportation and trade networks, as well as the associated challenges in accessing and sharing relevant spatial and genetic data. PMID:26702033

Massive MIMO-OFDM indoor visible light communication system downlink architecture design

NASA Astrophysics Data System (ADS)

Lang, Tian; Li, Zening; Chen, Gang

2014-10-01

Multiple-input multiple-output (MIMO) technique is now used in most new broadband communication system, and orthogonal frequency division multiplexing (OFDM) is also utilized within current 4th generation (4G) of mobile telecommunication technology. With MIMO and OFDM combined, visible light communication (VLC) system's diversity gain is increase, yet system capacity for dispersive channels is also enhanced. Moreover, with the emerging massive MIMO-OFDM VLC system, there are significant advantages than smaller systems' such as channel hardening, further increasing of energy efficiency (EE) and spectral efficiency (SE) based on law of large number. This paper addresses one of the major technological challenges, system architecture design, which was solved by semispherical beehive structure (SBS) receiver and so that diversity gain can be identified and applied in Massive MIMO VLC system. Simulation results shows that the proposed design clearly presents a spatial diversity over conventional VLC systems.

Spatial Factors Play a Major Role as Determinants of Endemic Ground Beetle Beta Diversity of Madeira Island Laurisilva

PubMed Central

Boieiro, Mário; Carvalho, José C.; Cardoso, Pedro; Aguiar, Carlos A. S.; Rego, Carla; de Faria e Silva, Israel; Amorim, Isabel R.; Pereira, Fernando; Azevedo, Eduardo B.; Borges, Paulo A. V.; Serrano, Artur R. M.

2013-01-01

The development in recent years of new beta diversity analytical approaches highlighted valuable information on the different processes structuring ecological communities. A crucial development for the understanding of beta diversity patterns was also its differentiation in two components: species turnover and richness differences. In this study, we evaluate beta diversity patterns of ground beetles from 26 sites in Madeira Island distributed throughout Laurisilva – a relict forest restricted to the Macaronesian archipelagos. We assess how the two components of ground beetle beta diversity (βrepl – species turnover and βrich - species richness differences) relate with differences in climate, geography, landscape composition matrix, woody plant species richness and soil characteristics and the relative importance of the effects of these variables at different spatial scales. We sampled 1025 specimens from 31 species, most of which are endemic to Madeira Island. A spatially explicit analysis was used to evaluate the contribution of pure environmental, pure spatial and environmental spatially structured effects on variation in ground beetle species richness and composition. Variation partitioning showed that 31.9% of species turnover (βrepl) and 40.7% of species richness variation (βrich) could be explained by the environmental and spatial variables. However, different environmental variables controlled the two types of beta diversity: βrepl was influenced by climate, disturbance and soil organic matter content whilst βrich was controlled by altitude and slope. Furthermore, spatial variables, represented through Moran’s eigenvector maps, played a significant role in explaining both βrepl and βrich, suggesting that both dispersal ability and Madeira Island complex orography are crucial for the understanding of beta diversity patterns in this group of beetles. PMID:23724065

The spatial sensitivity of the spectral diversity-biodiversity relationship: an experimental test in a prairie grassland.

PubMed

Wang, Ran; Gamon, John A; Cavender-Bares, Jeannine; Townsend, Philip A; Zygielbaum, Arthur I

2018-03-01

Remote sensing has been used to detect plant biodiversity in a range of ecosystems based on the varying spectral properties of different species or functional groups. However, the most appropriate spatial resolution necessary to detect diversity remains unclear. At coarse resolution, differences among spectral patterns may be too weak to detect. In contrast, at fine resolution, redundant information may be introduced. To explore the effect of spatial resolution, we studied the scale dependence of spectral diversity in a prairie ecosystem experiment at Cedar Creek Ecosystem Science Reserve, Minnesota, USA. Our study involved a scaling exercise comparing synthetic pixels resampled from high-resolution images within manipulated diversity treatments. Hyperspectral data were collected using several instruments on both ground and airborne platforms. We used the coefficient of variation (CV) of spectral reflectance in space as the indicator of spectral diversity and then compared CV at different scales ranging from 1 mm 2 to 1 m 2 to conventional biodiversity metrics, including species richness, Shannon's index, Simpson's index, phylogenetic species variation, and phylogenetic species evenness. In this study, higher species richness plots generally had higher CV. CV showed higher correlations with Shannon's index and Simpson's index than did species richness alone, indicating evenness contributed to the spectral diversity. Correlations with species richness and Simpson's index were generally higher than with phylogenetic species variation and evenness measured at comparable spatial scales, indicating weaker relationships between spectral diversity and phylogenetic diversity metrics than with species diversity metrics. High resolution imaging spectrometer data (1 mm 2 pixels) showed the highest sensitivity to diversity level. With decreasing spatial resolution, the difference in CV between diversity levels decreased and greatly reduced the optical detectability of biodiversity. The optimal pixel size for distinguishing α diversity in these prairie plots appeared to be around 1 mm to 10 cm, a spatial scale similar to the size of an individual herbaceous plant. These results indicate a strong scale-dependence of the spectral diversity-biodiversity relationships, with spectral diversity best able to detect a combination of species richness and evenness, and more weakly detecting phylogenetic diversity. These findings can be used to guide airborne studies of biodiversity and develop more effective large-scale biodiversity sampling methods. ©2018 The Authors Ecological Applications published by Wiley Periodicals, Inc. on behalf of Ecological Society of America.

Elevational Gradients in β-Diversity Reflect Variation in the Strength of Local Community Assembly Mechanisms across Spatial Scales

PubMed Central

Tello, J. Sebastián; Myers, Jonathan A.; Macía, Manuel J.; Fuentes, Alfredo F.; Cayola, Leslie; Arellano, Gabriel; Loza, M. Isabel; Torrez, Vania; Cornejo, Maritza; Miranda, Tatiana B.; Jørgensen, Peter M.

2015-01-01

Despite long-standing interest in elevational-diversity gradients, little is known about the processes that cause changes in the compositional variation of communities (β-diversity) across elevations. Recent studies have suggested that β-diversity gradients are driven by variation in species pools, rather than by variation in the strength of local community assembly mechanisms such as dispersal limitation, environmental filtering, or local biotic interactions. However, tests of this hypothesis have been limited to very small spatial scales that limit inferences about how the relative importance of assembly mechanisms may change across spatial scales. Here, we test the hypothesis that scale-dependent community assembly mechanisms shape biogeographic β-diversity gradients using one of the most well-characterized elevational gradients of tropical plant diversity. Using an extensive dataset on woody plant distributions along a 4,000-m elevational gradient in the Bolivian Andes, we compared observed patterns of β-diversity to null-model expectations. β-deviations (standardized differences from null values) were used to measure the relative effects of local community assembly mechanisms after removing sampling effects caused by variation in species pools. To test for scale-dependency, we compared elevational gradients at two contrasting spatial scales that differed in the size of local assemblages and regions by at least an order of magnitude. Elevational gradients in β-diversity persisted after accounting for regional variation in species pools. Moreover, the elevational gradient in β-deviations changed with spatial scale. At small scales, local assembly mechanisms were detectable, but variation in species pools accounted for most of the elevational gradient in β-diversity. At large spatial scales, in contrast, local assembly mechanisms were a dominant force driving changes in β-diversity. In contrast to the hypothesis that variation in species pools alone drives β-diversity gradients, we show that local community assembly mechanisms contribute strongly to systematic changes in β-diversity across elevations. We conclude that scale-dependent variation in community assembly mechanisms underlies these iconic gradients in global biodiversity. PMID:25803846

Grain-dependent responses of mammalian diversity to land use and the implications for conservation set-aside.

PubMed

Wearn, Oliver R; Carbone, Chris; Rowcliffe, J Marcus; Bernard, Henry; Ewers, Robert M

2016-07-01

Diversity responses to land-use change are poorly understood at local scales, hindering our ability to make forecasts and management recommendations at scales which are of practical relevance. A key barrier in this has been the underappreciation of grain-dependent diversity responses and the role that β-diversity (variation in community composition across space) plays in this. Decisions about the most effective spatial arrangement of conservation set-aside, for example high conservation value areas, have also neglected β-diversity, despite its role in determining the complementarity of sites. We examined local-scale mammalian species richness and β-diversity across old-growth forest, logged forest, and oil palm plantations in Borneo, using intensive camera- and live-trapping. For the first time, we were able to investigate diversity responses, as well as β-diversity, at multiple spatial grains, and across the whole terrestrial mammal community (large and small mammals); β-diversity was quantified by comparing observed β-diversity with that obtained under a null model, in order to control for sampling effects, and we refer to this as the β-diversity signal. Community responses to land use were grain dependent, with large mammals showing reduced richness in logged forest compared to old-growth forest at the grain of individual sampling points, but no change at the overall land-use level. Responses varied with species group, however, with small mammals increasing in richness at all grains in logged forest compared to old-growth forest. Both species groups were significantly depauperate in oil palm. Large mammal communities in old-growth forest became more heterogeneous at coarser spatial grains and small mammal communities became more homogeneous, while this pattern was reversed in logged forest. Both groups, however, showed a significant β-diversity signal at the finest grain in logged forest, likely due to logging-induced environmental heterogeneity. The β-diversity signal in oil palm was weak, but heterogeneity at the coarsest spatial grain was still evident, likely due to variation in landscape forest cover. Our findings suggest that the most effective spatial arrangement of set-aside will involve trade-offs between conserving large and small mammals. Greater consideration in the conservation and management of tropical landscapes needs to be given to β-diversity at a range of spatial grains. © 2016 by the Ecological Society of America.

Scale dependence of the diversity-stability relationship in a temperate grassland.

PubMed

Zhang, Yunhai; He, Nianpeng; Loreau, Michel; Pan, Qingmin; Han, Xingguo

2018-05-01

A positive relationship between biodiversity and ecosystem stability has been reported in many ecosystems; however, it has yet to be determined whether and how spatial scale affects this relationship. Here, for the first time, we assessed the effects of alpha, beta and gamma diversity on ecosystem stability and the scale dependence of the slope of the diversity-stability relationship.By employing a long-term (33 years) dataset from a temperate grassland, northern China, we calculated the all possible spatial scales with the complete combination from the basic 1-m 2 plots.Species richness was positively associated with ecosystem stability through species asynchrony and overyielding at all spatial scales (1, 2, 3, 4 and 5 m 2 ). Both alpha and beta diversity were positively associated with gamma stability.Moreover, the slope of the diversity-area relationship was significantly higher than that of the stability-area relationship, resulting in a decline of the slope of the diversity-stability relationship with increasing area. Synthesis. With the positive species diversity effect on ecosystem stability from small to large spatial scales, our findings demonstrate the need to maintain a high biodiversity and biotic heterogeneity as insurance against the risks incurred by ecosystems in the face of global environmental changes.

sGD: software for estimating spatially explicit indices of genetic diversity.

PubMed

Shirk, A J; Cushman, S A

2011-09-01

Anthropogenic landscape changes have greatly reduced the population size, range and migration rates of many terrestrial species. The small local effective population size of remnant populations favours loss of genetic diversity leading to reduced fitness and adaptive potential, and thus ultimately greater extinction risk. Accurately quantifying genetic diversity is therefore crucial to assessing the viability of small populations. Diversity indices are typically calculated from the multilocus genotypes of all individuals sampled within discretely defined habitat patches or larger regional extents. Importantly, discrete population approaches do not capture the clinal nature of populations genetically isolated by distance or landscape resistance. Here, we introduce spatial Genetic Diversity (sGD), a new spatially explicit tool to estimate genetic diversity based on grouping individuals into potentially overlapping genetic neighbourhoods that match the population structure, whether discrete or clinal. We compared the estimates and patterns of genetic diversity using patch or regional sampling and sGD on both simulated and empirical populations. When the population did not meet the assumptions of an island model, we found that patch and regional sampling generally overestimated local heterozygosity, inbreeding and allelic diversity. Moreover, sGD revealed fine-scale spatial heterogeneity in genetic diversity that was not evident with patch or regional sampling. These advantages should provide a more robust means to evaluate the potential for genetic factors to influence the viability of clinal populations and guide appropriate conservation plans. © 2011 Blackwell Publishing Ltd.

Biodiversity and ecosystem stability across scales in metacommunities.

PubMed

Wang, Shaopeng; Loreau, Michel

2016-05-01

Although diversity-stability relationships have been extensively studied in local ecosystems, the global biodiversity crisis calls for an improved understanding of these relationships in a spatial context. Here, we use a dynamical model of competitive metacommunities to study the relationships between species diversity and ecosystem variability across scales. We derive analytic relationships under a limiting case; these results are extended to more general cases with numerical simulations. Our model shows that, while alpha diversity decreases local ecosystem variability, beta diversity generally contributes to increasing spatial asynchrony among local ecosystems. Consequently, both alpha and beta diversity provide stabilising effects for regional ecosystems, through local and spatial insurance effects respectively. We further show that at the regional scale, the stabilising effect of biodiversity increases as spatial environmental correlation increases. Our findings have important implications for understanding the interactive effects of global environmental changes (e.g. environmental homogenisation) and biodiversity loss on ecosystem sustainability at large scales. © 2016 John Wiley & Sons Ltd/CNRS.

Operational Tree Species Mapping in a Diverse Tropical Forest with Airborne Imaging Spectroscopy.

PubMed

Baldeck, Claire A; Asner, Gregory P; Martin, Robin E; Anderson, Christopher B; Knapp, David E; Kellner, James R; Wright, S Joseph

2015-01-01

Remote identification and mapping of canopy tree species can contribute valuable information towards our understanding of ecosystem biodiversity and function over large spatial scales. However, the extreme challenges posed by highly diverse, closed-canopy tropical forests have prevented automated remote species mapping of non-flowering tree crowns in these ecosystems. We set out to identify individuals of three focal canopy tree species amongst a diverse background of tree and liana species on Barro Colorado Island, Panama, using airborne imaging spectroscopy data. First, we compared two leading single-class classification methods--binary support vector machine (SVM) and biased SVM--for their performance in identifying pixels of a single focal species. From this comparison we determined that biased SVM was more precise and created a multi-species classification model by combining the three biased SVM models. This model was applied to the imagery to identify pixels belonging to the three focal species and the prediction results were then processed to create a map of focal species crown objects. Crown-level cross-validation of the training data indicated that the multi-species classification model had pixel-level producer's accuracies of 94-97% for the three focal species, and field validation of the predicted crown objects indicated that these had user's accuracies of 94-100%. Our results demonstrate the ability of high spatial and spectral resolution remote sensing to accurately detect non-flowering crowns of focal species within a diverse tropical forest. We attribute the success of our model to recent classification and mapping techniques adapted to species detection in diverse closed-canopy forests, which can pave the way for remote species mapping in a wider variety of ecosystems.

Modelling patterns of pollinator species richness and diversity using satellite image texture.

PubMed

Hofmann, Sylvia; Everaars, Jeroen; Schweiger, Oliver; Frenzel, Mark; Bannehr, Lutz; Cord, Anna F

2017-01-01

Assessing species richness and diversity on the basis of standardised field sampling effort represents a cost- and time-consuming method. Satellite remote sensing (RS) can help overcome these limitations because it facilitates the collection of larger amounts of spatial data using cost-effective techniques. RS information is hence increasingly analysed to model biodiversity across space and time. Here, we focus on image texture measures as a proxy for spatial habitat heterogeneity, which has been recognized as an important determinant of species distributions and diversity. Using bee monitoring data of four years (2010-2013) from six 4 × 4 km field sites across Central Germany and a multimodel inference approach we test the ability of texture features derived from Landsat-TM imagery to model local pollinator biodiversity. Textures were shown to reflect patterns of bee diversity and species richness to some extent, with the first-order entropy texture and terrain roughness being the most relevant indicators. However, the texture measurements accounted for only 3-5% of up to 60% of the variability that was explained by our final models, although the results are largely consistent across different species groups (bumble bees, solitary bees). While our findings provide indications in support of the applicability of satellite imagery textures for modeling patterns of bee biodiversity, they are inconsistent with the high predictive power of texture metrics reported in previous studies for avian biodiversity. We assume that our texture data captured mainly heterogeneity resulting from landscape configuration, which might be functionally less important for wild bees than compositional diversity of plant communities. Our study also highlights the substantial variability among taxa in the applicability of texture metrics for modelling biodiversity.

Operational Tree Species Mapping in a Diverse Tropical Forest with Airborne Imaging Spectroscopy

PubMed Central

Baldeck, Claire A.; Asner, Gregory P.; Martin, Robin E.; Anderson, Christopher B.; Knapp, David E.; Kellner, James R.; Wright, S. Joseph

2015-01-01

Remote identification and mapping of canopy tree species can contribute valuable information towards our understanding of ecosystem biodiversity and function over large spatial scales. However, the extreme challenges posed by highly diverse, closed-canopy tropical forests have prevented automated remote species mapping of non-flowering tree crowns in these ecosystems. We set out to identify individuals of three focal canopy tree species amongst a diverse background of tree and liana species on Barro Colorado Island, Panama, using airborne imaging spectroscopy data. First, we compared two leading single-class classification methods—binary support vector machine (SVM) and biased SVM—for their performance in identifying pixels of a single focal species. From this comparison we determined that biased SVM was more precise and created a multi-species classification model by combining the three biased SVM models. This model was applied to the imagery to identify pixels belonging to the three focal species and the prediction results were then processed to create a map of focal species crown objects. Crown-level cross-validation of the training data indicated that the multi-species classification model had pixel-level producer’s accuracies of 94–97% for the three focal species, and field validation of the predicted crown objects indicated that these had user’s accuracies of 94–100%. Our results demonstrate the ability of high spatial and spectral resolution remote sensing to accurately detect non-flowering crowns of focal species within a diverse tropical forest. We attribute the success of our model to recent classification and mapping techniques adapted to species detection in diverse closed-canopy forests, which can pave the way for remote species mapping in a wider variety of ecosystems. PMID:26153693

Modelling patterns of pollinator species richness and diversity using satellite image texture

PubMed Central

Everaars, Jeroen; Schweiger, Oliver; Frenzel, Mark; Bannehr, Lutz; Cord, Anna F.

2017-01-01

Assessing species richness and diversity on the basis of standardised field sampling effort represents a cost- and time-consuming method. Satellite remote sensing (RS) can help overcome these limitations because it facilitates the collection of larger amounts of spatial data using cost-effective techniques. RS information is hence increasingly analysed to model biodiversity across space and time. Here, we focus on image texture measures as a proxy for spatial habitat heterogeneity, which has been recognized as an important determinant of species distributions and diversity. Using bee monitoring data of four years (2010–2013) from six 4 × 4 km field sites across Central Germany and a multimodel inference approach we test the ability of texture features derived from Landsat-TM imagery to model local pollinator biodiversity. Textures were shown to reflect patterns of bee diversity and species richness to some extent, with the first-order entropy texture and terrain roughness being the most relevant indicators. However, the texture measurements accounted for only 3–5% of up to 60% of the variability that was explained by our final models, although the results are largely consistent across different species groups (bumble bees, solitary bees). While our findings provide indications in support of the applicability of satellite imagery textures for modeling patterns of bee biodiversity, they are inconsistent with the high predictive power of texture metrics reported in previous studies for avian biodiversity. We assume that our texture data captured mainly heterogeneity resulting from landscape configuration, which might be functionally less important for wild bees than compositional diversity of plant communities. Our study also highlights the substantial variability among taxa in the applicability of texture metrics for modelling biodiversity. PMID:28973006

Patterns of seed bank and vegetation diversity along a tidal freshwater river.

PubMed

Elsey-Quirk, Tracy; Leck, Mary Allessio

2015-12-01

Species richness and diversity may increase with spatial scale related to increased area and heterogeneity of habitat. Yet, in bidirectional hydrologically connected tidal ecosystems, secondary dispersal via hydrochory has the potential to homogenize seed banks, and both life history characteristics and tolerances to environmental conditions influence the composition of plant communities. How species richness, diversity, and composition of seed banks and vegetation change along environmental gradients and at different spatial scales is not well understood. We explored the relationships of seed bank and vegetation diversity across 135 plots along a tidal freshwater river in the Delaware Estuary, USA. Species richness and diversity were partitioned across three hierarchical spatial scales: individual plots, transects perpendicular to the tidal channel, and river kilometers. Community structure was also examined as it related to distance from the tidal channel and location along the tidal river. Species richness was 89 in the seed bank and 54 in the vegetation. Species-area relationships revealed that species richness reached a near maximum asymptote inland (20 m from channel) for the seed bank and at the edge (0 m) for the vegetation. Rare occurrences of species in the seed bank and vegetation were greatest 5 m from the channel edge. As spatial scale increased, seed bank richness increased, associated with the progressive accumulation of species. Seed bank diversity, however, was maximized within small plot areas and along the river. Diversity of the vegetation was maximized locally due to the abundance of a few common species. These findings suggest that suites of common species contributed to high localized vegetation diversity, yet large spatial scales maximized the number and diversity of species in the seed bank and vegetation through rare encounters, as well as the complexity of the landscape. © 2015 Botanical Society of America.

Partitioning the impact of environment and spatial structure on alpha and beta components of taxonomic, functional, and phylogenetic diversity in European ants.

PubMed

Arnan, Xavier; Cerdá, Xim; Retana, Javier

2015-01-01

We analyze the relative contribution of environmental and spatial variables to the alpha and beta components of taxonomic (TD), phylogenetic (PD), and functional (FD) diversity in ant communities found along different climate and anthropogenic disturbance gradients across western and central Europe, in order to assess the mechanisms structuring ant biodiversity. To this aim we calculated alpha and beta TD, PD, and FD for 349 ant communities, which included a total of 155 ant species; we examined 10 functional traits and phylogenetic relatedness. Variation partitioning was used to examine how much variation in ant diversity was explained by environmental and spatial variables. Autocorrelation in diversity measures and each trait's phylogenetic signal were also analyzed. We found strong autocorrelation in diversity measures. Both environmental and spatial variables significantly contributed to variation in TD, PD, and FD at both alpha and beta scales; spatial structure had the larger influence. The different facets of diversity showed similar patterns along environmental gradients. Environment explained a much larger percentage of variation in FD than in TD or PD. All traits demonstrated strong phylogenetic signals. Our results indicate that environmental filtering and dispersal limitations structure all types of diversity in ant communities. Strong dispersal limitations appear to have led to clustering of TD, PD, and FD in western and central Europe, probably because different historical and evolutionary processes generated different pools of species. Remarkably, these three facets of diversity showed parallel patterns along environmental gradients. Trait-mediated species sorting and niche conservatism appear to structure ant diversity, as evidenced by the fact that more variation was explained for FD and that all traits had strong phylogenetic signals. Since environmental variables explained much more variation in FD than in PD, functional diversity should be a better indicator of community assembly processes than phylogenetic diversity.

Spatial Heterogeneity in the Effects of Immigration and Diversity on Neighborhood Homicide Rates

PubMed Central

Graif, Corina; Sampson, Robert J.

2010-01-01

This paper examines the connection of immigration and diversity to homicide by advancing a recently developed approach to modeling spatial dynamics—geographically weighted regression. In contrast to traditional global averaging, we argue on substantive grounds that neighborhood characteristics vary in their effects across neighborhood space, a process of “spatial heterogeneity.” Much like treatment-effect heterogeneity and distinct from spatial spillover, our analysis finds considerable evidence that neighborhood characteristics in Chicago vary significantly in predicting homicide, in some cases showing countervailing effects depending on spatial location. In general, however, immigrant concentration is either unrelated or inversely related to homicide, whereas language diversity is consistently linked to lower homicide. The results shed new light on the immigration-homicide nexus and suggest the pitfalls of global averaging models that hide the reality of a highly diversified and spatially stratified metropolis. PMID:20671811

Characterization of the bacterial community in a biotrickling filter treating high loads of H(2)S by molecular biology tools.

PubMed

Maestre, Juan P; Rovira, Roger; Gamisans, Xavier; Kinney, Kerry A; Kirisits, Mary Jo; Lafuente, Javier; Gabriel, David

2009-01-01

The diversity and spatial distribution of bacteria in a lab-scale biotrickling filter treating high loads of hydrogen sulfide (H(2)S) were investigated. Diversity and community structure were studied by terminal-restriction fragment length polymorphism (T-RFLP). A 16S rRNA gene clone library was established. Near Full-length 16S rRNA gene sequences were obtained, and clones were clustered into 24 operational taxonomic units (OTUs). Nearly 74% and 26% of the clones were affiliated with the phyla Proteobacteria and Bacteroidetes, respectively. Beta-, epsilon- and gamma-proteobacteria accounted for 15, 9 and 48%, respectively. Around 45% of the sequences retrieved were affiliated to bacteria of the sulfur cycle including Thiothrix spp., Thiobacillus spp. and Sulfurimonas denitrificans. Sequences related to Thiothrix lacustris accounted for a 38%. Rarefaction curve demonstrated that clone library constructed can be sufficient to describe the vast majority of the bacterial diversity of this reactor operating under strict conditions (2,000 ppm(v) of H(2)S). A spatial distribution of bacteria was found along the length of the reactor by means of the T-RFLP technique. Although aerobic species were predominant along the reactor, facultative anaerobes had a major relative abundance in the inlet part of the reactor, where the sulfide to oxygen ratio is higher.

System-Level Performance of Antenna Arrays in CDMA-Based Cellular Mobile Radio Systems

NASA Astrophysics Data System (ADS)

Czylwik, Andreas; Dekorsy, Armin

2004-12-01

Smart antennas exploit the inherent spatial diversity of the mobile radio channel, provide an antenna gain, and also enable spatial interference suppression leading to reduced intracell as well as intercell interference. Especially, for the downlink of future CDMA-based mobile communications systems, transmit beamforming is seen as a well-promising smart antenna technique. The main objective of this paper is to study the performance of diverse antenna array topologies when applied for transmit beamforming in the downlink of CDMA-based networks. In this paper, we focus on uniform linear array (ULA) and uniform circular array (UCA) topologies. For the ULA, we consider three-sector base stations with one linear array per sector. While recent research on downlink beamforming is often restricted to one single cell, this study takes into account the important impact of intercell interference on the performance by evaluating complete networks. Especially, from the operator perspective, system capacity and system coverage are very essential parameters of a cellular system so that there is a clear necessity of intensive system level investigations. Apart from delivering assessments on the performance of the diverse antenna array topologies, in the paper also different antenna array parameters, such as element spacing and beamwidth of the sector antennas, are optimized. Although we focus on the network level, fast channel fluctuations are taken into account by including them analytically into the signal-to-interference calculation.

Capacity of MIMO free space optical communications using multiple partially coherent beams propagation through non-Kolmogorov strong turbulence.

PubMed

Deng, Peng; Kavehrad, Mohsen; Liu, Zhiwen; Zhou, Zhou; Yuan, Xiuhua

2013-07-01

We study the average capacity performance for multiple-input multiple-output (MIMO) free-space optical (FSO) communication systems using multiple partially coherent beams propagating through non-Kolmogorov strong turbulence, assuming equal gain combining diversity configuration and the sum of multiple gamma-gamma random variables for multiple independent partially coherent beams. The closed-form expressions of scintillation and average capacity are derived and then used to analyze the dependence on the number of independent diversity branches, power law α, refractive-index structure parameter, propagation distance and spatial coherence length of source beams. Obtained results show that, the average capacity increases more significantly with the increase in the rank of MIMO channel matrix compared with the diversity order. The effect of the diversity order on the average capacity is independent of the power law, turbulence strength parameter and spatial coherence length, whereas these effects on average capacity are gradually mitigated as the diversity order increases. The average capacity increases and saturates with the decreasing spatial coherence length, at rates depending on the diversity order, power law and turbulence strength. There exist optimal values of the spatial coherence length and diversity configuration for maximizing the average capacity of MIMO FSO links over a variety of atmospheric turbulence conditions.

Beta diversity at different spatial scales: plant communities in organic and conventional agriculture.

PubMed

Gabriel, Doreen; Roschewitz, Indra; Tscharntke, Teja; Thies, Carsten

2006-10-01

Biodiversity studies that guide agricultural subsidy policy have generally compared farming systems at a single spatial scale: the field. However, diversity patterns vary across spatial scales. Here, we examined the effects of farming system (organic vs. conventional) and position in the field (edge vs. center) on plant species richness in wheat fields at three spatial scales. We quantified alpha-, beta-, and gamma-diversity at the microscale in 800 plots, at the mesoscale in 40 fields, and at the macroscale in three regions using the additive partitioning approach, and evaluated the relative contribution of beta-diversity at each spatial scale to total observed species richness. We found that alpha-, beta-, and gamma-diversity were higher in organic than conventional fields and higher at the field edge than in the field center at all spatial scales. In both farming systems, beta-diversity at the meso- and macroscale explained most of the overall species richness (up to 37% and 25%, respectively), indicating considerable differences in community composition among fields and regions due to environmental heterogeneity. The spatial scale at which beta-diversity contributed the most to overall species richness differed between rare and common species. Total richness of rare species (present in < or = 5% of total samples) was mainly explained by differences in community composition at the meso- and macroscale (up to 27% and 48%, respectively), but only in organic fields. Total richness of common species (present in > or = 25% of total samples) was explained by differences in community composition at the micro- and mesoscale (up to 29% and 47%, respectively), i.e., among plots and fields, independent of farming system. Our results show that organic farming made the greatest contribution to total species richness at the meso (among fields) and macro (among regions) scale due to environmental heterogeneity. Hence, agri-environment schemes should exploit this large-scale contribution of beta-diversity by tailoring schemes at regional scales to maximize dissimilarity between conservation areas using geographic information systems rather than focusing entirely at the classical local-field scale, which is the current practice.

Reduced fine-scale spatial genetic structure in grazed populations of Dianthus carthusianorum

PubMed Central

Rico, Y; Wagner, H H

2016-01-01

Strong spatial genetic structure in plant populations can increase homozygosity, reducing genetic diversity and adaptive potential. The strength of spatial genetic structure largely depends on rates of seed dispersal and pollen flow. Seeds without dispersal adaptations are likely to be dispersed over short distances within the vicinity of the mother plant, resulting in spatial clustering of related genotypes (fine-scale spatial genetic structure, hereafter spatial genetic structure (SGS)). However, primary seed dispersal by zoochory can promote effective dispersal, increasing the mixing of seeds and influencing SGS within plant populations. In this study, we investigated the effects of seed dispersal by rotational sheep grazing on the strength of SGS and genetic diversity using 11 nuclear microsatellites for 49 populations of the calcareous grassland forb Dianthus carthusianorum. Populations connected by rotational sheep grazing showed significantly weaker SGS and higher genetic diversity than populations in ungrazed grasslands. Independent of grazing treatment, small populations showed significantly stronger SGS and lower genetic diversity than larger populations, likely due to genetic drift. A lack of significant differences in the strength of SGS and genetic diversity between populations that were recently colonized and pre-existing populations suggested that populations colonized after the reintroduction of rotational sheep grazing were likely founded by colonists from diverse source populations. We conclude that dispersal by rotational sheep grazing has the potential to considerably reduce SGS within D. carthusianorum populations. Our study highlights the effectiveness of landscape management by rotational sheep grazing to importantly reduce genetic structure at local scales within restored plant populations. PMID:27381322

Reduced fine-scale spatial genetic structure in grazed populations of Dianthus carthusianorum.

PubMed

Rico, Y; Wagner, H H

2016-11-01

Strong spatial genetic structure in plant populations can increase homozygosity, reducing genetic diversity and adaptive potential. The strength of spatial genetic structure largely depends on rates of seed dispersal and pollen flow. Seeds without dispersal adaptations are likely to be dispersed over short distances within the vicinity of the mother plant, resulting in spatial clustering of related genotypes (fine-scale spatial genetic structure, hereafter spatial genetic structure (SGS)). However, primary seed dispersal by zoochory can promote effective dispersal, increasing the mixing of seeds and influencing SGS within plant populations. In this study, we investigated the effects of seed dispersal by rotational sheep grazing on the strength of SGS and genetic diversity using 11 nuclear microsatellites for 49 populations of the calcareous grassland forb Dianthus carthusianorum. Populations connected by rotational sheep grazing showed significantly weaker SGS and higher genetic diversity than populations in ungrazed grasslands. Independent of grazing treatment, small populations showed significantly stronger SGS and lower genetic diversity than larger populations, likely due to genetic drift. A lack of significant differences in the strength of SGS and genetic diversity between populations that were recently colonized and pre-existing populations suggested that populations colonized after the reintroduction of rotational sheep grazing were likely founded by colonists from diverse source populations. We conclude that dispersal by rotational sheep grazing has the potential to considerably reduce SGS within D. carthusianorum populations. Our study highlights the effectiveness of landscape management by rotational sheep grazing to importantly reduce genetic structure at local scales within restored plant populations.

imVisIR - a new tool for high resolution soil characterisation

NASA Astrophysics Data System (ADS)

Steffens, Markus; Buddenbaum, Henning

2014-05-01

The physical and chemical heterogeneities of soils are the source of a vast functional diversity of soil properties in a multitude of spatial domains. But many studies do not consider the spatial variability of soil types, diagnostic horizons and properties. These lateral and vertical heterogeneities of soils or soil horizons are mostly neglected due to the limitations in the available soil data and missing techniques to gather the information. We present an imaging technique that enables the spatially accurate, high resolution assessment (63×63 µm2 per pixel) of complete soil profiles consisting of mineral and organic horizons. We used a stainless steel box (100×100×300 mm3) to sample various soil types and a hyperspectral camera to record the bidirectional reflectance of the large undisturbed soil samples in the visible and near infrared (Vis-NIR) part of the electromagnetic spectrum (400-1000 nm in 160 spectral bands). Various statistical, geostatistical and image processing tools were used to 1) assess the spatial variability of the soil profile as a whole; 2) classify diagnostic horizons; 3) extrapolate elemental concentrations of small sampling areas to the complete image and calculate high resolution chemometric maps of up to five elements (C, N, Al, Fe, Mn); and 4) derive maps of the chemical composition of soil organic matter. Imaging Vis-NIR (imVisIR) has the potential to significantly improve soil classification, assessment of elemental budgets and balances and the understanding of soil forming processes and mechanisms. It will help to identify areas of interest for techniques working on smaller scales and enable the upscaling and referencing of this information to the complete pedon.

Remote Sensing Applications with High Reliability in Changjiang Water Resource Management

NASA Astrophysics Data System (ADS)

Ma, L.; Gao, S.; Yang, A.

2018-04-01

Remote sensing technology has been widely used in many fields. But most of the applications cannot get the information with high reliability and high accuracy in large scale, especially for the applications using automatic interpretation methods. We have designed an application-oriented technology system (PIR) composed of a series of accurate interpretation techniques,which can get over 85 % correctness in Water Resource Management from the view of photogrammetry and expert knowledge. The techniques compose of the spatial positioning techniques from the view of photogrammetry, the feature interpretation techniques from the view of expert knowledge, and the rationality analysis techniques from the view of data mining. Each interpreted polygon is accurate enough to be applied to the accuracy sensitive projects, such as the Three Gorge Project and the South - to - North Water Diversion Project. In this paper, we present several remote sensing applications with high reliability in Changjiang Water Resource Management,including water pollution investigation, illegal construction inspection, and water conservation monitoring, etc.

The design and implementation of hydrographical information management system (HIMS)

NASA Astrophysics Data System (ADS)

Sui, Haigang; Hua, Li; Wang, Qi; Zhang, Anming

2005-10-01

With the development of hydrographical work and information techniques, the large variety of hydrographical information including electronic charts, documents and other materials are widely used, and the traditional management mode and techniques are unsuitable for the development of the Chinese Marine Safety Administration Bureau (CMSAB). How to manage all kinds of hydrographical information has become an important and urgent problem. A lot of advanced techniques including GIS, RS, spatial database management and VR techniques are introduced for solving these problems. Some design principles and key techniques of the HIMS including the mixed mode base on B/S, C/S and stand-alone computer mode, multi-source & multi-scale data organization and management, multi-source data integration and diverse visualization of digital chart, efficient security control strategies are illustrated in detail. Based on the above ideas and strategies, an integrated system named Hydrographical Information Management System (HIMS) was developed. And the HIMS has been applied in the Shanghai Marine Safety Administration Bureau and obtained good evaluation.

Factors influencing geographic patterns in diversity of forest bird communities of eastern Connecticut, USA

USGS Publications Warehouse

Craig, Robert J.; Klaver, Robert W.

2012-01-01

At regional scales, the most important variables associated with diversity are latitudinally-based temperature and net primary productivity, although diversity is also influenced by habitat. We examined bird species richness, community density and community evenness in forests of eastern Connecticut to determine whether: 1) spatial and seasonal patterns exist in diversity, 2) energy explains the greatest proportion of variation in diversity parameters, 3) variation in habitat explains remaining diversity variance, and 4) seasonal shifts in diversity provide clues about how environmental variables shape communities. We sought to discover if our data supported predictions of the species–energy hypothesis. We used the variable circular plot technique to estimate bird populations and quantified the location, elevation, forest type, vegetation type, canopy cover, moisture regime, understory density and primary production for the study sites. We found that 1) summer richness and population densities are roughly equal in northeastern and southeastern Connecticut, whereas in winter both concentrate toward the coast, 2) variables linked with temperature explained much of the patterns in winter diversity, but energy-related variables showed little relationship to summer diversity, 3) the effect of habitat variables on diversity parameters predominated in summer, although their effect was weak, 4) contrary to theory, evenness increased from summer to winter, and 5) support for predictions of species–energy theory was primarily restricted to winter data. Although energy and habitat played a role in explaining community patterns, they left much of the variance in regional diversity unexplained, suggesting that a large stochastic component to diversity also may exist.

Multiscale mapping of species diversity under changed land use using imaging spectroscopy.

PubMed

Paz-Kagan, Tarin; Caras, Tamir; Herrmann, Ittai; Shachak, Moshe; Karnieli, Arnon

2017-07-01

Land use changes are one of the most important factors causing environmental transformations and species diversity alterations. The aim of the current study was to develop a geoinformatics-based framework to quantify alpha and beta diversity indices in two sites in Israel with different land uses, i.e., an agricultural system of fruit orchards, an afforestation system of planted groves, and an unmanaged system of groves. The framework comprises four scaling steps: (1) classification of a tree species distribution (SD) map using imaging spectroscopy (IS) at a pixel size of 1 m; (2) estimation of local species richness by calculating the alpha diversity index for 30-m grid cells; (3) calculation of beta diversity for different land use categories and sub-categories at different sizes; and (4) calculation of the beta diversity difference between the two sites. The SD was classified based on a hyperspectral image with 448 bands within the 380-2500 nm spectral range and a spatial resolution of 1 m. Twenty-three tree species were classified with high overall accuracy values of 82.57% and 86.93% for the two sites. Significantly high values of the alpha index characterize the unmanaged land use, and the lowest values were calculated for the agricultural land use. In addition, high values of alpha indices were found at the borders between the polygons related to the "edge-effect" phenomenon, whereas low alpha indices were found in areas with high invasion species rates. The beta index value, calculated for 58 polygons, was significantly lower in the agricultural land use. The suggested framework of this study succeeded in quantifying land use effects on tree species distribution, evenness, and richness. IS and spatial statistics techniques offer an opportunity to study woody plant species variation with a multiscale approach that is useful for managing land use, especially under increasing environmental changes. © 2017 by the Ecological Society of America.

Mushroom biomass and diversity are driven by different spatio-temporal scales along Mediterranean elevation gradients

NASA Astrophysics Data System (ADS)

Alday, Josu G.; Martínez de Aragón, Juan; de-Miguel, Sergio; Bonet, José Antonio

2017-04-01

Mushrooms are important non-wood-forest-products in many Mediterranean ecosystems, being highly vulnerable to climate change. However, the ecological scales of variation of mushroom productivity and diversity, and climate dependence has been usually overlooked due to a lack of available data. We determined the spatio-temporal variability of epigeous sporocarps and the climatic factors driving their fruiting to plan future sustainable management of wild mushrooms production. We collected fruiting bodies in Pinus sylvestris stands along an elevation gradient for 8 consecutive years. Overall, sporocarp biomass was mainly dependent on inter-annual variations, whereas richness was more spatial-scale dependent. Elevation was not significant, but there were clear elevational differences in biomass and richness patterns between ectomycorrhizal and saprotrophic guilds. The main driver of variation was late-summer-early-autumn precipitation. Thus, different scale processes (inter-annual vs. spatial-scale) drive sporocarp biomass and diversity patterns; temporal effects for biomass and ectomycorrhizal fungi vs. spatial scale for diversity and saprotrophic fungi. The significant role of precipitation across fungal guilds and spatio-temporal scales indicates that it is a limiting resource controlling sporocarp production and diversity in Mediterranean regions. The high spatial and temporal variability of mushrooms emphasize the need for long-term datasets of multiple spatial points to effectively characterize fungal fruiting patterns.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Majewski, Pawel W.; Yager, Kevin G.

Block-copolymers self-assemble into diverse morphologies, where nanoscale order can be finely tuned via block architecture and processing conditions. However, the ultimate usage of these materials in real-world applications may be hampered by the extremely long thermal annealing times—hours or days—required to achieve good order. Here, we provide an overview of the fundamentals of block-copolymer self-assembly kinetics, and review the techniques that have been demonstrated to influence, and enhance, these ordering kinetics. We discuss the inherent tradeoffs between oven annealing, solvent annealing, microwave annealing, zone annealing, and other directed self-assembly methods; including an assessment of spatial and temporal characteristics. Here, wemore » also review both real-space and reciprocal-space analysis techniques for quantifying order in these systems.« less

Rapid ordering of block copolymer thin films

NASA Astrophysics Data System (ADS)

Majewski, Pawel W.; Yager, Kevin G.

2016-10-01

Block-copolymers self-assemble into diverse morphologies, where nanoscale order can be finely tuned via block architecture and processing conditions. However, the ultimate usage of these materials in real-world applications may be hampered by the extremely long thermal annealing times—hours or days—required to achieve good order. Here, we provide an overview of the fundamentals of block-copolymer self-assembly kinetics, and review the techniques that have been demonstrated to influence, and enhance, these ordering kinetics. We discuss the inherent tradeoffs between oven annealing, solvent annealing, microwave annealing, zone annealing, and other directed self-assembly methods; including an assessment of spatial and temporal characteristics. We also review both real-space and reciprocal-space analysis techniques for quantifying order in these systems.

Mechanisms for increased soil C storage with increasing temporal and spatial plant diversity in Agroecosystems

NASA Astrophysics Data System (ADS)

Tiemann, L. K.; Grandy, S.; Marin-Spiotta, E.; Atkinson, E. E.

2012-12-01

Generally, there are positive relationships between plant species diversity and net primary production and other key ecosystem functions. However, the effects of aboveground diversity on soil microbial communities and ecosystem processes they mediate, such as soil C sequestration, remain unclear. In this study, we used an 11-y cropping diversity study where increases in diversity have increased crop yields. At the experimental site, temporal diversity is altered using combinations of annual crop rotations, while spatial diversity is altered using cover crop species. We used five treatments ranging in diversity from one to five species consisting of continuous corn with no cover crop or one cover crop and corn-soy-wheat rotations with no cover, one cover or two cover crop species. We collected soils from four replicate plots of each treatment and measured the distribution of mega- (>2 mm), macro- (0.25-2 mm), and micro- (0.053-0.25 mm) aggregates. Within each aggregate size class, we also measured total soil C and N, permanganate oxidizable C (POXC), extracellular enzyme activities (EEA), and microbial community structure with phospholipid fatty acid (PLFA) analysis. We use these data to address the impacts of both rotational and cover crop diversity on soil physical structure, associated microbial community structure and activity and soil C storage. As spatial diversity increased, we found concurrent increases in mega-aggregate abundance as well as increasing soil C in the mega- and micro-aggregates but not macro-aggregates. The proportion of total soil C in each aggregate size class that is relatively labile (POXC) was highest in the micro-aggregates, as was enzyme activity associated with labile C acquisition across all levels of diversity. Enzyme activity associated with more recalcitrant forms of soil C was highest in the mega-aggregate class, also across all diversity levels; however, the ratio of labile to recalcitrant EEA increased with increasing diversity in the mega- and micro-aggregates. In addition, soil N increased with diversity such that microbial C:N EEA simultaneously decreased in mega-aggregates. We also found that cropping diversity has created distinctive soil microbial communities, highlighted by variation in the abundance of gram positive bacteria and Actinomycetes. Further research will help us determine how these changes in community structure with increasing diversity are related to concomitant changes in aggregation and enzyme activities. We suggest that the additional organic matter inputs from cover crops in the high diversity treatments have increased aggregation processes and C pools. While microbial activity has also increased in association with this increased C availability, the activity of recalcitrant and N-acquiring enzymes has declined, suggesting an overall decrease in SOM mineralization with possible increased SOM stabilization. The addition of crop species in rotation (temporal diversity) had minimal influence on any of the measured parameters. We thus conclude that spatial diversity is a more important driver of soil structure and microbial activity, likely due to the high quality organic matter inputs derived from the leguminous cover crops; however, spatial diversity alone did not lead to the same level of C storage potential as mixtures of temporal and spatial diversity.

Complementarity of UV and IR differential absorption lidar for global measurements of atmospheric species

NASA Technical Reports Server (NTRS)

Megie, G.; Menzies, R. T.

1980-01-01

An analysis of the potential capabilities of a spectrally diversified DIAL technique for monitoring atmospheric species is presented assuming operation from an earth-orbiting platform. Emphasis is given to the measurement accuracies and spatial and temporal resolutions required to meet present atmospheric science objectives. The discussion points out advantages of spectral diversity to perform comprehensive studies of the atmosphere; in general it is shown that IR systems have an advantage in lower atmospheric measurements, while UV systems are superior for middle and upper atmospheric measurements.

High Performance Geostatistical Modeling of Biospheric Resources

NASA Astrophysics Data System (ADS)

Pedelty, J. A.; Morisette, J. T.; Smith, J. A.; Schnase, J. L.; Crosier, C. S.; Stohlgren, T. J.

2004-12-01

We are using parallel geostatistical codes to study spatial relationships among biospheric resources in several study areas. For example, spatial statistical models based on large- and small-scale variability have been used to predict species richness of both native and exotic plants (hot spots of diversity) and patterns of exotic plant invasion. However, broader use of geostastics in natural resource modeling, especially at regional and national scales, has been limited due to the large computing requirements of these applications. To address this problem, we implemented parallel versions of the kriging spatial interpolation algorithm. The first uses the Message Passing Interface (MPI) in a master/slave paradigm on an open source Linux Beowulf cluster, while the second is implemented with the new proprietary Xgrid distributed processing system on an Xserve G5 cluster from Apple Computer, Inc. These techniques are proving effective and provide the basis for a national decision support capability for invasive species management that is being jointly developed by NASA and the US Geological Survey.

Small-scale spatial variability of soil microbial community composition and functional diversity in a mixed forest

NASA Astrophysics Data System (ADS)

Wang, Qiufeng; Tian, Jing; Yu, Guirui

2014-05-01

Patterns in the spatial distribution of organisms provide important information about mechanisms that regulate the diversity and complexity of soil ecosystems. Therefore, information on spatial distribution of microbial community composition and functional diversity is urgently necessary. The spatial variability on a 26×36 m plot and vertical distribution (0-10 cm and 10-20 cm) of soil microbial community composition and functional diversity were studied in a natural broad-leaved Korean pine (Pinus koraiensis) mixed forest soil in Changbai Mountain. The phospholipid fatty acid (PLFA) pattern was used to characterize the soil microbial community composition and was compared with the community substrate utilization pattern using Biolog. Bacterial biomass dominated and showed higher variability than fungal biomass at all scales examined. The microbial biomass decreased with soil depths increased and showed less variability in lower 10-20 cm soil layer. The Shannon-Weaver index value for microbial functional diversity showed higher variability in upper 0-10 cm than lower 10-20 cm soil layer. Carbohydrates, carboxylic acids, polymers and amino acids are the main carbon sources possessing higher utilization efficiency or utilization intensity. At the same time, the four carbon source types contributed to the differentiation of soil microbial communities. This study suggests the higher diversity and complexity for this mix forest ecosystem. To determine the driving factors that affect this spatial variability of microorganism is the next step for our study.

Physicochemical characterization and failure analysis of military coating systems

NASA Astrophysics Data System (ADS)

Keene, Lionel Thomas

Modern military coating systems, as fielded by all branches of the U.S. military, generally consist of a diverse array of organic and inorganic components that can complicate their physicochemical analysis. These coating systems consist of VOC-solvent/waterborne automotive grade polyurethane matrix containing a variety of inorganic pigments and flattening agents. The research presented here was designed to overcome the practical difficulties regarding the study of such systems through the combined application of several cross-disciplinary techniques, including vibrational spectroscopy, electron microscopy, microtomy, ultra-fast laser ablation and optical interferometry. The goal of this research has been to determine the degree and spatial progression of weathering-induced alteration of military coating systems as a whole, as well as to determine the failure modes involved, and characterizing the impact of these failures on the physical barrier performance of the coatings. Transmission-mode Fourier Transform Infrared (FTIR) spectroscopy has been applied to cross-sections of both baseline and artificially weathered samples to elucidate weathering-induced spatial gradients to the baseline chemistry of the coatings. A large discrepancy in physical durability (as indicated by the spatial progression of these gradients) has been found between older and newer generation coatings. Data will be shown implicating silica fillers (previously considered inert) as the probable cause for this behavioral divergence. A case study is presented wherein the application of the aforementioned FTIR technique fails to predict the durability of the coating system as a whole. The exploitation of the ultra-fast optical phenomenon of femtosecond (10-15S) laser ablation is studied as a potential tool to facilitate spectroscopic depth profiling of composite materials. Finally, the interferometric technique of Phase Shifting was evaluated as a potential high-sensitivity technique applied to the problem of determining internal stress evolution in curing and aging coatings.

An overview assessment of the effectiveness and global popularity of some methods used in measuring riverbank filtration

NASA Astrophysics Data System (ADS)

Umar, Da'u. Abba; Ramli, Mohammad Firuz; Aris, Ahmad Zaharin; Sulaiman, Wan Nor Azmin; Kura, Nura Umar; Tukur, Abubakar Ibrahim

2017-07-01

This paper presents an overview assessment of the effectiveness and popularity of some methods adopted in measuring river bank filtration (RBF). The review is aim at understanding some of the appropriate methods used in measuring riverbank filtration, their frequencies of use, and their spatial applications worldwide. The most commonly used methods and techniques in riverbank filtration studies are: Geographical Information System (GIS) (site suitability/surface characterization), Geophysical, Pumping Test and borehole logging (sub-surface), Hydrochemical, Geochemical, and Statistical techniques (hydrochemistry of water), Numerical modelling, Tracer techniques and Stable Isotope Approaches (degradation and contaminants attenuation processes). From the summary in Table 1, hydrochemical, numerical modelling and pumping test are the frequently used and popular methods, while geophysical, GIS and statistical techniques are the less attractive. However, many researchers prefer integrated approach especially that riverbank filtration studies involve diverse and interrelated components. In term of spatial popularity and successful implementation of riverbank filtration, it is explicitly clear that the popularity and success of the technology is more pronounced in developed countries like U.S. and most European countries. However, it is gradually gaining ground in Asia and Africa, although it is not far from its infancy state in Africa, where the technology could be more important considering the economic status of the region and its peculiarity when it comes to water resources predicaments.

Different responses of functional traits and diversity of stream macroinvertebrates to environmental and spatial factors in the Xishuangbanna watershed of the upper Mekong River Basin, China.

PubMed

Ding, Ning; Yang, Weifang; Zhou, Yunlei; González-Bergonzoni, Ivan; Zhang, Jie; Chen, Kai; Vidal, Nicolas; Jeppesen, Erik; Liu, Zhengwen; Wang, Beixin

2017-01-01

Functional traits and diversity indices have provided new insights into community responses to stressors. Most traits of aquatic organisms have frequently been tested for predictability and geographical stability in response to environmental variables, but such tests of functional diversity indices are rare. We sampled macroinvertebrates at 18 reference sites (RS) and 35 disturbed sites (DS) from headwater streams in the upper Mekong River Basin, Xishuangbanna (XSBN), China. We selected 29 qualitative categories of eight traits and then calculated five functional diversity indices, namely functional richness (FRic), functional evenness (FEve), functional dispersion (FDis), functional divergence (FDiv) and Rao's Quadratic Entropy (RaoQ), and two trait diversity indices, namely trait richness (TR) and trait diversity (TD). We used combination of RLQ and fourth-corner to examine the response of traits and functional diversity to the disturbance and environmental variables. We used variance partitioning to explore the relative role of environmental variables and spatial factors in constraining trait composition and functional diversity. We found that the relative frequency of ten trait categories, and the values of TD, TR, FRic and FDis in RS were significantly different (p<0.05) from DS. In addition, the seven traits (except for "habit") demonstrated a predictable response of trait patterns along the integrative environmental gradients. Environmental variables significantly contributed to most of the traits, functional diversity and trait diversity. However, spatial variables were mainly significant in shaping ecological traits, FRic and FEve. Our results confirm the dominant role of environmental variables in the determination of community trait composition and functional diversity, and substantiate the contribution of spatial vectors in explaining the variance of functional traits and diversity. We conclude that the traits "Refuge", "External protection", "Respiration" and "Body shape", and diversity indices FDis, TD, and TR are promising indicators of stream conditions at XSBN. Copyright © 2016 Elsevier B.V. All rights reserved.

Gap formation following climatic events in spatially structured plant communities

PubMed Central

Liao, Jinbao; De Boeck, Hans J.; Li, Zhenqing; Nijs, Ivan

2015-01-01

Gaps play a crucial role in maintaining species diversity, yet how community structure and composition influence gap formation is still poorly understood. We apply a spatially structured community model to predict how species diversity and intraspecific aggregation shape gap patterns emerging after climatic events, based on species-specific mortality responses. In multispecies communities, average gap size and gap-size diversity increased rapidly with increasing mean mortality once a mortality threshold was exceeded, greatly promoting gap recolonization opportunity. This result was observed at all levels of species richness. Increasing interspecific difference likewise enhanced these metrics, which may promote not only diversity maintenance but also community invasibility, since more diverse niches for both local and exotic species are provided. The richness effects on gap size and gap-size diversity were positive, but only expressed when species were sufficiently different. Surprisingly, while intraspecific clumping strongly promoted gap-size diversity, it hardly influenced average gap size. Species evenness generally reduced gap metrics induced by climatic events, so the typical assumption of maximum evenness in many experiments and models may underestimate community diversity and invasibility. Overall, understanding the factors driving gap formation in spatially structured assemblages can help predict community secondary succession after climatic events. PMID:26114803

Changes in Species Diversity Patterns and Spatial Heterogeneity during the Secondary Succession of Grassland Vegetation on the Loess Plateau, China.

PubMed

Sun, Caili; Chai, Zongzheng; Liu, Guobin; Xue, Sha

2017-01-01

Analyzing the dynamic patterns of species diversity and spatial heterogeneity of vegetation in grasslands during secondary succession could help with the maintenance and management of these ecosystems. Here, we evaluated the influence of secondary succession on grassland plant diversity and spatial heterogeneity of abandoned croplands on the Loess Plateau (China) during four phases of recovery: 1-5, 5-10, 10-20, and 20-30 years. The species composition and dominance of the grassland vegetation changed markedly during secondary succession and formed a clear successional series, with the species assemblage dominated by Artemisia capillaris → Heteropappus altaicus→ A. sacrorum . The diversity pattern was one of low-high-low, with diversity peaking in the 10-20 year phase, thus corresponding to a hump-backed model in which maximum diversity occurring at the intermediate stages. A spatially aggregated pattern prevailed throughout the entire period of grassland recovery; this was likely linked to the dispersal properties of herbaceous plants and to high habitat heterogeneity. We conclude that natural succession was conducive to the successful recovery of native vegetation. From a management perspective, native pioneer tree species should be introduced about 20 years after abandoning croplands to accelerate the natural succession of grassland vegetation.

The role of competition – colonization tradeoffs and spatial heterogeneity in promoting trematode coexistence

USGS Publications Warehouse

Mordecai, Erin A.; Jaramillo, Alejandra G.; Ashford, Jacob E.; Hechinger, Ryan F.; Lafferty, Kevin D.

2016-01-01

Competition – colonization tradeoffs occur in many systems, and theory predicts that they can strongly promote species coexistence. However, there is little empirical evidence that observed competition – colonization tradeoffs are strong enough to maintain diversity in natural systems. This is due in part to a mismatch between theoretical assumptions and biological reality in some systems. We tested whether a competition – colonization tradeoff explains how a diverse trematode guild coexists in California horn snail populations, a system that meets the requisite criteria for the tradeoff to promote coexistence. A field experiment showed that subordinate trematode species tended to have higher colonization rates than dominant species. This tradeoff promoted coexistence in parameterized models but did not fully explain trematode diversity and abundance, suggesting a role of additional diversity maintenance mechanisms. Spatial heterogeneity is an alternative way to promote coexistence if it isolates competing species. We used scale transition theory to expand the competition – colonization tradeoff model to include spatial variation. The parameterized model showed that spatial variation in trematode prevalence did not isolate most species sufficiently to explain the overall high diversity, but could benefit some rare species. Together, the results suggest that several mechanisms combine to maintain diversity, even when a competition – colonization tradeoff occurs.

Changes in Species Diversity Patterns and Spatial Heterogeneity during the Secondary Succession of Grassland Vegetation on the Loess Plateau, China

PubMed Central

Sun, Caili; Chai, Zongzheng; Liu, Guobin; Xue, Sha

2017-01-01

Analyzing the dynamic patterns of species diversity and spatial heterogeneity of vegetation in grasslands during secondary succession could help with the maintenance and management of these ecosystems. Here, we evaluated the influence of secondary succession on grassland plant diversity and spatial heterogeneity of abandoned croplands on the Loess Plateau (China) during four phases of recovery: 1–5, 5–10, 10–20, and 20–30 years. The species composition and dominance of the grassland vegetation changed markedly during secondary succession and formed a clear successional series, with the species assemblage dominated by Artemisia capillaris→ Heteropappus altaicus→ A. sacrorum. The diversity pattern was one of low–high–low, with diversity peaking in the 10–20 year phase, thus corresponding to a hump-backed model in which maximum diversity occurring at the intermediate stages. A spatially aggregated pattern prevailed throughout the entire period of grassland recovery; this was likely linked to the dispersal properties of herbaceous plants and to high habitat heterogeneity. We conclude that natural succession was conducive to the successful recovery of native vegetation. From a management perspective, native pioneer tree species should be introduced about 20 years after abandoning croplands to accelerate the natural succession of grassland vegetation. PMID:28900433

Latitude delineates patterns of biogeography in terrestrial Streptomyces.

PubMed

Choudoir, Mallory J; Doroghazi, James R; Buckley, Daniel H

2016-12-01

The biogeography of Streptomyces was examined at regional spatial scales to identify factors that govern patterns of microbial diversity. Streptomyces are spore forming filamentous bacteria which are widespread in soil. Streptomyces strains were isolated from perennial grass habitats sampled across a spatial scale of more than 6000 km. Previous analysis of this geographically explicit culture collection provided evidence for a latitudinal diversity gradient in Streptomyces species. Here the hypothesis that this latitudinal diversity gradient is a result of evolutionary dynamics associated with historical demographic processes was evaluated. Historical demographic phenomena have genetic consequences that can be evaluated through analysis of population genetics. Population genetic approaches were applied to analyze population structure in six of the most numerically abundant and geographically widespread Streptomyces phylogroups from our culture collection. Streptomyces population structure varied at regional spatial scales, and allelic diversity correlated with geographic distance. In addition, allelic diversity and gene flow are partitioned by latitude. Finally, it was found that nucleotide diversity within phylogroups was negatively correlated with latitude. These results indicate that phylogroup diversification is constrained by dispersal limitation at regional spatial scales, and they are consistent with the hypothesis that historical demographic processes have influenced the contemporary biogeography of Streptomyces. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Phylogenetic congruence of lichenised fungi and algae is affected by spatial scale and taxonomic diversity.

PubMed

Buckley, Hannah L; Rafat, Arash; Ridden, Johnathon D; Cruickshank, Robert H; Ridgway, Hayley J; Paterson, Adrian M

2014-01-01

The role of species' interactions in structuring biological communities remains unclear. Mutualistic symbioses, involving close positive interactions between two distinct organismal lineages, provide an excellent means to explore the roles of both evolutionary and ecological processes in determining how positive interactions affect community structure. In this study, we investigate patterns of co-diversification between fungi and algae for a range of New Zealand lichens at the community, genus, and species levels and explore explanations for possible patterns related to spatial scale and pattern, taxonomic diversity of the lichens considered, and the level sampling replication. We assembled six independent datasets to compare patterns in phylogenetic congruence with varied spatial extent of sampling, taxonomic diversity and level of specimen replication. For each dataset, we used the DNA sequences from the ITS regions of both the fungal and algal genomes from lichen specimens to produce genetic distance matrices. Phylogenetic congruence between fungi and algae was quantified using distance-based redundancy analysis and we used geographic distance matrices in Moran's eigenvector mapping and variance partitioning to evaluate the effects of spatial variation on the quantification of phylogenetic congruence. Phylogenetic congruence was highly significant for all datasets and a large proportion of variance in both algal and fungal genetic distances was explained by partner genetic variation. Spatial variables, primarily at large and intermediate scales, were also important for explaining genetic diversity patterns in all datasets. Interestingly, spatial structuring was stronger for fungal than algal genetic variation. As the spatial extent of the samples increased, so too did the proportion of explained variation that was shared between the spatial variables and the partners' genetic variation. Different lichen taxa showed some variation in their phylogenetic congruence and spatial genetic patterns and where greater sample replication was used, the amount of variation explained by partner genetic variation increased. Our results suggest that the phylogenetic congruence pattern, at least at small spatial scales, is likely due to reciprocal co-adaptation or co-dispersal. However, the detection of these patterns varies among different lichen taxa, across spatial scales and with different levels of sample replication. This work provides insight into the complexities faced in determining how evolutionary and ecological processes may interact to generate diversity in symbiotic association patterns at the population and community levels. Further, it highlights the critical importance of considering sample replication, taxonomic diversity and spatial scale in designing studies of co-diversification.

Genetic diversity pattern of microeukaryotic communities and its relationship with the environment based on PCR-DGGE and T-RFLP techniques in Dongshan Bay, southeast China

NASA Astrophysics Data System (ADS)

Zhang, Wenjing; Mo, Yuanyuan; Yang, Jun; Zhou, Jing; Lin, Yuanshao; Isabwe, Alain; Zhang, Jian; Gao, Xiu; Yu, Zheng

2018-07-01

Microeukaryotes play important roles in aquatic ecosystems, and could act as drivers of the biological nutrient cycling processes. However, compared with prokaryotic ones, little is known about the genetic diversity pattern of their community, and the environmental factors affecting their ecological pattern, especially in marine ecosystems. In this study, we used denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) to explore the genetic diversity structure of microeukaryotic communities in Dongshan Bay, southeast China. Our results revealed that microeukaryotic diversity ranged from 31 to 48 phylotypes (on average, 42) using the DGGE approach, while from 22 to 38 phylotypes (on average, 30) based on T-RFLP method, and the Shannon-Wiener diversity (DGGE-based) was relatively higher, suggesting that DGGE displayed a slightly higher resolution than T-RFLP. Surprisingly, the DGGE showed significant horizontal difference among microeukaryotic communities, but was similar with T-RFLP analysis that had no significant influence on microeukaryotic diversity at vertical scale. Further, redundancy analysis (RDA) indicated that the DGGE-based microeukaryotic communities distribution was significantly correlated with three environmental factors (Chl-a, TP and salinity), whereas microeukaryotic community revealed by T-RFLP was affected by four environmental factors namely salinity, temperature, depth and NOX-N. Compared with RDA, BIO-ENV analysis showed that heterotrophic bacteria and NOX-N were important environmental variable influencing microeukaryotic communities in both methods. These differences may be attributed to the noisy effects caused by the relatively large number of environmental variables. Generally speaking, despite differences in beta-diversity ordination for both DGGE and T-RFLP methods, there exists some consistency in the results of both techniques in terms of microeukaryotes responses to the environmental variables. These results suggested that environmental parameters had a great effect on spatial distribution of microeukaryotic community and contributed to marine ecosystem health to be further evaluated.

The importance of taxonomic resolution for additive beta diversity as revealed through DNA barcoding.

PubMed

Bringloe, Trevor T; Cottenie, Karl; Martin, Gillian K; Adamowicz, Sarah J

2016-12-01

Additive diversity partitioning (α, β, and γ) is commonly used to study the distribution of species-level diversity across spatial scales. Here, we first investigate whether published studies of additive diversity partitioning show signs of difficulty attaining species-level resolution due to inherent limitations with morphological identifications. Second, we present a DNA barcoding approach to delineate specimens of stream caddisfly larvae (order Trichoptera) and consider the importance of taxonomic resolution on classical (additive) measures of beta (β) diversity. Caddisfly larvae were sampled using a hierarchical spatial design in two regions (subarctic Churchill, Manitoba, Canada; temperate Pennsylvania, USA) and then additively partitioned according to Barcode Index Numbers (molecular clusters that serve as a proxy for species), genus, and family levels; diversity components were expressed as proportional species turnover. We screened 114 articles of additive diversity partitioning and found that a third reported difficulties with achieving species-level identifications, with a clear taxonomic tendency towards challenges identifying invertebrate taxa. Regarding our own study, caddisfly BINs appeared to show greater subregional turnover (e.g., proportional additive β) compared to genus or family levels. Diversity component studies failing to achieve species resolution due to morphological identifications may therefore be underestimating diversity turnover at larger spatial scales.

A modeling study of the impacts of Mississippi River diversion and sea-level rise on water quality of a deltaic estuary

USGS Publications Warehouse

Wang, Hongqing; Chen, Qin; Hu, Kelin; LaPeyre, Megan K.

2017-01-01

Freshwater and sediment management in estuaries affects water quality, particularly in deltaic estuaries. Furthermore, climate change-induced sea-level rise (SLR) and land subsidence also affect estuarine water quality by changing salinity, circulation, stratification, sedimentation, erosion, residence time, and other physical and ecological processes. However, little is known about how the magnitudes and spatial and temporal patterns in estuarine water quality variables will change in response to freshwater and sediment management in the context of future SLR. In this study, we applied the Delft3D model that couples hydrodynamics and water quality processes to examine the spatial and temporal variations of salinity, total suspended solids, and chlorophyll-α concentration in response to small (142 m3 s−1) and large (7080 m3 s−1) Mississippi River (MR) diversions under low (0.38 m) and high (1.44 m) relative SLR (RSLR = eustatic SLR + subsidence) scenarios in the Breton Sound Estuary, Louisiana, USA. The hydrodynamics and water quality model were calibrated and validated via field observations at multiple stations across the estuary. Model results indicate that the large MR diversion would significantly affect the magnitude and spatial and temporal patterns of the studied water quality variables across the entire estuary, whereas the small diversion tends to influence water quality only in small areas near the diversion. RSLR would also play a significant role on the spatial heterogeneity in estuary water quality by acting as an opposite force to river diversions; however, RSLR plays a greater role than the small-scale diversion on the magnitude and spatial pattern of the water quality parameters in this deltaic estuary.

Demonstration of the Wide-Field Imaging Interferometer Testbed Using a Calibrated Hyperspectral Image Projector

NASA Technical Reports Server (NTRS)

Bolcar, Matthew R.; Leisawitz, David; Maher, Steve; Rinehart, Stephen

2012-01-01

The Wide-field Imaging Interferometer testbed (WIIT) at NASA's Goddard Space Flight Center uses a dual-Michelson interferometric technique. The WIIT combines stellar interferometry with Fourier-transform interferometry to produce high-resolution spatial-spectral data over a large field-of-view. This combined technique could be employed on future NASA missions such as the Space Infrared Interferometric Telescope (SPIRIT) and the Sub-millimeter Probe of the Evolution of Cosmic Structure (SPECS). While both SPIRIT and SPECS would operate at far-infrared wavelengths, the WIIT demonstrates the dual-interferometry technique at visible wavelengths. The WIIT will produce hyperspectral image data, so a true hyperspectral object is necessary. A calibrated hyperspectral image projector (CHIP) has been constructed to provide such an object. The CHIP uses Digital Light Processing (DLP) technology to produce customized, spectrally-diverse scenes. CHIP scenes will have approximately 1.6-micron spatial resolution and the capability of . producing arbitrary spectra in the band between 380 nm and 1.6 microns, with approximately 5-nm spectral resolution. Each pixel in the scene can take on a unique spectrum. Spectral calibration is achieved with an onboard fiber-coupled spectrometer. In this paper we describe the operation of the CHIP. Results from the WIIT observations of CHIP scenes will also be presented.

An algebraic algorithm for nonuniformity correction in focal-plane arrays.

PubMed

Ratliff, Bradley M; Hayat, Majeed M; Hardie, Russell C

2002-09-01

A scene-based algorithm is developed to compensate for bias nonuniformity in focal-plane arrays. Nonuniformity can be extremely problematic, especially for mid- to far-infrared imaging systems. The technique is based on use of estimates of interframe subpixel shifts in an image sequence, in conjunction with a linear-interpolation model for the motion, to extract information on the bias nonuniformity algebraically. The performance of the proposed algorithm is analyzed by using real infrared and simulated data. One advantage of this technique is its simplicity; it requires relatively few frames to generate an effective correction matrix, thereby permitting the execution of frequent on-the-fly nonuniformity correction as drift occurs. Additionally, the performance is shown to exhibit considerable robustness with respect to lack of the common types of temporal and spatial irradiance diversity that are typically required by statistical scene-based nonuniformity correction techniques.

Application of Time Series Insar Technique for Deformation Monitoring of Large-Scale Landslides in Mountainous Areas of Western China

NASA Astrophysics Data System (ADS)

Qu, T.; Lu, P.; Liu, C.; Wan, H.

2016-06-01

Western China is very susceptible to landslide hazards. As a result, landslide detection and early warning are of great importance. This work employs the SBAS (Small Baseline Subset) InSAR Technique for detection and monitoring of large-scale landslides that occurred in Li County, Sichuan Province, Western China. The time series INSAR is performed using descending scenes acquired from TerraSAR-X StripMap mode since 2014 to get the spatial distribution of surface displacements of this giant landslide. The time series results identify the distinct deformation zone on the landslide body with a rate of up to 150mm/yr. The deformation acquired by SBAS technique is validated by inclinometers from diverse boreholes of in-situ monitoring. The integration of InSAR time series displacements and ground-based monitoring data helps to provide reliable data support for the forecasting and monitoring of largescale landslide.

High-rate synthetic aperture communications in shallow water.

PubMed

Song, H C; Hodgkiss, W S; Kuperman, W A; Akal, T; Stevenson, M

2009-12-01

Time reversal communication exploits spatial diversity to achieve spatial and temporal focusing in complex ocean environments. Spatial diversity can be provided easily by a vertical array in a waveguide. Alternatively, spatial diversity can be obtained from a virtual horizontal array generated by two elements, a transmitter and a receiver, due to relative motion between them, referred to as a synthetic aperture. This paper presents coherent synthetic aperture communication results from at-sea experiments conducted in two different frequency bands: (1) 2-4 kHz and (2) 8-20 kHz. Case (1) employs binary-phase shift-keying modulation, while case (2) involves up to eight-phase shift keying modulation with a data rate of 30 kbits/s divided by the number of transmissions (diversity) to be accumulated. The receiver utilizes time reversal diversity combining followed by a single channel equalizer, with frequent channel updates to accommodate the time-varying channel due to coupling of space and time in the presence of motion. Two to five consecutive transmissions from a source moving at 4 kts over 3-6 km range in shallow water are combined successfully after Doppler compensation, confirming the feasibility of coherent synthetic aperture communications using time reversal.

Volumetric velocimetry for fluid flows

NASA Astrophysics Data System (ADS)

Discetti, Stefano; Coletti, Filippo

2018-04-01

In recent years, several techniques have been introduced that are capable of extracting 3D three-component velocity fields in fluid flows. Fast-paced developments in both hardware and processing algorithms have generated a diverse set of methods, with a growing range of applications in flow diagnostics. This has been further enriched by the increasingly marked trend of hybridization, in which the differences between techniques are fading. In this review, we carry out a survey of the prominent methods, including optical techniques and approaches based on medical imaging. An overview of each is given with an example of an application from the literature, while focusing on their respective strengths and challenges. A framework for the evaluation of velocimetry performance in terms of dynamic spatial range is discussed, along with technological trends and emerging strategies to exploit 3D data. While critical challenges still exist, these observations highlight how volumetric techniques are transforming experimental fluid mechanics, and that the possibilities they offer have just begun to be explored.

Sediment heavy metals and benthic diversities in Hun-Tai River, northeast of China.

PubMed

Qu, Xiaodong; Ren, Ze; Zhang, Min; Liu, Xiaobo; Peng, Wenqi

2017-04-01

In aquatic ecosystems, metal contamination in sediments has become a ubiquitous environmental problem, causing serious issues. Hun-Tai River, located in northeast of China, flows through an important heavy industry region and metropolitan area. This study examined the heavy metals (Cd, Cr, Cu, Fe, Mn, Pb, Ni, and Zn) of sediments and diversities (taxa richness, Shannon diversity, and evenness) of benthic assemblages (benthic algae and macroinvertebrate) in Hun-Tai River. The results clearly described the spatial patterns of metal contamination in terms of geo-accumulation index and contamination factor, as well as the spatial patterns of benthic diversities in terms of taxa richness, Shannon index, and evenness by kriging interpolation. The sediments were largely contaminated by Cd, followed by Cu, Fe, Zn, Mn, and Ni. Cd and Zn had similar spatial patterns and similar sources. Cu, Fe, Mn, and Ni showed similar spatial patterns and similar sources. The surface sediments were unpolluted by Cr and Pb. The metal mines and the heavy industry in the major cities were the potential pollution sources. Benthic algae and macroinvertebrate responded similarly to the heterogeneous environment and metal contamination, with high taxa richness and Shannon index in middle-upper reaches of Hun-Tai River. Evenness showed complex spatial patterns. Under low contamination, both taxa richness, Shannon diversity, and evenness had a large variation range. However, under the moderate and high contamination, the taxa richness and Shannon diversity kept to a low level but the evenness had a high level. This study provided insights into the sediment heavy metal contamination in Hun-Tai River.

Hydrological and environmental variables outperform spatial factors in structuring species, trait composition, and beta diversity of pelagic algae.

PubMed

Wu, Naicheng; Qu, Yueming; Guse, Björn; Makarevičiūtė, Kristė; To, Szewing; Riis, Tenna; Fohrer, Nicola

2018-03-01

There has been increasing interest in algae-based bioassessment, particularly, trait-based approaches are increasingly suggested. However, the main drivers, especially the contribution of hydrological variables, of species composition, trait composition, and beta diversity of algae communities are less studied. To link species and trait composition to multiple factors (i.e., hydrological variables, local environmental variables, and spatial factors) that potentially control species occurrence/abundance and to determine their relative roles in shaping species composition, trait composition, and beta diversities of pelagic algae communities, samples were collected from a German lowland catchment, where a well-proven ecohydrological modeling enabled to predict long-term discharges at each sampling site. Both trait and species composition showed significant correlations with hydrological, environmental, and spatial variables, and variation partitioning revealed that the hydrological and local environmental variables outperformed spatial variables. A higher variation of trait composition (57.0%) than species composition (37.5%) could be explained by abiotic factors. Mantel tests showed that both species and trait-based beta diversities were mostly related to hydrological and environmental heterogeneity with hydrological contributing more than environmental variables, while purely spatial impact was less important. Our findings revealed the relative importance of hydrological variables in shaping pelagic algae community and their spatial patterns of beta diversities, emphasizing the need to include hydrological variables in long-term biomonitoring campaigns and biodiversity conservation or restoration. A key implication for biodiversity conservation was that maintaining the instream flow regime and keeping various habitats among rivers are of vital importance. However, further investigations at multispatial and temporal scales are greatly needed.

Advances in Applications of Hierarchical Bayesian Methods with Hydrological Models

NASA Astrophysics Data System (ADS)

Alexander, R. B.; Schwarz, G. E.; Boyer, E. W.

2017-12-01

Mechanistic and empirical watershed models are increasingly used to inform water resource decisions. Growing access to historical stream measurements and data from in-situ sensor technologies has increased the need for improved techniques for coupling models with hydrological measurements. Techniques that account for the intrinsic uncertainties of both models and measurements are especially needed. Hierarchical Bayesian methods provide an efficient modeling tool for quantifying model and prediction uncertainties, including those associated with measurements. Hierarchical methods can also be used to explore spatial and temporal variations in model parameters and uncertainties that are informed by hydrological measurements. We used hierarchical Bayesian methods to develop a hybrid (statistical-mechanistic) SPARROW (SPAtially Referenced Regression On Watershed attributes) model of long-term mean annual streamflow across diverse environmental and climatic drainages in 18 U.S. hydrological regions. Our application illustrates the use of a new generation of Bayesian methods that offer more advanced computational efficiencies than the prior generation. Evaluations of the effects of hierarchical (regional) variations in model coefficients and uncertainties on model accuracy indicates improved prediction accuracies (median of 10-50%) but primarily in humid eastern regions, where model uncertainties are one-third of those in arid western regions. Generally moderate regional variability is observed for most hierarchical coefficients. Accounting for measurement and structural uncertainties, using hierarchical state-space techniques, revealed the effects of spatially-heterogeneous, latent hydrological processes in the "localized" drainages between calibration sites; this improved model precision, with only minor changes in regional coefficients. Our study can inform advances in the use of hierarchical methods with hydrological models to improve their integration with stream measurements.

Scale-Dependence of Processes Structuring Dung Beetle Metacommunities Using Functional Diversity and Community Deconstruction Approaches

PubMed Central

da Silva, Pedro Giovâni; Hernández, Malva Isabel Medina

2015-01-01

Community structure is driven by mechanisms linked to environmental, spatial and temporal processes, which have been successfully addressed using metacommunity framework. The relative importance of processes shaping community structure can be identified using several different approaches. Two approaches that are increasingly being used are functional diversity and community deconstruction. Functional diversity is measured using various indices that incorporate distinct community attributes. Community deconstruction is a way to disentangle species responses to ecological processes by grouping species with similar traits. We used these two approaches to determine whether they are improvements over traditional measures (e.g., species composition, abundance, biomass) for identification of the main processes driving dung beetle (Scarabaeinae) community structure in a fragmented mainland-island landscape in southern Brazilian Atlantic Forest. We sampled five sites in each of four large forest areas, two on the mainland and two on the island. Sampling was performed in 2012 and 2013. We collected abundance and biomass data from 100 sampling points distributed over 20 sampling sites. We studied environmental, spatial and temporal effects on dung beetle community across three spatial scales, i.e., between sites, between areas and mainland-island. The γ-diversity based on species abundance was mainly attributed to β-diversity as a consequence of the increase in mean α- and β-diversity between areas. Variation partitioning on abundance, biomass and functional diversity showed scale-dependence of processes structuring dung beetle metacommunities. We identified two major groups of responses among 17 functional groups. In general, environmental filters were important at both local and regional scales. Spatial factors were important at the intermediate scale. Our study supports the notion of scale-dependence of environmental, spatial and temporal processes in the distribution and functional organization of Scarabaeinae beetles. We conclude that functional diversity may be used as a complementary approach to traditional measures, and that community deconstruction allows sufficient disentangling of responses of different trait-based groups. PMID:25822150

Biozone Characterization of Foraminifera in Upper Pleistocene through Recent Shelf and Slope Sediments, Northern Gulf of Alaska: Integration of SHE-diversity and Polytopic Vector Analyses

NASA Astrophysics Data System (ADS)

Zellers, S.; Cowan, E. A.; Davies, M. H.

2014-12-01

Gulf of Alaska sediments contain distinct, low-diversity assemblages of benthic and planktic foraminifera, whose distribution is a function of food availability, water mass properties, ice proximity, transport/deposition, predation, and taphonomic processes. Spatial and temporal changes in diversity reflect these processes and provide insight into this margin's history. Two quantitative techniques are integrated to define and characterize benthic foraminferal biozones in Gulf of Alaska sediment core samples collected by the R/V Maurice Ewing in 2004 at shelf site EW0408-79JC (59.53° N, 141.76° W, 158 m depth), and slope site EW0408-85JC (59.56° N, 144.15° W, 682 m depth). Sediments date from the end of the most recent glaciation (diamict in 85JC) to the present (bioturbated, silty clay at both sites). We apply SHE analysis, a graphical, iterative technique, based on diversity trends in a plot of ln E vs. ln N, where E is species evenness and N is cumulative number of specimens. In each step, the plot is examined for the first change in slope between successive samples, representing a change in diversity. At this point a boundary is defined, samples before the break are removed, and the analysis is repeated until all samples are analyzed. Data are further analyzed using an unmixing algorithm known as polytopic vector analyses. This technique defines a small number of orthogonal end members that explain a majority of the variance, thus reducing data complexity and aiding interpretation. SHE-analysis of benthic foraminiferal data defines eighteen informal abundance biozones. Polytopic vector analyses indicate that the faunal assemblages reflect mixtures of up to seven distinct biofacies: outer neritic (2), upper bathyal (2), reduced oxygen (2), and inner neritic. Rapid changes in faunal diversity correspond with increased sedimentation rates, especially during the end of the most recent glaciation (17 to 16 ka). The same relationship occurs over the last 1000 years at the shelf site. Where the cores overlap in age, many more assemblage boundaries occur in the shelf core, suggesting a comparatively dynamic environment relative to the slope. The least amount of diversity change corresponds with the laminated intervals in 85JC, coincident with high productivity and development of anoxia during regional deglaciation.

Genomic and Resistance Gene Homolog Diversity of the Dominant Tallgrass Prairie Species across the U.S. Great Plains Precipitation Gradient

PubMed Central

Rouse, Matthew N.; Saleh, Amgad A.; Seck, Amadou; Keeler, Kathleen H.; Travers, Steven E.; Hulbert, Scot H.; Garrett, Karen A.

2011-01-01

Background Environmental variables such as moisture availability are often important in determining species prevalence and intraspecific diversity. The population genetic structure of dominant plant species in response to a cline of these variables has rarely been addressed. We evaluated the spatial genetic structure and diversity of Andropogon gerardii populations across the U.S. Great Plains precipitation gradient, ranging from approximately 48 cm/year to 105 cm/year. Methodology/Principal Findings Genomic diversity was evaluated with AFLP markers and diversity of a disease resistance gene homolog was evaluated by PCR-amplification and digestion with restriction enzymes. We determined the degree of spatial genetic structure using Mantel tests. Genomic and resistance gene homolog diversity were evaluated across prairies using Shannon's index and by averaging haplotype dissimilarity. Trends in diversity across prairies were determined using linear regression of diversity on average precipitation for each prairie. We identified significant spatial genetic structure, with genomic similarity decreasing as a function of distance between samples. However, our data indicated that genome-wide diversity did not vary consistently across the precipitation gradient. In contrast, we found that disease resistance gene homolog diversity was positively correlated with precipitation. Significance Prairie remnants differ in the genetic resources they maintain. Selection and evolution in this disease resistance homolog is environmentally dependent. Overall, we found that, though this environmental gradient may not predict genomic diversity, individual traits such as disease resistance genes may vary significantly. PMID:21532756

Historical biome distribution and recent human disturbance shape the diversity of arbuscular mycorrhizal fungi.

PubMed

Pärtel, Meelis; Öpik, Maarja; Moora, Mari; Tedersoo, Leho; Szava-Kovats, Robert; Rosendahl, Søren; Rillig, Matthias C; Lekberg, Ylva; Kreft, Holger; Helgason, Thorunn; Eriksson, Ove; Davison, John; de Bello, Francesco; Caruso, Tancredi; Zobel, Martin

2017-10-01

The availability of global microbial diversity data, collected using standardized metabarcoding techniques, makes microorganisms promising models for investigating the role of regional and local factors in driving biodiversity. Here we modelled the global diversity of symbiotic arbuscular mycorrhizal (AM) fungi using currently available data on AM fungal molecular diversity (small subunit (SSU) ribosomal RNA (rRNA) gene sequences) in field samples. To differentiate between regional and local effects, we estimated species pools (sets of potentially suitable taxa) for each site, which are expected to reflect regional processes. We then calculated community completeness, an index showing the fraction of the species pool present, which is expected to reflect local processes. We found significant spatial variation, globally in species pool size, as well as in local and dark diversity (absent members of the species pool). Species pool size was larger close to areas containing tropical grasslands during the last glacial maximum, which are possible centres of diversification. Community completeness was greater in regions of high wilderness (remoteness from human disturbance). Local diversity was correlated with wilderness and current connectivity to mountain grasslands. Applying the species pool concept to symbiotic fungi facilitated a better understanding of how biodiversity can be jointly shaped by large-scale historical processes and recent human disturbance. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Coexistence of species with different dispersal across landscapes: a critical role of spatial correlation in disturbance.

PubMed

Liao, Jinbao; Ying, Zhixia; Woolnough, Daelyn A; Miller, Adam D; Li, Zhenqing; Nijs, Ivan

2016-05-11

Disturbance is key to maintaining species diversity in plant communities. Although the effects of disturbance frequency and extent on species diversity have been studied, we do not yet have a mechanistic understanding of how these aspects of disturbance interact with spatial structure of disturbance to influence species diversity. Here we derive a novel pair approximation model to explore competitive outcomes in a two-species system subject to spatially correlated disturbance. Generally, spatial correlation in disturbance favoured long-range dispersers, while distance-limited dispersers were greatly suppressed. Interestingly, high levels of spatial aggregation of disturbance promoted long-term species coexistence that is not possible in the absence of disturbance, but only when the local disperser was intrinsically competitively superior. However, spatial correlation in disturbance led to different competitive outcomes, depending on the disturbed area. Concerning ecological conservation and management, we theoretically demonstrate that introducing a spatially correlated disturbance to the system or altering an existing disturbance regime can be a useful strategy either to control species invasion or to promote species coexistence. Disturbance pattern analysis may therefore provide new insights into biodiversity conservation. © 2016 The Author(s).

Conservation businesses and conservation planning in a biological diversity hotspot.

PubMed

Di Minin, Enrico; Macmillan, Douglas Craig; Goodman, Peter Styan; Escott, Boyd; Slotow, Rob; Moilanen, Atte

2013-08-01

The allocation of land to biological diversity conservation competes with other land uses and the needs of society for development, food, and extraction of natural resources. Trade-offs between biological diversity conservation and alternative land uses are unavoidable, given the realities of limited conservation resources and the competing demands of society. We developed a conservation-planning assessment for the South African province of KwaZulu-Natal, which forms the central component of the Maputaland-Pondoland-Albany biological diversity hotspot. Our objective was to enhance biological diversity protection while promoting sustainable development and providing spatial guidance in the resolution of potential policy conflicts over priority areas for conservation at risk of transformation. The conservation-planning assessment combined spatial-distribution models for 646 conservation features, spatial economic-return models for 28 alternative land uses, and spatial maps for 4 threats. Nature-based tourism businesses were competitive with other land uses and could provide revenues of >US$60 million/year to local stakeholders and simultaneously help meeting conservation goals for almost half the conservation features in the planning region. Accounting for opportunity costs substantially decreased conflicts between biological diversity, agricultural use, commercial forestry, and mining. Accounting for economic benefits arising from conservation and reducing potential policy conflicts with alternative plans for development can provide opportunities for successful strategies that combine conservation and sustainable development and facilitate conservation action. © 2013 Society for Conservation Biology.

Rapid ordering of block copolymer thin films

DOE PAGES

Majewski, Pawel W.; Yager, Kevin G.

2016-08-18

Block-copolymers self-assemble into diverse morphologies, where nanoscale order can be finely tuned via block architecture and processing conditions. However, the ultimate usage of these materials in real-world applications may be hampered by the extremely long thermal annealing times—hours or days—required to achieve good order. Here, we provide an overview of the fundamentals of block-copolymer self-assembly kinetics, and review the techniques that have been demonstrated to influence, and enhance, these ordering kinetics. We discuss the inherent tradeoffs between oven annealing, solvent annealing, microwave annealing, zone annealing, and other directed self-assembly methods; including an assessment of spatial and temporal characteristics. Here, wemore » also review both real-space and reciprocal-space analysis techniques for quantifying order in these systems.« less

Metacommunity versus Biogeography: A Case Study of Two Groups of Neotropical Vegetation-Dwelling Arthropods

PubMed Central

Gonçalves-Souza, Thiago; Romero, Gustavo Q.; Cottenie, Karl

2014-01-01

Biogeography and metacommunity ecology provide two different perspectives on species diversity. Both are spatial in nature but their spatial scales do not necessarily match. With recent boom of metacommunity studies, we see an increasing need for clear discrimination of spatial scales relevant for both perspectives. This discrimination is a necessary prerequisite for improved understanding of ecological phenomena across scales. Here we provide a case study to illustrate some spatial scale-dependent concepts in recent metacommunity studies and identify potential pitfalls. We presented here the diversity patterns of Neotropical lepidopterans and spiders viewed both from metacommunity and biogeographical perspectives. Specifically, we investigated how the relative importance of niche- and dispersal-based processes for community assembly change at two spatial scales: metacommunity scale, i.e. within a locality, and biogeographical scale, i.e. among localities widely scattered along a macroclimatic gradient. As expected, niche-based processes dominated the community assembly at metacommunity scale, while dispersal-based processes played a major role at biogeographical scale for both taxonomical groups. However, we also observed small but significant spatial effects at metacommunity scale and environmental effects at biogeographical scale. We also observed differences in diversity patterns between the two taxonomical groups corresponding to differences in their dispersal modes. Our results thus support the idea of continuity of processes interactively shaping diversity patterns across scales and emphasize the necessity of integration of metacommunity and biogeographical perspectives. PMID:25549332

Spatial heterogeneity of physicochemical properties explains differences in microbial composition in arid soils from Cuatro Cienegas, Mexico.

PubMed

Pajares, Silvia; Escalante, Ana E; Noguez, Ana M; García-Oliva, Felipe; Martínez-Piedragil, Celeste; Cram, Silke S; Eguiarte, Luis Enrique; Souza, Valeria

2016-01-01

Arid ecosystems are characterized by high spatial heterogeneity, and the variation among vegetation patches is a clear example. Soil biotic and abiotic factors associated with these patches have also been well documented as highly heterogeneous in space. Given the low vegetation cover and little precipitation in arid ecosystems, soil microorganisms are the main drivers of nutrient cycling. Nonetheless, little is known about the spatial distribution of microorganisms and the relationship that their diversity holds with nutrients and other physicochemical gradients in arid soils. In this study, we evaluated the spatial variability of soil microbial diversity and chemical parameters (nutrients and ion content) at local scale (meters) occurring in a gypsum-based desert soil, to gain knowledge on what soil abiotic factors control the distribution of microbes in arid ecosystems. We analyzed 32 soil samples within a 64 m(2) plot and: (a) characterized microbial diversity using T-RFLPs of the bacterial 16S rRNA gene, (b) determined soil chemical parameters, and (c) identified relationships between microbial diversity and chemical properties. Overall, we found a strong correlation between microbial composition heterogeneity and spatial variation of cations (Ca(2), K(+)) and anions (HCO[Formula: see text], Cl(-), SO[Formula: see text]) content in this small plot. Our results could be attributable to spatial differences of soil saline content, favoring the patchy emergence of salt and soil microbial communities.

Imaging spectroscopy links aspen genotype with below-ground processes at landscape scales

PubMed Central

Madritch, Michael D.; Kingdon, Clayton C.; Singh, Aditya; Mock, Karen E.; Lindroth, Richard L.; Townsend, Philip A.

2014-01-01

Fine-scale biodiversity is increasingly recognized as important to ecosystem-level processes. Remote sensing technologies have great potential to estimate both biodiversity and ecosystem function over large spatial scales. Here, we demonstrate the capacity of imaging spectroscopy to discriminate among genotypes of Populus tremuloides (trembling aspen), one of the most genetically diverse and widespread forest species in North America. We combine imaging spectroscopy (AVIRIS) data with genetic, phytochemical, microbial and biogeochemical data to determine how intraspecific plant genetic variation influences below-ground processes at landscape scales. We demonstrate that both canopy chemistry and below-ground processes vary over large spatial scales (continental) according to aspen genotype. Imaging spectrometer data distinguish aspen genotypes through variation in canopy spectral signature. In addition, foliar spectral variation correlates well with variation in canopy chemistry, especially condensed tannins. Variation in aspen canopy chemistry, in turn, is correlated with variation in below-ground processes. Variation in spectra also correlates well with variation in soil traits. These findings indicate that forest tree species can create spatial mosaics of ecosystem functioning across large spatial scales and that these patterns can be quantified via remote sensing techniques. Moreover, they demonstrate the utility of using optical properties as proxies for fine-scale measurements of biodiversity over large spatial scales. PMID:24733949

Integrating spatially explicit representations of landscape perceptions into land change research

USGS Publications Warehouse

Dorning, Monica; Van Berkel, Derek B.; Semmens, Darius J.

2017-01-01

Purpose of ReviewHuman perceptions of the landscape can influence land-use and land-management decisions. Recognizing the diversity of landscape perceptions across space and time is essential to understanding land change processes and emergent landscape patterns. We summarize the role of landscape perceptions in the land change process, demonstrate advances in quantifying and mapping landscape perceptions, and describe how these spatially explicit techniques have and may benefit land change research.Recent FindingsMapping landscape perceptions is becoming increasingly common, particularly in research focused on quantifying ecosystem services provision. Spatial representations of landscape perceptions, often measured in terms of landscape values and functions, provide an avenue for matching social and environmental data in land change studies. Integrating these data can provide new insights into land change processes, contribute to landscape planning strategies, and guide the design and implementation of land change models.SummaryChallenges remain in creating spatial representations of human perceptions. Maps must be accompanied by descriptions of whose perceptions are being represented and the validity and uncertainty of those representations across space. With these considerations, rapid advancements in mapping landscape perceptions hold great promise for improving representation of human dimensions in landscape ecology and land change research.

Stand Structure and Substrate Diversity as Two Major Drivers for Bryophyte Distribution in a Temperate Montane Ecosystem

PubMed Central

Chen, Yun; Niu, Shuai; Li, Peikun; Jia, Hongru; Wang, Hailiang; Ye, Yongzhong; Yuan, Zhiliang

2017-01-01

Elucidating the major drivers of bryophyte distribution is the first step to protecting bryophyte diversity. Topography, forest, substrates (ground, tree trunks, roots, rocks, and rotten wood), and spatial factor, which factors are the major drivers of bryophyte distribution? In this study, 53 plots were set in 400 m2 along the elevation gradient in Xiaoqinling, China. All bryophytes in the plots were collected and identified. Regression analysis was used to examine the relationship between bryophyte and substrate diversity. We compared the patterns of overall bryophyte diversity and diversity of bryophytes found on the ground, tree, and rock along elevational gradients. Canonical correspondence analysis was applied to relate species composition to selected environmental variables. The importance of topography, forest, substrates, and spatial factors was determined by variance partitioning. A total of 1378 bryophyte specimens were collected, and 240 species were identified. Bryophyte diversity was closely related to substrate diversity. The overall bryophyte diversity significantly increased with elevation; however, the response varied among ground, tree, and rock bryophytes. Tree diversity and herb layer were considered important environmental factors in determining bryophyte distribution. Species abundance was best explained by stand structure (17%), and species diversity was best explained by stand structure (35%) and substrate (40%). Results directly indicated that substrate diversity can improve bryophyte species diversity. The effects of micro-habitat formed by stand structure and substrate diversity were higher than those of spatial processes and topography factors on bryophyte distribution. This study proved that the determinant factors influencing bryophyte diversity reflect the trends in recent forest management, providing a real opportunity to improve forest biodiversity conservation. PMID:28603535

Stand Structure and Substrate Diversity as Two Major Drivers for Bryophyte Distribution in a Temperate Montane Ecosystem.

PubMed

Chen, Yun; Niu, Shuai; Li, Peikun; Jia, Hongru; Wang, Hailiang; Ye, Yongzhong; Yuan, Zhiliang

2017-01-01

Elucidating the major drivers of bryophyte distribution is the first step to protecting bryophyte diversity. Topography, forest, substrates (ground, tree trunks, roots, rocks, and rotten wood), and spatial factor, which factors are the major drivers of bryophyte distribution? In this study, 53 plots were set in 400 m 2 along the elevation gradient in Xiaoqinling, China. All bryophytes in the plots were collected and identified. Regression analysis was used to examine the relationship between bryophyte and substrate diversity. We compared the patterns of overall bryophyte diversity and diversity of bryophytes found on the ground, tree, and rock along elevational gradients. Canonical correspondence analysis was applied to relate species composition to selected environmental variables. The importance of topography, forest, substrates, and spatial factors was determined by variance partitioning. A total of 1378 bryophyte specimens were collected, and 240 species were identified. Bryophyte diversity was closely related to substrate diversity. The overall bryophyte diversity significantly increased with elevation; however, the response varied among ground, tree, and rock bryophytes. Tree diversity and herb layer were considered important environmental factors in determining bryophyte distribution. Species abundance was best explained by stand structure (17%), and species diversity was best explained by stand structure (35%) and substrate (40%). Results directly indicated that substrate diversity can improve bryophyte species diversity. The effects of micro-habitat formed by stand structure and substrate diversity were higher than those of spatial processes and topography factors on bryophyte distribution. This study proved that the determinant factors influencing bryophyte diversity reflect the trends in recent forest management, providing a real opportunity to improve forest biodiversity conservation.

A Rapidly Prototyped Vegetation Dryness Index Evaluated for Wildfire Risk Assessment at Stennis Space Center

NASA Technical Reports Server (NTRS)

Ross, Kenton; Graham, William; Prados, Don; Spruce, Joseph

2007-01-01

MVDI, which effectively involves the differencing of NDMI and NDVI, appears to display increased noise that is consistent with a differencing technique. This effect masks finer variations in vegetation moisture, preventing MVDI from fulfilling the requirement of giving decision makers insight into spatial variation of fire risk. MVDI shows dependencies on land cover and phenology which also argue against its use as a fire risk proxy in an area of diverse and fragmented land covers. The conclusion of the rapid prototyping effort is that MVDI should not be implemented for SSC decision support.

Evolution in High Spatial Resolution Imaging of Faint, Complex Objects

NASA Astrophysics Data System (ADS)

van Belle, G.

The astrophysical community has been working at the task of obtaining image information of the smallest structures in the sky via the use of optical interferometry for well over a century. A richly diverse family of technology architectures has been explored over the years, and yet the current family of facilities are all striking similar. Although there may be other, heretofore undeployed, architectures that support the goal of collecting image information at the highest resolutions, we expect dramatic advances at the component level of long-baseline interferometry to be the best avenue for advancing the technique, rather than entirely new architectures.

Relative importance of local habitat complexity and regional factors for assemblages of oribatid mites (Acari: Oribatida) in Sphagnum peat bogs.

PubMed

Minor, M A; Ermilov, S G; Philippov, D A; Prokin, A A

2016-11-01

We investigated communities of oribatid mites in five peat bogs in the north-west of the East European plain. We aimed to determine the extent to which geographic factors (latitude, separation distance), local environment (Sphagnum moss species, ground water level, biogeochemistry) and local habitat complexity (diversity of vascular plants and bryophytes in the surrounding plant community) influence diversity and community composition of Oribatida. There was a significant north-to-south increase in Oribatida abundance. In the variance partitioning, spatial factors explained 33.1 % of variability in abundance across samples; none of the environmental factors were significant. Across all bogs, Oribatida species richness and community composition were similar in Sphagnum rubellum and Sphagnum magellanicum, but significantly different and less diverse in Sphagnum cuspidatum. Sphagnum microhabitat explained 52.2 % of variability in Oribatida species richness, whereas spatial variables explained only 8.7 %. There was no distance decay in community similarity between bogs with increased geographical distance. The environmental variables explained 34.9 % of the variance in community structure, with vascular plants diversity, bryophytes diversity, and ground water level all contributing significantly; spatial variables explained 15.1 % of the total variance. Overall, only 50 % of the Oribatida community variance was explained by the spatial structure and environmental variables. We discuss relative importance of spatial and local environmental factors, and make general inferences about the formation of fauna in Sphagnum bogs.

Landscape-Scale Controls on Aboveground Forest Carbon Stocks on the Osa Peninsula, Costa Rica

PubMed Central

Taylor, Philip; Asner, Gregory; Dahlin, Kyla; Anderson, Christopher; Knapp, David; Martin, Roberta; Mascaro, Joseph; Chazdon, Robin; Cole, Rebecca; Wanek, Wolfgang; Hofhansl, Florian; Malavassi, Edgar; Vilchez-Alvarado, Braulio; Townsend, Alan

2015-01-01

Tropical forests store large amounts of carbon in tree biomass, although the environmental controls on forest carbon stocks remain poorly resolved. Emerging airborne remote sensing techniques offer a powerful approach to understand how aboveground carbon density (ACD) varies across tropical landscapes. In this study, we evaluate the accuracy of the Carnegie Airborne Observatory (CAO) Light Detection and Ranging (LiDAR) system to detect top-of-canopy tree height (TCH) and ACD across the Osa Peninsula, Costa Rica. LiDAR and field-estimated TCH and ACD were highly correlated across a wide range of forest ages and types. Top-of-canopy height (TCH) reached 67 m, and ACD surpassed 225 Mg C ha-1, indicating both that airborne CAO LiDAR-based estimates of ACD are accurate in tall, high-biomass forests and that the Osa Peninsula harbors some of the most carbon-rich forests in the Neotropics. We also examined the relative influence of lithologic, topoedaphic and climatic factors on regional patterns in ACD, which are known to influence ACD by regulating forest productivity and turnover. Analyses revealed a spatially nested set of factors controlling ACD patterns, with geologic variation explaining up to 16% of the mapped ACD variation at the regional scale, while local variation in topographic slope explained an additional 18%. Lithologic and topoedaphic factors also explained more ACD variation at 30-m than at 100-m spatial resolution, suggesting that environmental filtering depends on the spatial scale of terrain variation. Our result indicate that patterns in ACD are partially controlled by spatial variation in geologic history and geomorphic processes underpinning topographic diversity across landscapes. ACD also exhibited spatial autocorrelation, which may reflect biological processes that influence ACD, such as the assembly of species or phenotypes across the landscape, but additional research is needed to resolve how abiotic and biotic factors contribute to ACD variation across high biomass, high diversity tropical landscapes. PMID:26061884

Coherent and Noncoherent Joint Processing of Sonar for Detection of Small Targets in Shallow Water.

PubMed

Pan, Xiang; Jiang, Jingning; Li, Si; Ding, Zhenping; Pan, Chen; Gong, Xianyi

2018-04-10

A coherent-noncoherent joint processing framework is proposed for active sonar to combine diversity gain and beamforming gain for detection of a small target in shallow water environments. Sonar utilizes widely-spaced arrays to sense environments and illuminate a target of interest from multiple angles. Meanwhile, it exploits spatial diversity for time-reversal focusing to suppress reverberation, mainly strong bottom reverberation. For enhancement of robustness of time-reversal focusing, an adaptive iterative strategy is utilized in the processing framework. A probing signal is firstly transmitted and echoes of a likely target are utilized as steering vectors for the second transmission. With spatial diversity, target bearing and range are estimated using a broadband signal model. Numerical simulations show that the novel sonar outperforms the traditional phased-array sonar due to benefits of spatial diversity. The effectiveness of the proposed framework has been validated by localization of a small target in at-lake experiments.

Temporal and Spatial Diversity of Bacterial Communities in Coastal Waters of the South China Sea

PubMed Central

Du, Jikun; Xiao, Kai; Li, Li; Ding, Xian; Liu, Helu; Lu, Yongjun; Zhou, Shining

2013-01-01

Bacteria are recognized as important drivers of biogeochemical processes in all aquatic ecosystems. Temporal and geographical patterns in ocean bacterial communities have been observed in many studies, but the temporal and spatial patterns in the bacterial communities from the South China Sea remained unexplored. To determine the spatiotemporal patterns, we generated 16S rRNA datasets for 15 samples collected from the five regularly distributed sites of the South China Sea in three seasons (spring, summer, winter). A total of 491 representative sequences were analyzed by MOTHUR, yielding 282 operational taxonomic units (OTUs) grouped at 97% stringency. Significant temporal variations of bacterial diversity were observed. Richness and diversity indices indicated that summer samples were the most diverse. The main bacterial group in spring and summer samples was Alphaproteobacteria, followed by Cyanobacteria and Gammaproteobacteria, whereas Cyanobacteria dominated the winter samples. Spatial patterns in the samples were observed that samples collected from the coastal (D151, D221) waters and offshore (D157, D1512, D224) waters clustered separately, the coastal samples harbored more diverse bacterial communities. However, the temporal pattern of the coastal site D151 was contrary to that of the coastal site D221. The LIBSHUFF statistics revealed noticeable differences among the spring, summer and winter libraries collected at five sites. The UPGMA tree showed there were temporal and spatial heterogeneity of bacterial community composition in coastal waters of the South China Sea. The water salinity (P=0.001) contributed significantly to the bacteria-environment relationship. Our results revealed that bacterial community structures were influenced by environmental factors and community-level changes in 16S-based diversity were better explained by spatial patterns than by temporal patterns. PMID:23785512

Comparing spatial diversification and meta-population models in the Indo-Australian Archipelago

PubMed Central

Chalmandrier, Loïc; Albouy, Camille; Descombes, Patrice; Sandel, Brody; Faurby, Soren; Svenning, Jens-Christian; Zimmermann, Niklaus E.

2018-01-01

Reconstructing the processes that have shaped the emergence of biodiversity gradients is critical to understand the dynamics of diversification of life on Earth. Islands have traditionally been used as model systems to unravel the processes shaping biological diversity. MacArthur and Wilson's island biogeographic model predicts diversity to be based on dynamic interactions between colonization and extinction rates, while treating islands themselves as geologically static entities. The current spatial configuration of islands should influence meta-population dynamics, but long-term geological changes within archipelagos are also expected to have shaped island biodiversity, in part by driving diversification. Here, we compare two mechanistic models providing inferences on species richness at a biogeographic scale: a mechanistic spatial-temporal model of species diversification and a spatial meta-population model. While the meta-population model operates over a static landscape, the diversification model is driven by changes in the size and spatial configuration of islands through time. We compare the inferences of both models to floristic diversity patterns among land patches of the Indo-Australian Archipelago. Simulation results from the diversification model better matched observed diversity than a meta-population model constrained only by the contemporary landscape. The diversification model suggests that the dynamic re-positioning of islands promoting land disconnection and reconnection induced an accumulation of particularly high species diversity on Borneo, which is central within the island network. By contrast, the meta-population model predicts a higher diversity on the mainlands, which is less compatible with empirical data. Our analyses highlight that, by comparing models with contrasting assumptions, we can pinpoint the processes that are most compatible with extant biodiversity patterns. PMID:29657753

Comparing spatial diversification and meta-population models in the Indo-Australian Archipelago.

PubMed

Chalmandrier, Loïc; Albouy, Camille; Descombes, Patrice; Sandel, Brody; Faurby, Soren; Svenning, Jens-Christian; Zimmermann, Niklaus E; Pellissier, Loïc

2018-03-01

Reconstructing the processes that have shaped the emergence of biodiversity gradients is critical to understand the dynamics of diversification of life on Earth. Islands have traditionally been used as model systems to unravel the processes shaping biological diversity. MacArthur and Wilson's island biogeographic model predicts diversity to be based on dynamic interactions between colonization and extinction rates, while treating islands themselves as geologically static entities. The current spatial configuration of islands should influence meta-population dynamics, but long-term geological changes within archipelagos are also expected to have shaped island biodiversity, in part by driving diversification. Here, we compare two mechanistic models providing inferences on species richness at a biogeographic scale: a mechanistic spatial-temporal model of species diversification and a spatial meta-population model. While the meta-population model operates over a static landscape, the diversification model is driven by changes in the size and spatial configuration of islands through time. We compare the inferences of both models to floristic diversity patterns among land patches of the Indo-Australian Archipelago. Simulation results from the diversification model better matched observed diversity than a meta-population model constrained only by the contemporary landscape. The diversification model suggests that the dynamic re-positioning of islands promoting land disconnection and reconnection induced an accumulation of particularly high species diversity on Borneo, which is central within the island network. By contrast, the meta-population model predicts a higher diversity on the mainlands, which is less compatible with empirical data. Our analyses highlight that, by comparing models with contrasting assumptions, we can pinpoint the processes that are most compatible with extant biodiversity patterns.

Geographic distance and ecosystem size determine the distribution of smallest protists in lacustrine ecosystems.

PubMed

Lepère, Cécile; Domaizon, Isabelle; Taïb, Najwa; Mangot, Jean-François; Bronner, Gisèle; Boucher, Delphine; Debroas, Didier

2013-07-01

Understanding the spatial distribution of aquatic microbial diversity and the underlying mechanisms causing differences in community composition is a challenging and central goal for ecologists. Recent insights into protistan diversity and ecology are increasing the debate over their spatial distribution. In this study, we investigate the importance of spatial and environmental factors in shaping the small protists community structure in lakes. We analyzed small protists community composition (beta-diversity) and richness (alpha-diversity) at regional scale by different molecular methods targeting the gene coding for 18S rRNA gene (T-RFLP and 454 pyrosequencing). Our results show a distance-decay pattern for rare and dominant taxa and the spatial distribution of the latter followed the prediction of the island biogeography theory. Furthermore, geographic distances between lakes seem to be the main force shaping the protists community composition in the lakes studied here. Finally, the spatial distribution of protists was discussed at the global scale (11 worldwide distributed lakes) by comparing these results with those present in the public database. UniFrac analysis showed 18S rRNA gene OTUs compositions significantly different among most of lakes, and this difference does not seem to be related to the trophic status. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Cross-taxon congruence and environmental conditions.

PubMed

Toranza, Carolina; Arim, Matías

2010-07-16

Diversity patterns of different taxa typically covary in space, a phenomenon called cross-taxon congruence. This pattern has been explained by the effect of one taxon diversity on taxon diversity, shared biogeographic histories of different taxa, and/or common responses to environmental conditions. A meta-analysis of the association between environment and diversity patterns found that in 83 out of 85 studies, more than 60% of the spatial variability in species richness was related to variables representing energy, water or their interaction. The role of the environment determining taxa diversity patterns leads us to hypothesize that this would explain the observed cross-taxon congruence. However, recent analyses reported the persistence of cross-taxon congruence when environmental effect was statistically removed. Here we evaluate this hypothesis, analyzing the cross-taxon congruence between birds and mammals in the Brazilian Cerrado, and assess the environmental role on the spatial covariation in diversity patterns. We found a positive association between avian and mammal richness and a positive latitudinal trend for both groups in the Brazilian Cerrado. Regression analyses indicated an effect of latitude, PET, and mean temperature over both biological groups. In addition, we show that NDVI was only associated with avian diversity; while the annual relative humidity, was only correlated with mammal diversity. We determined the environmental effects on diversity in a path analysis that accounted for 73% and 76% of the spatial variation in avian and mammal richness. However, an association between avian and mammal diversity remains significant. Indeed, the importance of this link between bird and mammal diversity was also supported by a significant association between birds and mammal spatial autoregressive model residuals. Our study corroborates the main role of environmental conditions on diversity patterns, but suggests that other important mechanisms, which have not been properly evaluated, are involved in the observed cross-taxon congruence. The approaches introduced here indicate that the prevalence of a significant association among taxa, after considering the environmental determinant, could indicate both the need to incorporate additional processes (e.g. biogeographic and evolutionary history or trophic interactions) and/or the existence of a shared trend in detection biases among taxa and regions.

Raman Imaging in Cell Membranes, Lipid-Rich Organelles, and Lipid Bilayers.

PubMed

Syed, Aleem; Smith, Emily A

2017-06-12

Raman-based optical imaging is a promising analytical tool for noninvasive, label-free chemical imaging of lipid bilayers and cellular membranes. Imaging using spontaneous Raman scattering suffers from a low intensity that hinders its use in some cellular applications. However, developments in coherent Raman imaging, surface-enhanced Raman imaging, and tip-enhanced Raman imaging have enabled video-rate imaging, excellent detection limits, and nanometer spatial resolution, respectively. After a brief introduction to these commonly used Raman imaging techniques for cell membrane studies, this review discusses selected applications of these modalities for chemical imaging of membrane proteins and lipids. Finally, recent developments in chemical tags for Raman imaging and their applications in the analysis of selected cell membrane components are summarized. Ongoing developments toward improving the temporal and spatial resolution of Raman imaging and small-molecule tags with strong Raman scattering cross sections continue to expand the utility of Raman imaging for diverse cell membrane studies.

An investigation of site diversity and comparison with ITU-R recommendations

NASA Astrophysics Data System (ADS)

Callaghan, S. A.; Boyes, B.; Couchman, A.; Waight, J.; Walden, C. J.; Ventouras, S.

2008-08-01

Earth-space radio systems operating at frequencies of 10 GHz and above are badly attenuated by rain, cloud, and atmospheric gases. As the frequencies of operational systems increase, it becomes increasingly uneconomic to compensate for the effects of fading through the use of a fixed fade margin, hence the implementation of fade mitigation techniques (FMT). The spatial and temporal variation of rain provides the justification for the use of site diversity as an FMT. Site diversity employs two or more ground stations receiving the same satellite signal with a separation distance such that the sites encounter intense rainfall at different times, and switching to the site experiencing the least fading improves system performance considerably. Measurements of the 20.7 GHz beacon carried as part of the Global Broadcast Service (GBS) payload on the U.S. Department of Defense satellite UFO-9 have been made at three sites: two are located in the South of England (˜8 km apart), and the third receiver was located in Scotland. These beacon measurements have produced long term attenuation exceedance and site diversity gain and improvement statistics. This attenuation time series data can simulate the performance of an Earth-space system using site diversity, indicating the optimum method of implementing this FMT. In this paper, unbalanced site diversity is investigated, as this is a more likely scenario than the balanced site diversity modeled by the ITU-R recommendations. This paper also investigates the implementation of site diversity from a commercial context, including cost-benefit analysis and technical feasibility.

Social diversity promotes cooperation in spatial multigames

NASA Astrophysics Data System (ADS)

Qin, Jiahu; Chen, Yaming; Kang, Yu; Perc, Matjaž

2017-04-01

Social diversity is omnipresent in the modern world. Here we introduce this diversity into spatial multigames and study its impact on the evolution of cooperation. Multigames are characterized by two or more different social dilemmas being contested among players in the population. When a fraction of players plays the prisoner's dilemma game while the remainder plays the snowdrift game cooperation becomes a difficult proposition. We show that social diversity, determined by the payoff scaling factors from the uniform, exponential or power-law distribution, significantly promotes cooperation. In particular, the stronger the social diversity, the more widespread cooperative behavior becomes. Monte Carlo simulations on the square lattice reveal that a power-law distribution of social diversity is in fact optimal for socially favorable states, thus resonating with findings previously reported for single social dilemmas. We also show that the same promotion mechanism works in time-varying environments, thus further generalizing the important role of social diversity for cooperation in social dilemmas.

Disentangling the drivers of taxonomic and phylogenetic beta diversities in disturbed and undisturbed subtropical forests

NASA Astrophysics Data System (ADS)

Liu, Jinliang; Qian, Hong; Jin, Yi; Wu, Chuping; Chen, Jianhua; Yu, Shuquan; Wei, Xinliang; Jin, Xiaofeng; Liu, Jiajia; Yu, Mingjian

2016-10-01

Understanding the relative importance of dispersal limitation and environmental filtering processes in structuring the beta diversities of subtropical forests in human disturbed landscapes is still limited. Here we used taxonomic (TBD) and phylogenetic (PBD), including terminal PBD (PBDt) and basal PBD (PBDb), beta diversity indices to quantify the taxonomic and phylogenetic turnovers at different depths of evolutionary history in disturbed and undisturbed subtropical forests. Multiple linear regression model and distance-based redundancy analysis were used to disentangle the relative importance of environmental and spatial variables. Environmental variables were significantly correlated with TBD and PBDt metrics. Temperature and precipitation were major environmental drivers of beta diversity patterns, which explained 7-27% of the variance in TBD and PBDt, whereas the spatial variables independently explained less than 1% of the variation for all forests. The relative importance of environmental and spatial variables differed between disturbed and undisturbed forests (e.g., when Bray-Curtis was used as a beta diversity metric, environmental variable had a significant effect on beta diversity for disturbed forests but had no effect on undisturbed forests). We conclude that environmental filtering plays a more important role than geographical limitation and disturbance history in driving taxonomic and terminal phylogenetic beta diversity.

Disentangling the drivers of taxonomic and phylogenetic beta diversities in disturbed and undisturbed subtropical forests

PubMed Central

Liu, Jinliang; Qian, Hong; Jin, Yi; Wu, Chuping; Chen, Jianhua; Yu, Shuquan; Wei, Xinliang; Jin, Xiaofeng; Liu, Jiajia; Yu, Mingjian

2016-01-01

Understanding the relative importance of dispersal limitation and environmental filtering processes in structuring the beta diversities of subtropical forests in human disturbed landscapes is still limited. Here we used taxonomic (TBD) and phylogenetic (PBD), including terminal PBD (PBDt) and basal PBD (PBDb), beta diversity indices to quantify the taxonomic and phylogenetic turnovers at different depths of evolutionary history in disturbed and undisturbed subtropical forests. Multiple linear regression model and distance-based redundancy analysis were used to disentangle the relative importance of environmental and spatial variables. Environmental variables were significantly correlated with TBD and PBDt metrics. Temperature and precipitation were major environmental drivers of beta diversity patterns, which explained 7–27% of the variance in TBD and PBDt, whereas the spatial variables independently explained less than 1% of the variation for all forests. The relative importance of environmental and spatial variables differed between disturbed and undisturbed forests (e.g., when Bray-Curtis was used as a beta diversity metric, environmental variable had a significant effect on beta diversity for disturbed forests but had no effect on undisturbed forests). We conclude that environmental filtering plays a more important role than geographical limitation and disturbance history in driving taxonomic and terminal phylogenetic beta diversity. PMID:27775021

Identification, prediction, and mitigation of sinkhole hazards in evaporite karst areas

USGS Publications Warehouse

Gutierrez, F.; Cooper, A.H.; Johnson, K.S.

2008-01-01

Sinkholes usually have a higher probability of occurrence and a greater genetic diversity in evaporite terrains than in carbonate karst areas. This is because evaporites have a higher solubility and, commonly, a lower mechanical strength. Subsidence damage resulting from evaporite dissolution generates substantial losses throughout the world, but the causes are only well understood in a few areas. To deal with these hazards, a phased approach is needed for sinkhole identification, investigation, prediction, and mitigation. Identification techniques include field surveys and geomorphological mapping combined with accounts from local people and historical sources. Detailed sinkhole maps can be constructed from sequential historical maps, recent topographical maps, and digital elevation models (DEMs) complemented with building-damage surveying, remote sensing, and high-resolution geodetic surveys. On a more detailed level, information from exposed paleosubsidence features (paleokarst), speleological explorations, geophysical investigations, trenching, dating techniques, and boreholes may help in investigating dissolution and subsidence features. Information on the hydrogeological pathways including caves, springs, and swallow holes are particularly important especially when corroborated by tracer tests. These diverse data sources make a valuable database-the karst inventory. From this dataset, sinkhole susceptibility zonations (relative probability) may be produced based on the spatial distribution of the features and good knowledge of the local geology. Sinkhole distribution can be investigated by spatial distribution analysis techniques including studies of preferential elongation, alignment, and nearest neighbor analysis. More objective susceptibility models may be obtained by analyzing the statistical relationships between the known sinkholes and the conditioning factors. Chronological information on sinkhole formation is required to estimate the probability of occurrence of sinkholes (number of sinkholes/km2 year). Such spatial and temporal predictions, frequently derived from limited records and based on the assumption that past sinkhole activity may be extrapolated to the future, are non-corroborated hypotheses. Validation methods allow us to assess the predictive capability of the susceptibility maps and to transform them into probability maps. Avoiding the most hazardous areas by preventive planning is the safest strategy for development in sinkhole-prone areas. Corrective measures could be applied to reduce the dissolution activity and subsidence processes. A more practical solution for safe development is to reduce the vulnerability of the structures by using subsidence-proof designs. ?? 2007 Springer-Verlag.

Atmospheric turbulence mitigation in an OAM-based MIMO free-space optical link using spatial diversity combined with MIMO equalization.

PubMed

Ren, Yongxiong; Wang, Zhe; Xie, Guodong; Li, Long; Willner, Asher J; Cao, Yinwen; Zhao, Zhe; Yan, Yan; Ahmed, Nisar; Ashrafi, Nima; Ashrafi, Solyman; Bock, Robert; Tur, Moshe; Willner, Alan E

2016-06-01

We explore the mitigation of atmospheric turbulence effects for orbital angular momentum (OAM)-based free-space optical (FSO) communications with multiple-input multiple-output (MIMO) architecture. Such a system employs multiple spatially separated aperture elements at the transmitter/receiver, and each transmitter aperture contains multiplexed data-carrying OAM beams. We propose to use spatial diversity combined with MIMO equalization to mitigate both weak and strong turbulence distortions. In a 2×2 FSO link with each transmitter aperture containing two multiplexed OAM modes of ℓ=+1 and ℓ=+3, we experimentally show that at least two OAM data channels could be recovered under both weak and strong turbulence distortions using selection diversity assisted with MIMO equalization.

The Value of Learning about Natural History in Biodiversity Markets

PubMed Central

Bruggeman, Douglas J.

2015-01-01

Markets for biodiversity have generated much controversy because of the often unstated and untested assumptions included in transactions rules. Simple trading rules are favored to reduce transaction costs, but others have argued that this leads to markets that favor development and erode biodiversity. Here, I describe how embracing complexity and uncertainty within a tradable credit system for the Red-cockaded Woodpecker (Picoides borealis) creates opportunities to achieve financial and conservation goals simultaneously. Reversing the effects of habitat fragmentation is one of the main reasons for developing markets. I include uncertainty in habitat fragmentation effects by evaluating market transactions using five alternative dispersal models that were able to approximate observed patterns of occupancy and movement. Further, because dispersal habitat is often not included in market transactions, I contrast how changes in breeding versus dispersal habitat affect credit values. I use an individually-based, spatially-explicit population model for the Red-cockaded Woodpecker (Picoides borealis) to predict spatial- and temporal- influences of landscape change on species occurrence and genetic diversity. Results indicated that the probability of no net loss of abundance and genetic diversity responded differently to the transient dynamics in breeding and dispersal habitat. Trades that do not violate the abundance cap may simultaneously violate the cap for the erosion of genetic diversity. To highlight how economic incentives may help reduce uncertainty, I demonstrate tradeoffs between the value of tradable credits and the value of information needed to predict the influence of habitat trades on population viability. For the trade with the greatest uncertainty regarding the change in habitat fragmentation, I estimate that the value of using 13-years of data to reduce uncertainty in dispersal behaviors is $6.2 million. Future guidance for biodiversity markets should at least encourage the use of spatially- and temporally-explicit techniques that include population genetic estimates and the influence of uncertainty. PMID:26675488

Impact of phytoplankton community structure and function on marine particulate optical properties

NASA Astrophysics Data System (ADS)

McFarland, Malcolm Neil

Phytoplankton are an ecologically important and diverse group of organisms whose distribution, abundance, and population dynamics vary significantly over small spatial (cm) and temporal (minutes) scales in the coastal ocean. Our inability to observe phytoplankton community structure and function at these small scales has severely limited our understanding of the fundamental ecological and evolutionary mechanisms that drive phytoplankton growth, mortality, adaptation and speciation. The goal of this dissertation was to enhance our understanding of phytoplankton ecology by improving in situ observational techniques based on the optical properties of cells, colonies, populations, and communities. Field and laboratory studies were used to determine the effects of phytoplankton species composition, morphology, and physiology on the inherent optical properties of communities and to explore the adaptive significance of bio-optically important cellular characteristics. Initial field studies found a strong association between species composition and the relative magnitude and shape of particulate absorption, scattering, and attenuation coefficient spectra. Subsequent field studies using scanning flow cytometry to directly measure optically important phytoplankton and non-algal particle characteristics demonstrated that the size and pigment content of large (>20 microm) phytoplankton cells and colonies vary significantly with the slope of particulate attenuation and absorption spectra, and with the ratio of particulate scattering to absorption. These relationships enabled visualization of phytoplankton community composition and mortality over small spatial and temporal scales derived from high resolution optical measurements acquired with an autonomous profiling system. Laboratory studies with diverse uni-algal cultures showed that morphological and physiological characteristics of cells and colonies can account for ˜30% of the optical variation observed in natural communities and that complex morphologies and low intracellular pigment concentrations minimize pigment self-shading that could otherwise limit bio-optical fitness. These results demonstrate that optical properties reveal detailed information about the distribution, abundance, morphology, and physiology of phytoplankton that can help explain their ecological dynamics over small spatial scales and the bio-optical function of diverse forms in the ocean.

The Value of Learning about Natural History in Biodiversity Markets.

PubMed

Bruggeman, Douglas J

2015-01-01

Markets for biodiversity have generated much controversy because of the often unstated and untested assumptions included in transactions rules. Simple trading rules are favored to reduce transaction costs, but others have argued that this leads to markets that favor development and erode biodiversity. Here, I describe how embracing complexity and uncertainty within a tradable credit system for the Red-cockaded Woodpecker (Picoides borealis) creates opportunities to achieve financial and conservation goals simultaneously. Reversing the effects of habitat fragmentation is one of the main reasons for developing markets. I include uncertainty in habitat fragmentation effects by evaluating market transactions using five alternative dispersal models that were able to approximate observed patterns of occupancy and movement. Further, because dispersal habitat is often not included in market transactions, I contrast how changes in breeding versus dispersal habitat affect credit values. I use an individually-based, spatially-explicit population model for the Red-cockaded Woodpecker (Picoides borealis) to predict spatial- and temporal- influences of landscape change on species occurrence and genetic diversity. Results indicated that the probability of no net loss of abundance and genetic diversity responded differently to the transient dynamics in breeding and dispersal habitat. Trades that do not violate the abundance cap may simultaneously violate the cap for the erosion of genetic diversity. To highlight how economic incentives may help reduce uncertainty, I demonstrate tradeoffs between the value of tradable credits and the value of information needed to predict the influence of habitat trades on population viability. For the trade with the greatest uncertainty regarding the change in habitat fragmentation, I estimate that the value of using 13-years of data to reduce uncertainty in dispersal behaviors is $6.2 million. Future guidance for biodiversity markets should at least encourage the use of spatially- and temporally-explicit techniques that include population genetic estimates and the influence of uncertainty.

Reconstruction of explicit structural properties at the nanoscale via spectroscopic microscopy

NASA Astrophysics Data System (ADS)

Cherkezyan, Lusik; Zhang, Di; Subramanian, Hariharan; Taflove, Allen; Backman, Vadim

2016-02-01

The spectrum registered by a reflected-light bright-field spectroscopic microscope (SM) can quantify the microscopically indiscernible, deeply subdiffractional length scales within samples such as biological cells and tissues. Nevertheless, quantification of biological specimens via any optical measures most often reveals ambiguous information about the specific structural properties within the studied samples. Thus, optical quantification remains nonintuitive to users from the diverse fields of technique application. In this work, we demonstrate that the SM signal can be analyzed to reconstruct explicit physical measures of internal structure within label-free, weakly scattering samples: characteristic length scale and the amplitude of spatial refractive-index (RI) fluctuations. We present and validate the reconstruction algorithm via finite-difference time-domain solutions of Maxwell's equations on an example of exponential spatial correlation of RI. We apply the validated algorithm to experimentally measure structural properties within isolated cells from two genetic variants of HT29 colon cancer cell line as well as within a prostate tissue biopsy section. The presented methodology can lead to the development of novel biophotonics techniques that create two-dimensional maps of explicit structural properties within biomaterials: the characteristic size of macromolecular complexes and the variance of local mass density.

Elimination of sulphur odours at landfills by bioconversion and the corona discharge plasma technique.

PubMed

Xia, Fangfang; Liu, Xin; Kang, Ying; He, Ruo; Wu, Zucheng

2015-01-01

Hydrogen sulphide (H2S) contributes a lot to odours at landfills, which is a threat to the environment and the health of the staff therein. To mitigate its emission, the bioconversion within landfill cover soils (LCSs) was introduced. H2S emission and concentration both in the field air above the landfill and in microcosm testing were surveyed. Results indicated that H2S emission and concentration in the landfill varied with landfill seasons and sites. There existed relationship between H2S concentration and fluxes spatially and temporally. To characterize and assess the spatial and temporal diversity of sulphur-oxidizing bacteria (SOB) and sulphate-reducing bacteria (SRB) in the LCSs, the terminal-restriction fragment length polymorphism technique was employed. Using the functional genes of dsrB and soxB, SOB, including Halothiobacillus, Rhodothalassium, Paracocccus, Allochromatium, and Thiobacillus, and SRB, including Desulfovibrio, Syntrophobacter, Desulfomonile and Desulfobacca, were identical and exhibited the dominant role in the LCSs. By employing an alternative available corona reactor, more than 90% removal efficiencies of sulphides were demonstrated, suggesting that the LCSs for eliminating odours in a lower concentration would be feasible.

Mapping Planetary Volcanic Deposits: Identifying Vents and Distinguishing between Effects of Eruption Conditions and Local Storage and Release on Flow Field Morphology

NASA Technical Reports Server (NTRS)

Bleacher, J. E.; Eppler, D. B.; Skinner, J. A.; Evans, C. A.; Feng, W.; Gruener, J. E.; Hurwitz, D. M.; Whitson, P.; Janoiko, B.

2014-01-01

Terrestrial geologic mapping techniques are regularly used for "photogeologic" mapping of other planets, but these approaches are complicated by the diverse type, areal coverage, and spatial resolution of available data sets. When available, spatially-limited in-situ human and/or robotic surface observations can sometimes introduce a level of detail that is difficult to integrate with regional or global interpretations. To assess best practices for utilizing observations acquired from orbit and on the surface, our team conducted a comparative study of geologic mapping and interpretation techniques. We compared maps generated for the same area in the San Francisco Volcanic Field (SFVF) in northern Arizona using 1) data collected for reconnaissance before and during the 2010 Desert Research And Technology Studies campaign, and 2) during a traditional, terrestrial field geology study. The operations, related results, and direct mapping comparisons are discussed in companion LPSC abstracts. Here we present new geologic interpretations for a volcanic cone and related lava flows as derived from all approaches involved in this study. Mapping results indicate a need for caution when interpreting past eruption conditions on other planetary surfaces from orbital data alone.

Mapping Planetary Volcanic Deposits: Identifying Vents and Distingushing between Effects of Eruption Conditions and Local Lava Storage and Release on Flow Field Morphology

NASA Technical Reports Server (NTRS)

Bleacher, J. E.; Eppler, D. B.; Skinner, J. A.; Evans, C. A.; Feng, W.; Gruener, J. E.; Hurwitz, D. M.; Whitson, P.; Janoiko, B.

2014-01-01

Terrestrial geologic mapping techniques are regularly used for "photogeologic" mapping of other planets, but these approaches are complicated by the diverse type, areal coverage, and spatial resolution of available data sets. When available, spatially-limited in-situ human and/or robotic surface observations can sometimes introduce a level of detail that is difficult to integrate with regional or global interpretations. To assess best practices for utilizing observations acquired from orbit and on the surface, our team conducted a comparative study of geologic mapping and interpretation techniques. We compared maps generated for the same area in the San Francisco Volcanic Field (SFVF) in northern Arizona using 1) data collected for reconnaissance before and during the 2010 Desert Research And Technology Studies campaign, and 2) during a traditional, terrestrial field geology study. The operations, related results, and direct mapping comparisons are discussed in companion LPSC abstracts [1-3]. Here we present new geologic interpretations for a volcanic cone and related lava flows as derived from all approaches involved in this study. Mapping results indicate a need for caution when interpreting past eruption conditions on other planetary surfaces from orbital data alone.

Regional zooplankton dispersal provides spatial insurance for ecosystem function.

PubMed

Symons, Celia C; Arnott, Shelley E

2013-05-01

Changing environmental conditions are affecting diversity and ecosystem function globally. Theory suggests that dispersal from a regional species pool may buffer against changes in local community diversity and ecosystem function after a disturbance through the establishment of functionally redundant tolerant species. The spatial insurance provided by dispersal may decrease through time after environmental change as the local community monopolizes resources and reduces community invasibility. To test for evidence of the spatial insurance hypothesis and to determine the role dispersal timing plays in this response we conducted a field experiment using crustacean zooplankton communities in a subarctic region that is expected to be highly impacted by climate change - Churchill, Canada. Three experiments were conducted where nutrients, salt, and dispersal were manipulated. The three experiments differed in time-since-disturbance that the dispersers were added. We found that coarse measures of diversity (i.e. species richness, evenness, and Shannon-Weiner diversity) were generally resistant to large magnitude disturbances, and that dispersal had the most impact on diversity when dispersers were added shortly after disturbance. Ecosystem functioning (chl-a) was degraded in disturbed communities, but dispersal recovered ecosystem function to undisturbed levels. This spatial insurance for ecosystem function was mediated through changes in community composition and the relative abundance of functional groups. Results suggest that regional diversity and habitat connectivity will be important in the future to maintain ecosystem function by introducing functionally redundant species to promote compensatory dynamics. © 2012 Blackwell Publishing Ltd.

Development of synchrotron X-ray micro-tomography under extreme conditions of pressure and temperature.

PubMed

Álvarez-Murga, M; Perrillat, J P; Le Godec, Y; Bergame, F; Philippe, J; King, A; Guignot, N; Mezouar, M; Hodeau, J L

2017-01-01

X-ray tomography is a non-destructive three-dimensional imaging/microanalysis technique selective to a wide range of properties such as density, chemical composition, chemical states and crystallographic structure with extremely high sensitivity and spatial resolution. Here the development of in situ high-pressure high-temperature micro-tomography using a rotating module for the Paris-Edinburgh cell combined with synchrotron radiation is described. By rotating the sample chamber by 360°, the limited angular aperture of ordinary high-pressure cells is surmounted. Such a non-destructive high-resolution probe provides three-dimensional insight on the morphological and structural evolution of crystalline as well as amorphous phases during high pressure and temperature treatment. To demonstrate the potentials of this new experimental technique the compression behavior of a basalt glass is investigated by X-ray absorption tomography, and diffraction/scattering tomography imaging of the structural changes during the polymerization of C 60 molecules under pressure is performed. Small size and weight of the loading frame and rotating module means that this apparatus is portable, and can be readily installed on most synchrotron facilities to take advantage of the diversity of three-dimensional imaging techniques available at beamlines. This experimental breakthrough should open new ways for in situ imaging of materials under extreme pressure-temperature-stress conditions, impacting diverse areas in physics, chemistry, geology or materials sciences.

Communication: Two-dimensional gas-phase coherent anti-Stokes Raman spectroscopy (2D-CARS): Simultaneous planar imaging and multiplex spectroscopy in a single laser shot

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bohlin, Alexis; Kliewer, Christopher J.

2013-01-01

Coherent anti-Stokes Raman spectroscopy (CARS) has been widely used as a powerful tool for chemical sensing, molecular dynamics measurements, and rovibrational spectroscopy since its development over 30 years ago, finding use in fields of study as diverse as combustion diagnostics, cell biology, plasma physics, and the standoff detection of explosives. The capability for acquiring resolved CARS spectra in multiple spatial dimensions within a single laser shot has been a long-standing goal for the study of dynamical processes, but has proven elusive because of both phase-matching and detection considerations. Here, by combining new phase matching and detection schemes with the highmore » efficiency of femtosecond excitation of Raman coherences, we introduce a technique for single-shot two-dimensional (2D) spatial measurements of gas phase CARS spectra. We demonstrate a spectrometer enabling both 2D plane imaging and spectroscopy simultaneously, and present the instantaneous measurement of 15, 000 spatially correlated rotational CARS spectra in N 2 and air over a 2D field of 40 mm 2.« less

Multi-scale Homogenization of Caddisfly Metacomminities in Human-modified Landscapes

NASA Astrophysics Data System (ADS)

Simião-Ferreira, Juliana; Nogueira, Denis Silva; Santos, Anna Claudia; De Marco, Paulo; Angelini, Ronaldo

2018-04-01

The multiple scale of stream networks spatial organization reflects the hierarchical arrangement of streams habitats with increasingly levels of complexity from sub-catchments until entire hydrographic basins. Through these multiple spatial scales, local stream habitats form nested subsets of increasingly landscape scale and habitat size with varying contributions of both alpha and beta diversity for the regional diversity. Here, we aimed to test the relative importance of multiple nested hierarchical levels of spatial scales while determining alpha and beta diversity of caddisflies in regions with different levels of landscape degradation in a core Cerrado area in Brazil. We used quantitative environmental variables to test the hypothesis that landscape homogenization affects the contribution of alpha and beta diversity of caddisflies to regional diversity. We found that the contribution of alpha and beta diversity for gamma diversity varied according to landscape degradation. Sub-catchments with more intense agriculture had lower diversity at multiple levels, markedly alpha and beta diversities. We have also found that environmental predictors mainly associated with water quality, channel size, and habitat integrity (lower scores indicate stream degradation) were related to community dissimilarity at the catchment scale. For an effective management of the headwater biodiversity of caddisfly, towards the conservation of these catchments, heterogeneous streams with more pristine riparian vegetation found within the river basin need to be preserved in protected areas. Additionally, in the most degraded areas the restoration of riparian vegetation and size increase of protected areas will be needed to accomplish such effort.

Mitochondrial phylogeography of a Beringian relict: the endemic freshwater genus of blackfish Dallia (Esociformes).

PubMed

Campbell, M A; Lopéz, J A

2014-02-01

Mitochondrial genetic variability among populations of the blackfish genus Dallia (Esociformes) across Beringia was examined. Levels of divergence and patterns of geographic distribution of mitochondrial DNA lineages were characterized using phylogenetic inference, median-joining haplotype networks, Bayesian skyline plots, mismatch analysis and spatial analysis of molecular variance (SAMOVA) to infer genealogical relationships and to assess patterns of phylogeography among extant mitochondrial lineages in populations of species of Dallia. The observed variation includes extensive standing mitochondrial genetic diversity and patterns of distinct spatial segregation corresponding to historical and contemporary barriers with minimal or no mixing of mitochondrial haplotypes between geographic areas. Mitochondrial diversity is highest in the common delta formed by the Yukon and Kuskokwim Rivers where they meet the Bering Sea. Other regions sampled in this study host comparatively low levels of mitochondrial diversity. The observed levels of mitochondrial diversity and the spatial distribution of that diversity are consistent with persistence of mitochondrial lineages in multiple refugia through the last glacial maximum. © 2014 The Fisheries Society of the British Isles.

Infrared atmospheric sounding interferometer correlation interferometry for the retrieval of atmospheric gases: the case of H2O and CO2.

PubMed

Grieco, Giuseppe; Masiello, Guido; Serio, Carmine; Jones, Roderic L; Mead, Mohammed I

2011-08-01

Correlation interferometry is a particular application of Fourier transform spectroscopy with partially scanned interferograms. Basically, it is a technique to obtain the difference between the spectra of atmospheric radiance at two diverse spectral resolutions. Although the technique could be exploited to design an appropriate correlation interferometer, in this paper we are concerned with the analytical aspects of the method and its application to high-spectral-resolution infrared observations in order to separate the emission of a given atmospheric gas from a spectral signal dominated by surface emission, such as in the case of satellite spectrometers operated in the nadir looking mode. The tool will be used to address some basic questions concerning the vertical spatial resolution of H2O and to develop an algorithm to retrieve the columnar amount of CO2. An application to complete interferograms from the Infrared Atmospheric Sounding Interferometer will be presented and discussed. For H2O, we have concluded that the vertical spatial resolution in the lower troposphere mostly depends on broad features associated with the spectrum, whereas for CO2, we have derived a technique capable of retrieving a CO2 columnar amount with accuracy of ≈±7 parts per million by volume at the level of each single field of view.

Fish assemblage in a semi-arid Neotropical reservoir: composition, structure and patterns of diversity and abundance.

PubMed

Novaes, J L C; Moreira, S I L; Freire, C E C; Sousa, M M O; Costa, R S

2014-05-01

The aim of this study was to analyse the composition, structure and spatial and temporal patterns of diversity and abundance of the ichthyofauna of the Santa Cruz Reservoir in semi-arid Brazil. Data were collected quarterly at eight sampling locations on the reservoir between February 2010 and November 2011 using gillnets from 12- to 70-mm mesh that were left in the water for 12h00min during the night. We evaluated the composition, structure and assemblage descriptors (Shannon-Wiener diversity index and equitability, respectively) and catch per unit effort by the number (CPUEn) and biomass (CPUEb) of the ichthyofauna. The 6,047 individuals (399,211.6 g) captured represented three orders, ten families and 20 species, of which four belonged to introduced species. The family Characidae was the most abundant with a total of 2,772 (45.8%) individuals captured. The species-abundance curve fit the log-normal model. In the spatial analysis of diversity, there were significant differences between sampling sites in the lacustrine and fluvial regions, and the highest values were found in the lacustrine region. In the temporal analysis of diversity, significant differences were also observed between the rainy and dry seasons, and the higher values were found during the dry season. Equitability followed the same spatiotemporal pattern as diversity. The Spearman correlation was significantly negative between diversity and rainfall. A cluster analysis spatially separated the ichthyofauna into two groups: one group formed by sampling sites in the fluvial region and another group formed by the remainder of the points in the lacustrine region. Both the CPUEn and CPUEb values were higher at point 8 (fluvial region) and during the rainy season. A two-way ANOVA showed that the CPUEn and CPUEb values were spatially and temporally significant. We conclude that the spatial and temporal trends of diversity in the Santa Cruz reservoir differ from those of other Brazilian reservoirs but that the fish community composition and spatiotemporal patterns of abundance were similar.

Intensive agriculture erodes β-diversity at large scales.

PubMed

Karp, Daniel S; Rominger, Andrew J; Zook, Jim; Ranganathan, Jai; Ehrlich, Paul R; Daily, Gretchen C

2012-09-01

Biodiversity is declining from unprecedented land conversions that replace diverse, low-intensity agriculture with vast expanses under homogeneous, intensive production. Despite documented losses of species richness, consequences for β-diversity, changes in community composition between sites, are largely unknown, especially in the tropics. Using a 10-year data set on Costa Rican birds, we find that low-intensity agriculture sustained β-diversity across large scales on a par with forest. In high-intensity agriculture, low local (α) diversity inflated β-diversity as a statistical artefact. Therefore, at small spatial scales, intensive agriculture appeared to retain β-diversity. Unlike in forest or low-intensity systems, however, high-intensity agriculture also homogenised vegetation structure over large distances, thereby decoupling the fundamental ecological pattern of bird communities changing with geographical distance. This ~40% decline in species turnover indicates a significant decline in β-diversity at large spatial scales. These findings point the way towards multi-functional agricultural systems that maintain agricultural productivity while simultaneously conserving biodiversity. © 2012 Blackwell Publishing Ltd/CNRS.

The relationship between satellite-derived indices and species diversity across African savanna ecosystems

NASA Astrophysics Data System (ADS)

Mapfumo, Ratidzo B.; Murwira, Amon; Masocha, Mhosisi; Andriani, R.

2016-10-01

The ability to use remotely sensed diversity is important for the management of ecosystems at large spatial extents. However, to achieve this, there is still need to develop robust methods and approaches that enable large-scale mapping of species diversity. In this study, we tested the relationship between species diversity measured in situ with the Normalized Difference Vegetation Index (NDVI) and the Coefficient of Variation in the NDVI (CVNDVI) derived from high and medium spatial resolution satellite data at dry, wet and coastal savanna woodlands. We further tested the effect of logging on NDVI along the transects and between transects as disturbance may be a mechanism driving the patterns observed. Overall, the results of this study suggest that high tree species diversity is associated with low and high NDVI and at intermediate levels is associated with low tree species diversity and NDVI. High tree species diversity is associated with high CVNDVI and vice versa and at intermediate levels is associated with high tree species diversity and CVNDVI.

Assessing exotic plant species invasions and associated soil characteristics: A case study in eastern Rocky Mountain National Park, Colorado, USA, using the pixel nested plot design

USGS Publications Warehouse

Kalkhan, M.A.; Stafford, E.J.; Woodly, P.J.; Stohlgren, T.J.

2007-01-01

Rocky Mountain National Park (RMNP), Colorado, USA, contains a diversity of plant species. However, many exotic plant species have become established, potentially impacting the structure and function of native plant communities. Our goal was to quantify patterns of exotic plant species in relation to native plant species, soil characteristics, and other abiotic factors that may indicate or predict their establishment and success. Our research approach for field data collection was based on a field plot design called the pixel nested plot. The pixel nested plot provides a link to multi-phase and multi-scale spatial modeling-mapping techniques that can be used to estimate total species richness and patterns of plant diversity at finer landscape scales. Within the eastern region of RMNP, in an area of approximately 35,000 ha, we established a total of 60 pixel nested plots in 9 vegetation types. We used canonical correspondence analysis (CCA) and multiple linear regressions to quantify relationships between soil characteristics and native and exotic plant species richness and cover. We also used linear correlation, spatial autocorrelation and cross correlation statistics to test for the spatial patterns of variables of interest. CCA showed that exotic species were significantly (P < 0.05) associated with photosynthetically active radiation (r = 0.55), soil nitrogen (r = 0.58) and bare ground (r = -0.66). Pearson's correlation statistic showed significant linear relationships between exotic species, organic carbon, soil nitrogen, and bare ground. While spatial autocorrelations indicated that our 60 pixel nested plots were spatially independent, the cross correlation statistics indicated that exotic plant species were spatially associated with bare ground, in general, exotic plant species were most abundant in areas of high native species richness. This indicates that resource managers should focus on the protection of relatively rare native rich sites with little canopy cover, and fertile soils. Using the pixel nested plot approach for data collection can facilitate the ecological monitoring of these vulnerable areas at the landscape scale in a time- and cost-effective manner. ?? 2006 Elsevier B.V. All rights reserved.

3D shape representation with spatial probabilistic distribution of intrinsic shape keypoints

NASA Astrophysics Data System (ADS)

Ghorpade, Vijaya K.; Checchin, Paul; Malaterre, Laurent; Trassoudaine, Laurent

2017-12-01

The accelerated advancement in modeling, digitizing, and visualizing techniques for 3D shapes has led to an increasing amount of 3D models creation and usage, thanks to the 3D sensors which are readily available and easy to utilize. As a result, determining the similarity between 3D shapes has become consequential and is a fundamental task in shape-based recognition, retrieval, clustering, and classification. Several decades of research in Content-Based Information Retrieval (CBIR) has resulted in diverse techniques for 2D and 3D shape or object classification/retrieval and many benchmark data sets. In this article, a novel technique for 3D shape representation and object classification has been proposed based on analyses of spatial, geometric distributions of 3D keypoints. These distributions capture the intrinsic geometric structure of 3D objects. The result of the approach is a probability distribution function (PDF) produced from spatial disposition of 3D keypoints, keypoints which are stable on object surface and invariant to pose changes. Each class/instance of an object can be uniquely represented by a PDF. This shape representation is robust yet with a simple idea, easy to implement but fast enough to compute. Both Euclidean and topological space on object's surface are considered to build the PDFs. Topology-based geodesic distances between keypoints exploit the non-planar surface properties of the object. The performance of the novel shape signature is tested with object classification accuracy. The classification efficacy of the new shape analysis method is evaluated on a new dataset acquired with a Time-of-Flight camera, and also, a comparative evaluation on a standard benchmark dataset with state-of-the-art methods is performed. Experimental results demonstrate superior classification performance of the new approach on RGB-D dataset and depth data.

Video Salient Object Detection via Fully Convolutional Networks.

PubMed

Wang, Wenguan; Shen, Jianbing; Shao, Ling

This paper proposes a deep learning model to efficiently detect salient regions in videos. It addresses two important issues: 1) deep video saliency model training with the absence of sufficiently large and pixel-wise annotated video data and 2) fast video saliency training and detection. The proposed deep video saliency network consists of two modules, for capturing the spatial and temporal saliency information, respectively. The dynamic saliency model, explicitly incorporating saliency estimates from the static saliency model, directly produces spatiotemporal saliency inference without time-consuming optical flow computation. We further propose a novel data augmentation technique that simulates video training data from existing annotated image data sets, which enables our network to learn diverse saliency information and prevents overfitting with the limited number of training videos. Leveraging our synthetic video data (150K video sequences) and real videos, our deep video saliency model successfully learns both spatial and temporal saliency cues, thus producing accurate spatiotemporal saliency estimate. We advance the state-of-the-art on the densely annotated video segmentation data set (MAE of .06) and the Freiburg-Berkeley Motion Segmentation data set (MAE of .07), and do so with much improved speed (2 fps with all steps).This paper proposes a deep learning model to efficiently detect salient regions in videos. It addresses two important issues: 1) deep video saliency model training with the absence of sufficiently large and pixel-wise annotated video data and 2) fast video saliency training and detection. The proposed deep video saliency network consists of two modules, for capturing the spatial and temporal saliency information, respectively. The dynamic saliency model, explicitly incorporating saliency estimates from the static saliency model, directly produces spatiotemporal saliency inference without time-consuming optical flow computation. We further propose a novel data augmentation technique that simulates video training data from existing annotated image data sets, which enables our network to learn diverse saliency information and prevents overfitting with the limited number of training videos. Leveraging our synthetic video data (150K video sequences) and real videos, our deep video saliency model successfully learns both spatial and temporal saliency cues, thus producing accurate spatiotemporal saliency estimate. We advance the state-of-the-art on the densely annotated video segmentation data set (MAE of .06) and the Freiburg-Berkeley Motion Segmentation data set (MAE of .07), and do so with much improved speed (2 fps with all steps).

MRI of chemical reactions and processes.

PubMed

Britton, Melanie M

2017-08-01

As magnetic resonance imaging (MRI) can spatially resolve a wealth of molecular information available from nuclear magnetic resonance (NMR), it is able to non-invasively visualise the composition, properties and reactions of a broad range of spatially-heterogeneous molecular systems. Hence, MRI is increasingly finding applications in the study of chemical reactions and processes in a diverse range of environments and technologies. This article will explain the basic principles of MRI and how it can be used to visualise chemical composition and molecular properties, providing an overview of the variety of information available. Examples are drawn from the disciplines of chemistry, chemical engineering, environmental science, physics, electrochemistry and materials science. The review introduces a range of techniques used to produce image contrast, along with the chemical and molecular insight accessible through them. Methods for mapping the distribution of chemical species, using chemical shift imaging or spatially-resolved spectroscopy, are reviewed, as well as methods for visualising physical state, temperature, current density, flow velocities and molecular diffusion. Strategies for imaging materials with low signal intensity, such as those containing gases or low sensitivity nuclei, using compressed sensing, para-hydrogen or polarisation transfer, are discussed. Systems are presented which encapsulate the diversity of chemical and physical parameters observable by MRI, including one- and two-phase flow in porous media, chemical pattern formation, phase transformations and hydrodynamic (fingering) instabilities. Lastly, the emerging area of electrochemical MRI is discussed, with studies presented on the visualisation of electrochemical deposition and dissolution processes during corrosion and the operation of batteries, supercapacitors and fuel cells. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Detection of forest stand-level spatial structure in ectomycorrhizal fungal communities

Treesearch

Erik A. Lilleskov; Thomas D. Bruns; Thomas R. Horton; D. Lee Taylor; Paul Grogan

2004-01-01

Ectomycorrhizal fungal (EMF) communities are highly diverse at the stand level. To begin to understand what might lead to such diversity, and to improve sampling designs, we investigated the spatial structure of these communities. We used EMF community data from a number of studies carried out in seven mature and one recently fire-initiated forest stand. We applied...

Species dispersal rates alter diversity and ecosystem stability in pond metacommunities.

PubMed

Howeth, Jennifer G; Leibold, Mathew A

2010-09-01

Metacommunity theory suggests that relationships between diversity and ecosystem stability can be determined by the rate of species dispersal among local communities. The predicted relationships, however, may depend upon the relative strength of local environmental processes and disturbance. Here we evaluate the role of dispersal frequency and local predation perturbations in affecting patterns of diversity and stability in pond plankton metacommunities. Pond metacommunities were composed of three mesocosm communities: one of the three communities maintained constant "press" predation from a selective predator, bluegill sunfish (Lepomis macrochirus); the second community maintained "press" conditions without predation; and the third community experienced recurrent "pulsed" predation from bluegill sunfish. The triads of pond communities were connected at either no, low (0.7%/d), or high (20%/d) planktonic dispersal. Richness and composition of zooplankton and stability of plankton biomass and ecosystem productivity were measured at local and regional spatial scales. Dispersal significantly affected diversity such that local and regional biotas at the low dispersal rate maintained the greatest number of species. The unimodal local dispersal-diversity relationship was predator-dependent, however, as selective press predation excluded species regardless of dispersal. Further, there was no effect of dispersal on beta diversity because predation generated local conditions that selected for distinct community assemblages. Spatial and temporal ecosystem stability responded to dispersal frequency but not predation. Low dispersal destabilized the spatial stability of producer biomass but stabilized temporal ecosystem productivity. The results indicate that selective predation can prevent species augmentation from mass effects but has no apparent influence on stability. Dispersal rates, in contrast, can have significant effects on both species diversity and ecosystem stability at multiple spatial scales in metacommunities.

Baseflow physical characteristics differ at multiple spatial scales in stream networks across diverse biomes

Treesearch

Janine Ruegg; Walter K. Dodds; Melinda D. Daniels; Ken R. Sheehan; Christina L. Baker; William B. Bowden; Kaitlin J. Farrell; Michael B. Flinn; Tamara K. Harms; Jeremy B. Jones; Lauren E. Koenig; John S. Kominoski; William H. McDowell; Samuel P. Parker; Amy D. Rosemond; Matt T. Trentman; Matt Whiles; Wilfred M. Wollheim

2016-01-01

ContextSpatial scaling of ecological processes is facilitated by quantifying underlying habitat attributes. Physical and ecological patterns are often measured at disparate spatial scales limiting our ability to quantify ecological processes at broader spatial scales using physical attributes.

How beta diversity and the underlying causes vary with sampling scales in the Changbai mountain forests.

PubMed

Tan, Lingzhao; Fan, Chunyu; Zhang, Chunyu; von Gadow, Klaus; Fan, Xiuhua

2017-12-01

This study aims to establish a relationship between the sampling scale and tree species beta diversity temperate forests and to identify the underlying causes of beta diversity at different sampling scales. The data were obtained from three large observational study areas in the Changbai mountain region in northeastern China. All trees with a dbh ≥1 cm were stem-mapped and measured. The beta diversity was calculated for four different grain sizes, and the associated variances were partitioned into components explained by environmental and spatial variables to determine the contributions of environmental filtering and dispersal limitation to beta diversity. The results showed that both beta diversity and the causes of beta diversity were dependent on the sampling scale. Beta diversity decreased with increasing scales. The best-explained beta diversity variation was up to about 60% which was discovered in the secondary conifer and broad-leaved mixed forest (CBF) study area at the 40 × 40 m scale. The variation partitioning result indicated that environmental filtering showed greater effects at bigger grain sizes, while dispersal limitation was found to be more important at smaller grain sizes. What is more, the result showed an increasing explanatory ability of environmental effects with increasing sampling grains but no clearly trend of spatial effects. The study emphasized that the underlying causes of beta diversity variation may be quite different within the same region depending on varying sampling scales. Therefore, scale effects should be taken into account in future studies on beta diversity, which is critical in identifying different relative importance of spatial and environmental drivers on species composition variation.

Genetic diversity and structure of managed and semi-natural populations of cocoa (Theobroma cacao) in the Huallaga and Ucayali Valleys of Peru.

PubMed

Zhang, Dapeng; Arevalo-Gardini, Enrique; Mischke, Sue; Zúñiga-Cernades, Luis; Barreto-Chavez, Alejandro; Del Aguila, Jorge Adriazola

2006-09-01

Cocoa (Theobroma cacao) is indigenous to the Amazon region of South America, and it is well known that the Peruvian Amazon harbours a large number of diverse cocoa populations. A small fraction of the diversity has been collected and maintained as an ex-situ germplasm repository in Peru. However, incorrect labelling of accessions and lack of information on genetic diversity have hindered efficient conservation and use of this germplasm. This study targeted assessment of genetic diversity and population structure in a managed and a semi-natural population. Using a capillary electrophoresis genotyping system, 105 cocoa accessions collected from the Huallaga and Ucayali valleys of Peru were fingerprinted. Based on 15 loci SSR profiles, genetic identity was examined for each accession and duplicates identified, population structure assessed and genetic diversity analysed in these two populations. Ten synonymous mislabelled groups were identified among the 105 accessions. The germplasm group in the Huallaga valley was clearly separated from the group in Ucayali valley by the Bayesian assignment test. The Huallaga group has lower genetic diversity, both in terms of allelic richness and of gene diversity, than the Ucayali group. Analysis of molecular variance suggested genetic substructure in the Ucayali group. Significant spatial correlation between genetic distance and geographical distances was detected in the Ucayali group by Mantel tests. These results substantiate the hypothesis that the Peruvian Amazon hosts a high level of cocoa genetic diversity, and the diversity has a spatial structure. The introduction of exotic seed populations into the Peruvian Amazon is changing the cocoa germplasm spectrum in this region. The spatial structure of cocoa diversity recorded here highlights the need for additional collecting and conservation measures for natural and semi-natural cocoa populations.

The rich get richer: Patterns of plant invasions in the United States

USGS Publications Warehouse

Stohlgren, T.J.; Barnett, D.T.; Kartesz, J.T.

2003-01-01

Observations from islands, small-scale experiments, and mathematical models have generally supported the paradigm that habitats of low plant diversity are more vulnerable to plant invasions than areas of high plant diversity. We summarize two independent data sets to show exactly the opposite pattern at multiple spatial scales. More significant, and alarming, is that hotspots of native plant diversity have been far more heavily invaded than areas of low plant diversity in most parts of the United States when considered at larger spatial scales. Our findings suggest that we cannot expect such hotspots to repel invasions, and that the threat of invasion is significant and predictably greatest in these areas.

Ultrafast imaging of cell elasticity with optical microelastography

PubMed Central

Grasland-Mongrain, Pol; Zorgani, Ali; Nakagawa, Shoma; Bernard, Simon; Paim, Lia Gomes; Fitzharris, Greg; Catheline, Stefan

2018-01-01

Elasticity is a fundamental cellular property that is related to the anatomy, functionality, and pathological state of cells and tissues. However, current techniques based on cell deformation, atomic force microscopy, or Brillouin scattering are rather slow and do not always accurately represent cell elasticity. Here, we have developed an alternative technique by applying shear wave elastography to the micrometer scale. Elastic waves were mechanically induced in live mammalian oocytes using a vibrating micropipette. These audible frequency waves were observed optically at 200,000 frames per second and tracked with an optical flow algorithm. Whole-cell elasticity was then mapped using an elastography method inspired by the seismology field. Using this approach we show that the elasticity of mouse oocytes is decreased when the oocyte cytoskeleton is disrupted with cytochalasin B. The technique is fast (less than 1 ms for data acquisition), precise (spatial resolution of a few micrometers), able to map internal cell structures, and robust and thus represents a tractable option for interrogating biomechanical properties of diverse cell types. PMID:29339488

A Phytochemical-Sensing Strategy Based on Mass Spectrometry Imaging and Metabolic Profiling for Understanding the Functionality of the Medicinal Herb Green Tea.

PubMed

Fujimura, Yoshinori; Miura, Daisuke; Tachibana, Hirofumi

2017-09-27

Low-molecular-weight phytochemicals have health benefits and reduce the risk of diseases, but the mechanisms underlying their activities have remained elusive because of the lack of a methodology that can easily visualize the exact behavior of such small molecules. Recently, we developed an in situ label-free imaging technique, called mass spectrometry imaging, for visualizing spatially-resolved biotransformations based on simultaneous mapping of the major bioactive green tea polyphenol and its phase II metabolites. In addition, we established a mass spectrometry-based metabolic profiling technique capable of evaluating the bioactivities of diverse green tea extracts, which contain multiple phytochemicals, by focusing on their compositional balances. This methodology allowed us to simultaneously evaluate the relative contributions of the multiple compounds present in a multicomponent system to its bioactivity. This review highlights small molecule-sensing techniques for visualizing the complex behaviors of herbal components and linking such information to an enhanced understanding of the functionalities of multicomponent medicinal herbs.

Infrared spectroscopic imaging: Label-free biochemical analysis of stroma and tissue fibrosis.

PubMed

Nazeer, Shaiju S; Sreedhar, Hari; Varma, Vishal K; Martinez-Marin, David; Massie, Christine; Walsh, Michael J

2017-11-01

Infrared spectroscopic tissue imaging is a potentially powerful adjunct tool to current histopathology techniques. By coupling the biochemical signature obtained through infrared spectroscopy to the spatial information offered by microscopy, this technique can selectively analyze the chemical composition of different features of unlabeled, unstained tissue sections. In the past, the tissue features that have received the most interest were parenchymal and epithelial cells, chiefly due to their involvement in dysplasia and progression to carcinoma; however, the field has recently turned its focus toward stroma and areas of fibrotic change. These components of tissue present an untapped source of biochemical information that can shed light on many diverse disease processes, and potentially hold useful predictive markers for these same pathologies. Here we review the recent applications of infrared spectroscopic imaging to stromal and fibrotic regions of diseased tissue, and explore the potential of this technique to advance current capabilities for tissue analysis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Temporally variable environments maintain more beta-diversity in Mediterranean landscapes

NASA Astrophysics Data System (ADS)

Martin, Beatriz; Ferrer, Miguel

2015-10-01

We examined the relationships between different environmental factors and the alpha and beta-diversity of terrestrial vertebrates (birds, mammals, amphibians and reptiles) in a Mediterranean region at the landscape level. We investigated whether the mechanisms underlying alpha and beta-diversity patterns are influenced by energy availability, habitat heterogeneity and temporal variability and if the drivers of the diversity patterns differed between both components of diversity. We defined alpha-diversity as synonym of species richness whereas beta-diversity was measured as distinctiveness. We evaluated a total of 13 different predictors using generalized linear mixed model (GLMM) analysis. Habitat spatial heterogeneity increased alpha-diversity, but contrastingly, it did not significantly affect beta-diversity among sites. Disturbed landscapes may show higher habitat spatial variation and higher alpha-diversity due to the contribution of highly generalist species that are wide-distributed and do not differ in composition (beta-diversity) among different sites within the region. Contrastingly, higher beta-diversity levels were negatively related to more stable sites in terms of temporal environmental variation. This negative relationship between environmental stability and beta-diversity levels is explained in terms of species adaptation to the local environmental conditions. Our study highlights the importance of temporal environmental variability in maintaining beta-diversity patterns under highly variable environmental conditions.

Phylogenetic Diversity of Bacteria Associated with the Marine Sponge Rhopaloeides odorabile†

PubMed Central

Webster, Nicole S.; Wilson, Kate J.; Blackall, Linda L.; Hill, Russell T.

2001-01-01

Molecular techniques were employed to document the microbial diversity associated with the marine sponge Rhopaloeides odorabile. The phylogenetic affiliation of sponge-associated bacteria was assessed by 16S rRNA sequencing of cloned DNA fragments. Fluorescence in situ hybridization (FISH) was used to confirm the presence of the predominant groups indicated by 16S rDNA analysis. The community structure was extremely diverse with representatives of the Actinobacteria, low-G+C gram-positive bacteria, the β- and γ-subdivisions of the Proteobacteria, Cytophaga/Flavobacterium, green sulfur bacteria, green nonsulfur bacteria, planctomycetes, and other sequence types with no known close relatives. FISH probes revealed the spatial location of these bacteria within the sponge tissue, in some cases suggesting possible symbiotic functions. The high proportion of 16S rRNA sequences derived from novel actinomycetes is good evidence for the presence of an indigenous marine actinomycete assemblage in R. odorabile. High microbial diversity was inferred from low duplication of clones in a library with 70 representatives. Determining the phylogenetic affiliation of sponge-associated microorganisms by 16S rRNA analysis facilitated the rational selection of culture media and isolation conditions to target specific groups of well-represented bacteria for laboratory culture. Novel media incorporating sponge extracts were used to isolate bacteria not previously recovered from this sponge. PMID:11133476

Coherent and Noncoherent Joint Processing of Sonar for Detection of Small Targets in Shallow Water

PubMed Central

Jiang, Jingning; Li, Si; Ding, Zhenping; Pan, Chen; Gong, Xianyi

2018-01-01

A coherent-noncoherent joint processing framework is proposed for active sonar to combine diversity gain and beamforming gain for detection of a small target in shallow water environments. Sonar utilizes widely-spaced arrays to sense environments and illuminate a target of interest from multiple angles. Meanwhile, it exploits spatial diversity for time-reversal focusing to suppress reverberation, mainly strong bottom reverberation. For enhancement of robustness of time-reversal focusing, an adaptive iterative strategy is utilized in the processing framework. A probing signal is firstly transmitted and echoes of a likely target are utilized as steering vectors for the second transmission. With spatial diversity, target bearing and range are estimated using a broadband signal model. Numerical simulations show that the novel sonar outperforms the traditional phased-array sonar due to benefits of spatial diversity. The effectiveness of the proposed framework has been validated by localization of a small target in at-lake experiments. PMID:29642637

Spatio-temporal dynamics of genetic diversity in Sorghum bicolor in Niger.

PubMed

Deu, Monique; Sagnard, F; Chantereau, J; Calatayud, C; Vigouroux, Y; Pham, J L; Mariac, C; Kapran, I; Mamadou, A; Gérard, B; Ndjeunga, J; Bezançon, G

2010-05-01

The dynamics of crop genetic diversity need to be assessed to draw up monitoring and conservation priorities. However, few surveys have been conducted in centres of diversity. Sub-Saharan Africa is the centre of origin of sorghum. Most Sahel countries have been faced with major human, environmental and social changes in recent decades, which are suspected to cause genetic erosion. Sorghum is the second staple cereal in Niger, a centre of diversity for this crop. Niger was submitted to recurrent drought period and to major social changes during these last decades. We report here on a spatio-temporal analysis of sorghum genetic diversity, conducted in 71 villages covering the rainfall gradient and range of agro-ecological conditions in Niger's agricultural areas. We used 28 microsatellite markers and applied spatial and genetic clustering methods to investigate change in genetic diversity over a 26-year period (1976-2003). Global genetic differentiation between the two collections was very low (F (st) = 0.0025). Most of the spatial clusters presented no major differentiation, as measured by F (st), and showed stability or an increase in allelic richness, except for two of them located in eastern Niger. The genetic clusters identified by Bayesian analysis did not show a major change between the two collections in the distribution of accessions between them or in their spatial location. These results suggest that farmers' management has globally preserved sorghum genetic diversity in Niger.

Spatial patterns of littoral zooplankton assemblages along a salinity gradient in a brackish sea: A functional diversity perspective

NASA Astrophysics Data System (ADS)

Helenius, Laura K.; Leskinen, Elina; Lehtonen, Hannu; Nurminen, Leena

2017-11-01

The distribution patterns and diversity of littoral zooplankton are both key baseline information for understanding the functioning of coastal ecosystems, and for identifying the mechanisms by which the impacts of recently increased eutrophication are transferred through littoral food webs. In this study, zooplankton community structure and diversity along a shallow coastal area of the northern Baltic Sea were determined in terms of horizontal environmental gradients. Spatial heterogeneity of the zooplankton community was examined along the gradient. Altogether 31 sites in shallow sandy bays on the coast of southwest Finland were sampled in the summer periods of 2009 and 2010 for zooplankton and environmental variables (surface water temperature, salinity, turbidity, wave exposure, macrophyte coverage, chlorophyll a and nutrients). Zooplankton diversity was measured as both taxonomic as well as functional diversity, using trait-based classification of planktonic crustaceans. Salinity, and to a lesser extent turbidity and temperature, were found to be the main predictors of the spatial patterns and functional diversity of the zooplankton community. Occurrence of cyclopoid copepods, as well as abundances of the calanoid copepod genus Acartia and the rotifer genus Keratella were found to be key factors in differentiating sites along the gradient. As far as we know, this is the first extensive study of functional diversity in Baltic Sea coastal zooplankton communities.

Niger-wide assessment of in situ sorghum genetic diversity with microsatellite markers.

PubMed

Deu, M; Sagnard, F; Chantereau, J; Calatayud, C; Hérault, D; Mariac, C; Pham, J-L; Vigouroux, Y; Kapran, I; Traore, P S; Mamadou, A; Gerard, B; Ndjeunga, J; Bezançon, G

2008-05-01

Understanding the geographical, environmental and social patterns of genetic diversity on different spatial scales is key to the sustainable in situ management of genetic resources. However, few surveys have been conducted on crop genetic diversity using exhaustive in situ germplasm collections on a country scale and such data are missing for sorghum in sub-Saharan Africa, its centre of origin. We report here a genetic analysis of 484 sorghum varieties collected in 79 villages evenly distributed across Niger, using 28 microsatellite markers. We found a high level of SSR diversity in Niger. Diversity varied between eastern and western Niger, and allelic richness was lower in the eastern part of the country. Genetic differentiation between botanical races was the first structuring factor (Fst = 0.19), but the geographical distribution and the ethnic group to which farmers belonged were also significantly associated with genetic diversity partitioning. Gene pools are poorly differentiated among climatic zones. The geographical situation of Niger, where typical western African (guinea), central African (caudatum) and eastern Sahelian African (durra) sorghum races converge, explained the high observed genetic diversity and was responsible for the interactions among the ethnic, geographical and botanical structure revealed in our study. After correcting for the structure of botanical races, spatial correlation of genetic diversity was still detected within 100 km, which may hint at limited seed exchanges between farmers. Sorghum domestication history, in relation to the spatial organisation of human societies, is therefore key information for sorghum in situ conservation programs in sub-Saharan Africa.

Mapping and determinism of soil microbial community distribution across an agricultural landscape

PubMed Central

Constancias, Florentin; Terrat, Sébastien; Saby, Nicolas P A; Horrigue, Walid; Villerd, Jean; Guillemin, Jean-Philippe; Biju-Duval, Luc; Nowak, Virginie; Dequiedt, Samuel; Ranjard, Lionel; Chemidlin Prévost-Bouré, Nicolas

2015-01-01

Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity. PMID:25833770

Developing spectral, structural, and phenological diversity proxies for monitoring biodiversity change across space and time using ESA's Sentinel satellites

NASA Astrophysics Data System (ADS)

Ma, X.; Mahecha, M. D.; Migliavacca, M.; Luo, Y.; Urban, M.; Bohn, F. J.; Huth, A.; Reichstein, M.

2017-12-01

A key challenge for monitoring biodiversity change is the lack of consistent measures of biodiversity across space and time. This challenge may be addressed by exploring the potentials provided by novel remote sensing observations. By continuously observing broad-scale patterns of vegetation and land surface parameters, remote sensing can complement the restricted coverage afforded by field measurements. Here we develop methods to infer spatial patterns of biodiversity at ecosystem level from ESA's next-generation Sentinel sensors (Sentinel-1: C-band radar & Sentinel-2: multispectral). Both satellites offer very high spatial (10 m) and temporal resolutions (5 days) measurements with global coverage. We propose and test several ecosystem biodiversity proxies, including landscape spectral diversity, phenological diversity, and canopy structural diversity. These diversity proxies are highly related to some key aspects of essential biodiversity variables (EBVs) as defined by GEO-BON, such as habitat structure, community composition, ecosystem function and structure. We verify spaceborne retrievals of these biodiversity proxies with in situ measurements from drone (spectral diversity), phenocam (phenological diversity), and airborne LiDAR (canopy structural diversity) over multiple flux tower sites within the Mediterranean region. We further compare our remote sensing retrievals of biodiversity proxies against several biodiversity indices as derived from field measurements (incl. ⍺-/β- diversity and Shannon-index) to explore the limitations and potentials of extending the RS proxies to a greater spatial extent. We expect the new concept as to maximize the potential of remote sensing information might help to monitor key aspects of EBVs on a global scale.

Remote Sensing of a Manipulated Prairie Grassland Experiment to Predict Belowground Processes

NASA Astrophysics Data System (ADS)

Cavender-Bares, J.; Schweiger, A. K.; Hobbie, S. E.; Madritch, M. D.; Wang, Z.; Couture, J. J.; Gamon, J. A.; Townsend, P. A.

2017-12-01

Given the importance of plant biodiversity for providing the ecosystem functions and services on which humans depend, rapid and remote methods of monitoring plant biodiversity across large spatial extents and biological scales are increasingly critical. In North American prairie systems, the ecosystem benefits of diversity are a subject of ongoing investigation and relevance to policy. However, detecting belowground components of ecosystem biodiversity, composition and associated functions are not possible directly through remote sensing. Nevertheless, belowground components of diversity may be linked to aboveground components allowing indirect inferences. Here we test a series of hypotheses about how aboveground functional and chemical diversity and composition of plant communities drive belowground functions, including N mineralization, enzyme activity and microbial biomass, as well as microbial diversity and composition. We hypothesize that the quantity and chemical composition of aboveground inputs to soil drive belowground processes, including decomposition and microbial enzyme activity. We use plant spectra (400 nm to 2500 nm) measured at the leaf and airborne level to determine chemical and functional composition of leaves and canopies in a long-term grassland experiment where diversity is manipulated at the Cedar Creek Ecosystem Science Reserve. We then assess the extent to which belowground chemistry, microbial diversity and composition are predicted from aboveground plant diversity, biomass and chemical composition. We find strong associations between aboveground inputs and belowground enzyme activity and microbial biomass but only weak linkages between aboveground diversity and belowground diversity. We discuss the potential for such approaches and the caveats related to the spatial scale of measurements and spatial resolution of airborne detection.

Particle image diffusometry: Resolving diffusion coefficient field from microscopy movie data without particle tracking

NASA Astrophysics Data System (ADS)

Hanasaki, Itsuo; Ooi, Yuto

2018-06-01

We propose a technique to evaluate the field of diffusion coefficient for particle dispersion where the Brownian motion is heterogeneous in space and single particle tracking (SPT) analysis is hindered by high concentration of the particles and/or their small size. We realize this "particle image diffusometry" by the principle of the differential dynamic microscopy (DDM). We extend the DDM by introducing the automated objective decision of the scaling regime itself. Label-free evaluation of spatially non-uniform diffusion coefficients without SPT is useful in the diverse applications including crystal nucleation and glass transition where non-invasive observation is desired.

Advances in Parameter and Uncertainty Quantification Using Bayesian Hierarchical Techniques with a Spatially Referenced Watershed Model (Invited)

NASA Astrophysics Data System (ADS)

Alexander, R. B.; Boyer, E. W.; Schwarz, G. E.; Smith, R. A.

2013-12-01

Estimating water and material stores and fluxes in watershed studies is frequently complicated by uncertainties in quantifying hydrological and biogeochemical effects of factors such as land use, soils, and climate. Although these process-related effects are commonly measured and modeled in separate catchments, researchers are especially challenged by their complexity across catchments and diverse environmental settings, leading to a poor understanding of how model parameters and prediction uncertainties vary spatially. To address these concerns, we illustrate the use of Bayesian hierarchical modeling techniques with a dynamic version of the spatially referenced watershed model SPARROW (SPAtially Referenced Regression On Watershed attributes). The dynamic SPARROW model is designed to predict streamflow and other water cycle components (e.g., evapotranspiration, soil and groundwater storage) for monthly varying hydrological regimes, using mechanistic functions, mass conservation constraints, and statistically estimated parameters. In this application, the model domain includes nearly 30,000 NHD (National Hydrologic Data) stream reaches and their associated catchments in the Susquehanna River Basin. We report the results of our comparisons of alternative models of varying complexity, including models with different explanatory variables as well as hierarchical models that account for spatial and temporal variability in model parameters and variance (error) components. The model errors are evaluated for changes with season and catchment size and correlations in time and space. The hierarchical models consist of a two-tiered structure in which climate forcing parameters are modeled as random variables, conditioned on watershed properties. Quantification of spatial and temporal variations in the hydrological parameters and model uncertainties in this approach leads to more efficient (lower variance) and less biased model predictions throughout the river network. Moreover, predictions of water-balance components are reported according to probabilistic metrics (e.g., percentiles, prediction intervals) that include both parameter and model uncertainties. These improvements in predictions of streamflow dynamics can inform the development of more accurate predictions of spatial and temporal variations in biogeochemical stores and fluxes (e.g., nutrients and carbon) in watersheds.

Catfish science: Status and trends in the 21st century

USGS Publications Warehouse

Kwak, Thomas J.; Porath, Mark T.; Michaletz, Paul H.; Travnichek, Vincent H.

2011-01-01

Catfish science, the study of the fish order Siluriformes, is a diverse and expanding field in terms of advances and breadth of topics. We compiled literature from primary fisheries journals as an index of interest and advances in catfish science to examine temporal trends in the field. The number of catfish scientific publications varied over the past century with strong peaks during 1975–1979 and 2005–2010, which may be the result of interactive scientific and societal influences. Catfish biology was the predominant publication topic until the late 1990s, when ecology, techniques, and management publications became more prevalent. Articles on catfish ecology were most numerous in both the first and second international catfish symposia, but publications on techniques and conservation were more numerous in the second catfish symposium than the first. We summarize the state of knowledge, recent advances, and areas for future attention among topics in catfish science, including sampling and aging techniques, population dynamics, ecology, fisheries management, species diversity, nonnative catfish, and human dimensions, with an emphasis on the gains in this second symposium. Areas that we expect to be pursued in the future are development of new techniques and validation of existing methods; expansion of research to less-studied catfish species; broadening temporal, spatial, and organizational scales; interdisciplinary approaches; and research on societal views and constituent demands. Meeting these challenges will require scientists to span beyond their professional comfort zones to effectively reach higher standards. We look forward to the coming decade and the many advances in the conservation, ecology, and management of catfish that will be shared.

Spatial storage effect promotes biodiversity during adaptive radiation.

PubMed

Tan, Jiaqi; Rattray, Jennifer B; Yang, Xian; Jiang, Lin

2017-07-12

Many ecological communities are enormously diverse. Variation in environmental conditions over time and space provides opportunities for temporal and spatial storage effects to operate, potentially promoting species coexistence and biodiversity. While several studies have provided empirical evidence supporting the significance of the temporal storage effect for coexistence, empirical tests of the role of the spatial storage effect are rare. In particular, we know little about how the spatial storage effect contributes to biodiversity over evolutionary timescales. Here, we report the first experimental study on the role of the spatial storage effect in the maintenance of biodiversity in evolving metacommunities, using the bacterium Pseudomonas fluorescens SBW25 as a laboratory model of adaptive radiation. We found that intercommunity spatial heterogeneity promoted phenotypic diversity of P. fluorescens in the presence of dispersal among local communities, by allowing the spatial storage effect to operate. Mechanistically, greater niche differences among P. fluorescens phenotypes arose in metacommunities with intercommunity spatial heterogeneity, facilitating negative frequency-dependent selection, and thus, the coexistence among P. fluorescens phenotypes. These results highlight the importance of the spatial storage effect for biodiversity over evolutionary timescales. © 2017 The Author(s).

Mapping genetic diversity of cherimoya (Annona cherimola Mill.): application of spatial analysis for conservation and use of plant genetic resources.

PubMed

Zonneveld, Maarten van; Scheldeman, Xavier; Escribano, Pilar; Viruel, María A; Van Damme, Patrick; Garcia, Willman; Tapia, César; Romero, José; Sigueñas, Manuel; Hormaza, José I

2012-01-01

There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at province and department level in Ecuador and Peru, respectively.

Mapping Genetic Diversity of Cherimoya (Annona cherimola Mill.): Application of Spatial Analysis for Conservation and Use of Plant Genetic Resources

PubMed Central

van Zonneveld, Maarten; Scheldeman, Xavier; Escribano, Pilar; Viruel, María A.; Van Damme, Patrick; Garcia, Willman; Tapia, César; Romero, José; Sigueñas, Manuel; Hormaza, José I.

2012-01-01

There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at province and department level in Ecuador and Peru, respectively. PMID:22253801

Exploring component-based approaches in forest landscape modeling

Treesearch

H. S. He; D. R. Larsen; D. J. Mladenoff

2002-01-01

Forest management issues are increasingly required to be addressed in a spatial context, which has led to the development of spatially explicit forest landscape models. The numerous processes, complex spatial interactions, and diverse applications in spatial modeling make the development of forest landscape models difficult for any single research group. New...

The beta-diversity of species interactions: Untangling the drivers of geographic variation in plant-pollinator diversity and function across scales.

PubMed

Burkle, Laura A; Myers, Jonathan A; Belote, R Travis

2016-01-01

Geographic patterns of biodiversity have long inspired interest in processes that shape the assembly, diversity, and dynamics of communities at different spatial scales. To study mechanisms of community assembly, ecologists often compare spatial variation in community composition (beta-diversity) across environmental and spatial gradients. These same patterns inspired evolutionary biologists to investigate how micro- and macro-evolutionary processes create gradients in biodiversity. Central to these perspectives are species interactions, which contribute to community assembly and geographic variation in evolutionary processes. However, studies of beta-diversity have predominantly focused on single trophic levels, resulting in gaps in our understanding of variation in species-interaction networks (interaction beta-diversity), especially at scales most relevant to evolutionary studies of geographic variation. We outline two challenges and their consequences in scaling-up studies of interaction beta-diversity from local to biogeographic scales using plant-pollinator interactions as a model system in ecology, evolution, and conservation. First, we highlight how variation in regional species pools may contribute to variation in interaction beta-diversity among biogeographic regions with dissimilar evolutionary history. Second, we highlight how pollinator behavior (host-switching) links ecological networks to geographic patterns of plant-pollinator interactions and evolutionary processes. Third, we outline key unanswered questions regarding the role of geographic variation in plant-pollinator interactions for conservation and ecosystem services (pollination) in changing environments. We conclude that the largest advances in the burgeoning field of interaction beta-diversity will come from studies that integrate frameworks in ecology, evolution, and conservation to understand the causes and consequences of interaction beta-diversity across scales. © 2016 Botanical Society of America.

Spatial Patterns in Water Temperature in Pacific Northwest Rivers: Diversity at Multiple Scales and Potential Influence of Climate Change

NASA Astrophysics Data System (ADS)

Torgersen, C. E.; Fullerton, A.; Lawler, J. J.; Ebersole, J. L.; Leibowitz, S. G.; Steel, E. A.; Beechie, T. J.; Faux, R.

2016-12-01

Understanding spatial patterns in water temperature will be essential for evaluating vulnerability of aquatic biota to future climate and for identifying and protecting diverse thermal habitats. We used high-resolution remotely sensed water temperature data for over 16,000 km of 2nd to 7th-order rivers throughout the Pacific Northwest and California to evaluate spatial patterns of summertime water temperature at multiple spatial scales. We found a diverse and geographically distributed suite of whole-river patterns. About half of rivers warmed asymptotically in a downstream direction, whereas the rest exhibited complex and unique spatial patterns. Patterns were associated with both broad-scale hydroclimatic variables as well as characteristics unique to each basin. Within-river thermal heterogeneity patterns were highly river-specific; across rivers, median size and spacing of cool patches <15 °C were around 250 m. Patches of this size are large enough for juvenile salmon rearing and for resting during migration, and the distance between patches is well within the movement capabilities of both juvenile and adult salmon. We found considerable thermal heterogeneity at fine spatial scales that may be important to fish that would be missed if data were analyzed at coarser scales. We estimated future thermal heterogeneity and concluded that climate change will cause warmer temperatures overall, but that thermal heterogeneity patterns may remain similar in the future for many rivers. We demonstrated considerable spatial complexity in both current and future water temperature, and resolved spatial patterns that could not have been perceived without spatially continuous data.

Additive Partitioning of Coral Reef Fish Diversity across Hierarchical Spatial Scales throughout the Caribbean

PubMed Central

Francisco-Ramos, Vanessa; Arias-González, Jesús Ernesto

2013-01-01

There is an increasing need to examine regional patterns of diversity in coral-reef systems since their biodiversity is declining globally. In this sense, additive partitioning might be useful since it quantifies the contribution of alpha and beta to total diversity across different scales. We applied this approach using an unbalanced design across four hierarchical scales (80 sites, 22 subregions, six ecoregions, and the Caribbean basin). Reef-fish species were compiled from the Reef Environmental Education Foundation (REEF) database and distributions were confirmed with published data. Permutation tests were used to compare observed values to those expected by chance. The primary objective was to identify patterns of reef-fish diversity across multiple spatial scales under different scenarios, examining factors such as fisheries and demographic connectivity. Total diversity at the Caribbean scale was attributed to β-diversity (nearly 62% of the species), with the highest β-diversity at the site scale. α¯-diversity was higher than expected by chance in all scenarios and at all studied scales. This suggests that fish assemblages are more homogenous than expected, particularly at the ecoregion scale. Within each ecoregion, diversity was mainly attributed to alpha, except for the Southern ecoregion where there was a greater difference in species among sites. β-components were lower than expected in all ecoregions, indicating that fishes within each ecoregion are a subsample of the same species pool. The scenario involving the effects of fisheries showed a shift in dominance for β-diversity from regions to subregions, with no major changes to the diversity patterns. In contrast, demographic connectivity partially explained the diversity pattern. β-components were low within connectivity regions and higher than expected by chance when comparing between them. Our results highlight the importance of ecoregions as a spatial scale to conserve local and regional coral reef-fish diversity. PMID:24205311

Geostatistics and Geographic Information System to Analyze the Spatial Distribution of the Diversity of Anastrepha Species (Diptera: Tephritidae): the Effect of Forest Fragments in an Urban Area.

PubMed

Garcia, A G; Araujo, M R; Uramoto, K; Walder, J M M; Zucchi, R A

2017-12-08

Fruit flies are among the most damaging insect pests of commercial fruit in Brazil. It is important to understand the landscape elements that may favor these flies. In the present study, spatial data from surveys of species of Anastrepha Schiner (Diptera: Tephritidae) in an urban area with forest fragments were analyzed, using geostatistics and Geographic Information System (GIS) to map the diversity of insects and evaluate how the forest fragments drive the spatial patterns. The results indicated a high diversity of species associated with large fragments, and a trend toward lower diversity in the more urbanized area, as the fragment sizes decreased. We concluded that the diversity of Anastrepha species is directly and positively related to large and continuous forest fragments in urbanized areas, and that combining geostatistics and GIS is a promising method for use in insect-pest management and sampling involving fruit flies. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Stochastic and deterministic processes regulate spatio-temporal variation in seed bank diversity

Treesearch

Alejandro A. Royo; Todd E. Ristau

2013-01-01

Seed banks often serve as reservoirs of taxonomic and genetic diversity that buffer plant populations and influence post-disturbance vegetation trajectories; yet evaluating their importance requires understanding how their composition varies within and across spatial and temporal scales (α- and β-diversity). Shifts in seed bank diversity are strongly...

Selective extinction drives taxonomic and functional alpha and beta diversities in island bird assemblages.

PubMed

Si, Xingfeng; Baselga, Andrés; Leprieur, Fabien; Song, Xiao; Ding, Ping

2016-03-01

Taxonomic diversity considers all species being equally different from each other and thus disregards species' different ecological functions. Exploring taxonomic and functional aspects of biodiversity simultaneously can better understand the processes of community assembly. We analysed taxonomic and functional alpha and beta diversities of breeding bird assemblages on land-bridge islands in the Thousand Island Lake, China. Given the high dispersal ability of most birds at this spatial scale (several kilometres), we predicted (i) selective extinction driving alpha and beta diversities after the creation of land-bridge islands of varying area and (ii) low taxonomic and functional beta diversities that were not correlated to spatial distance. Breeding birds were surveyed on 37 islands annually from 2007 to 2014. We decomposed beta diversity of breeding birds into spatial turnover and nestedness-resultant components, and related taxonomic and functional diversities to island area and isolation using power regression models (for alpha diversity) and multiple regression models on distance matrices (for beta diversity). We then ran simulations to assess the strength of the correlations between taxonomic and functional diversities. Results revealed that both taxonomic and functional alpha diversities increased with island area. The taxonomic nestedness-resultant and turnover components increased and decreased with difference in area, respectively, but functional counterparts did not. Isolation played a minor role in explaining alpha- and beta-diversity patterns. By partitioning beta diversity, we found low levels of overall taxonomic and functional beta diversities. The functional nestedness-resultant component dominated overall functional beta diversity, whereas taxonomic turnover was the dominant component for taxonomic beta diversity. The simulation showed that functional alpha and beta diversities were significantly correlated with taxonomic diversities, and the observed values of correlations were significantly different from null expectations of random extinction. Our assessment of island bird assemblages validated the predictions of no distance effects and low beta diversity due to pervasive dispersal events among islands and also suggested that selective extinction drives taxonomic and functional alpha and beta diversities. The contrasting turnover and nestedness-resultant components of taxonomic and functional beta diversities demonstrate the importance of considering the multifaceted nature of biodiversity when examining community assembly. © 2015 The Authors. Journal of Animal Ecology © 2015 British Ecological Society.

Dispersal responses override density effects on genetic diversity during post-disturbance succession

PubMed Central

Landguth, Erin L.; Bull, C. Michael; Banks, Sam C.; Gardner, Michael G.; Driscoll, Don A.

2016-01-01

Dispersal fundamentally influences spatial population dynamics but little is known about dispersal variation in landscapes where spatial heterogeneity is generated predominantly by disturbance and succession. We tested the hypothesis that habitat succession following fire inhibits dispersal, leading to declines over time in genetic diversity in the early successional gecko Nephrurus stellatus. We combined a landscape genetics field study with a spatially explicit simulation experiment to determine whether successional patterns in genetic diversity were driven by habitat-mediated dispersal or demographic effects (declines in population density leading to genetic drift). Initial increases in genetic structure following fire were likely driven by direct mortality and rapid population expansion. Subsequent habitat succession increased resistance to gene flow and decreased dispersal and genetic diversity in N. stellatus. Simulated changes in population density alone did not reproduce these results. Habitat-mediated reductions in dispersal, combined with changes in population density, were essential to drive the field-observed patterns. Our study provides a framework for combining demographic, movement and genetic data with simulations to discover the relative influence of demography and dispersal on patterns of landscape genetic structure. Our results suggest that succession can inhibit connectivity among individuals, opening new avenues for understanding how disturbance regimes influence spatial population dynamics. PMID:27009225

Floral abundance, richness, and spatial distribution drive urban garden bee communities.

PubMed

Plascencia, M; Philpott, S M

2017-10-01

In urban landscapes, gardens provide refuges for bee diversity, but conservation potential may depend on local and landscape features. Foraging and population persistence of bee species, as well as overall pollinator community structure, may be supported by the abundance, richness, and spatial distribution of floral resources. Floral resources strongly differ in urban gardens. Using hand netting and pan traps to survey bees, we examined whether abundance, richness, and spatial distribution of floral resources, as well as ground cover and garden landscape surroundings influence bee abundance, species richness, and diversity on the central coast of California. Differences in floral abundance and spatial distribution, as well as urban cover in the landscape, predicted different bee community variables. Abundance of all bees and of honeybees (Apis mellifera) was lower in sites with more urban land cover surrounding the gardens. Honeybee abundance was higher in sites with patchy floral resources, whereas bee species richness and bee diversity was higher in sites with more clustered floral resources. Surprisingly, bee species richness and bee diversity was lower in sites with very high floral abundance, possibly due to interactions with honeybees. Other studies have documented the importance of floral abundance and landscape surroundings for bees in urban gardens, but this study is the first to document that the spatial arrangement of flowers strongly predicts bee abundance and richness. Based on these findings, it is likely that garden managers may promote bee conservation by managing for floral connectivity and abundance within these ubiquitous urban habitats.

The Interaction of CuS and Halothiobacillus HT1 Biofilm in Microscale Using Synchrotron Radiation-Based Techniques

PubMed Central

Lin, Huirong; Chen, Guangcun; Zhu, Shenhai; Chen, Yingxu; Chen, Dongliang; Xu, Wei; Yu, Xiaohan; Shi, Jiyan

2013-01-01

In order to investigate the microbe-mineral interaction in the micro scale, spatial distribution and speciation of Cu and S in Halothiobacillus HT1 biofilm formed on a CuS surface was examined using synchrotron-based X-ray techniques. Confocal laser scanning microscope (CLSM) results indicated that Halothiobacillus HT1 biofilm formation gave rise to distinct chemical and redox gradients, leading to diverse niches in the biofilm. Live cells were distributed at the air-biofilm and membrane-biofilm interface. CuS was oxidized by Halothiobacillus HT1 biofilm, and copper penetrated into the biofilm. Sulfide was oxidized to cysteine (77.3%), sulfite (3.8%) and sulfonate (18.9%). Cu-cysteine-like species were involved in the copper homeostasis. These results significantly improve our understanding of the interfacial properties of the biofilm-mineral interface. PMID:23708108

Electrophysiological models of neural processing.

PubMed

Nelson, Mark E

2011-01-01

The brain is an amazing information processing system that allows organisms to adaptively monitor and control complex dynamic interactions with their environment across multiple spatial and temporal scales. Mathematical modeling and computer simulation techniques have become essential tools in understanding diverse aspects of neural processing ranging from sub-millisecond temporal coding in the sound localization circuity of barn owls to long-term memory storage and retrieval in humans that can span decades. The processing capabilities of individual neurons lie at the core of these models, with the emphasis shifting upward and downward across different levels of biological organization depending on the nature of the questions being addressed. This review provides an introduction to the techniques for constructing biophysically based models of individual neurons and local networks. Topics include Hodgkin-Huxley-type models of macroscopic membrane currents, Markov models of individual ion-channel currents, compartmental models of neuronal morphology, and network models involving synaptic interactions among multiple neurons.

Quantitative ultrasonic evaluation of concrete structures using one-sided access

NASA Astrophysics Data System (ADS)

Khazanovich, Lev; Hoegh, Kyle

2016-02-01

Nondestructive diagnostics of concrete structures is an important and challenging problem. A recent introduction of array ultrasonic dry point contact transducer systems offers opportunities for quantitative assessment of the subsurface condition of concrete structures, including detection of defects and inclusions. The methods described in this paper are developed for signal interpretation of shear wave impulse response time histories from multiple fixed distance transducer pairs in a self-contained ultrasonic linear array. This included generalizing Kirchoff migration-based synthetic aperture focusing technique (SAFT) reconstruction methods to handle the spatially diverse transducer pair locations, creating expanded virtual arrays with associated reconstruction methods, and creating automated reconstruction interpretation methods for reinforcement detection and stochastic flaw detection. Interpretation of the reconstruction techniques developed in this study were validated using the results of laboratory and field forensic studies. Applicability of the developed methods for solving practical engineering problems was demonstrated.

Prey dispersal rate affects prey species composition and trait diversity in response to multiple predators in metacommunities.

PubMed

Howeth, Jennifer G; Leibold, Mathew A

2010-09-01

1. Recent studies indicate that large-scale spatial processes can alter local community structuring mechanisms to determine local and regional assemblages of predators and their prey. In metacommunities, this may occur when the functional diversity represented in the regional predator species pool interacts with the rate of prey dispersal among local communities to affect prey species diversity and trait composition at multiple scales. 2. Here, we test for effects of prey dispersal rate and spatially and temporally heterogeneous predation from functionally dissimilar predators on prey structure in pond mesocosm metacommunities. An experimental metacommunity consisted of three pond mesocosm communities supporting two differentially size-selective invertebrate predators and their zooplankton prey. In each metacommunity, two communities maintained constant predation and supported either Gyrinus sp. (Coleoptera) or Notonecta ungulata (Hemiptera) predators generating a spatial prey refuge while the third community supported alternating predation from Gyrinus sp. and N. ungulata generating a temporal prey refuge. Mesocosm metacommunities were connected at either low (0.7% day(-1)) or high (10% day(-1)) planktonic prey dispersal. The diversity, composition and body size of zooplankton prey were measured at local and regional (metacommunity) scales. 3. Metacommunities experiencing the low prey dispersal rate supported the greatest regional prey species diversity (H') and evenness (J'). Neither dispersal rate nor predation regime affected local prey diversity or evenness. The spatial prey refuge at low dispersal maintained the largest difference in species composition and body size diversity between communities under Gyrinus and Notonecta predation, suggesting that species sorting was operating at the low dispersal rate. There was no effect of dispersal rate on species diversity or body size distribution in the temporal prey refuge. 4. The frequency distribution, but not the range, of prey body sizes within communities depended upon prey dispersal rate and predator identity. Taken together, these results demonstrate that prey dispersal rate can moderate the strength of predation to influence prey species diversity and the local frequency distribution of prey traits in metacommunities supporting ecologically different predators.

Projecting malaria hazard from climate change in eastern Africa using large ensembles to estimate uncertainty.

PubMed

Leedale, Joseph; Tompkins, Adrian M; Caminade, Cyril; Jones, Anne E; Nikulin, Grigory; Morse, Andrew P

2016-03-31

The effect of climate change on the spatiotemporal dynamics of malaria transmission is studied using an unprecedented ensemble of climate projections, employing three diverse bias correction and downscaling techniques, in order to partially account for uncertainty in climate- driven malaria projections. These large climate ensembles drive two dynamical and spatially explicit epidemiological malaria models to provide future hazard projections for the focus region of eastern Africa. While the two malaria models produce very distinct transmission patterns for the recent climate, their response to future climate change is similar in terms of sign and spatial distribution, with malaria transmission moving to higher altitudes in the East African Community (EAC) region, while transmission reduces in lowland, marginal transmission zones such as South Sudan. The climate model ensemble generally projects warmer and wetter conditions over EAC. The simulated malaria response appears to be driven by temperature rather than precipitation effects. This reduces the uncertainty due to the climate models, as precipitation trends in tropical regions are very diverse, projecting both drier and wetter conditions with the current state-of-the-art climate model ensemble. The magnitude of the projected changes differed considerably between the two dynamical malaria models, with one much more sensitive to climate change, highlighting that uncertainty in the malaria projections is also associated with the disease modelling approach.

A phylogenetic perspective on species diversity, β-diversity and biogeography for the microbial world.

PubMed

Barberán, Albert; Casamayor, Emilio O

2014-12-01

There is an increasing interest to combine phylogenetic data with distributional and ecological records to assess how natural communities arrange under an evolutionary perspective. In the microbial world, there is also a need to go beyond the problematic species definition to deeply explore ecological patterns using genetic data. We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high-altitude lakes district data set. We described phylogenetic community composition, spatial distribution, and β-diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition. High-altitude lakes districts usually contain a large mosaic of highly diverse small water bodies and conform a fine biogeographical model of spatially close but environmentally heterogeneous ecosystems. We sampled 18 lakes in the Pyrenees with a selection criteria focused on capturing the maximum environmental variation within the smallest geographical area. The results showed highly diverse communities nonrandomly distributed with phylogenetic β-diversity patterns mainly shaped by the environment and not by the spatial distance. Community similarity based on both bacterial taxonomic composition and phylogenetic β-diversity shared similar patterns and was primarily structured by similar environmental drivers. We observed a positive relationship between lake area and phylogenetic diversity with a slope consistent with highly dispersive planktonic organisms. The phylogenetic approach incorporated patterns of common ancestry into bacterial community analysis and emerged as a very convenient analytical tool for direct inter- and intrabiome biodiversity comparisons and sorting out microbial habitats with potential application in conservation studies. © 2014 John Wiley & Sons Ltd.

Disturbance, neutral theory, and patterns of beta diversity in soil communities.

PubMed

Maaß, Stefanie; Migliorini, Massimo; Rillig, Matthias C; Caruso, Tancredi

2014-12-01

Beta diversity describes how local communities within an area or region differ in species composition/abundance. There have been attempts to use changes in beta diversity as a biotic indicator of disturbance, but lack of theory and methodological caveats have hampered progress. We here propose that the neutral theory of biodiversity plus the definition of beta diversity as the total variance of a community matrix provide a suitable, novel, starting point for ecological applications. Observed levels of beta diversity (BD) can be compared to neutral predictions with three possible outcomes: Observed BD equals neutral prediction or is larger (divergence) or smaller (convergence) than the neutral prediction. Disturbance might lead to either divergence or convergence, depending on type and strength. We here apply these ideas to datasets collected on oribatid mites (a key, very diverse soil taxon) under several regimes of disturbances. When disturbance is expected to increase the heterogeneity of soil spatial properties or the sampling strategy encompassed a range of diverging environmental conditions, we observed diverging assemblages. On the contrary, we observed patterns consistent with neutrality when disturbance could determine homogenization of soil properties in space or the sampling strategy encompassed fairly homogeneous areas. With our method, spatial and temporal changes in beta diversity can be directly and easily monitored to detect significant changes in community dynamics, although the method itself cannot inform on underlying mechanisms. However, human-driven disturbances and the spatial scales at which they operate are usually known. In this case, our approach allows the formulation of testable predictions in terms of expected changes in beta diversity, thereby offering a promising monitoring tool.

Exploring links between greenspace and sudden unexpected death: A spatial analysis.

PubMed

Wu, Jianyong; Rappazzo, Kristen M; Simpson, Ross J; Joodi, Golsa; Pursell, Irion W; Mounsey, J Paul; Cascio, Wayne E; Jackson, Laura E

2018-04-01

Greenspace has been increasingly recognized as having numerous health benefits. However, its effects are unknown concerning sudden unexpected death (SUD), commonly referred to as sudden cardiac death, which constitutes a large proportion of mortality in the United States. Because greenspace can promote physical activity, reduce stress and buffer air pollutants, it may have beneficial effects for people at risk of SUD, such as those with heart disease, hypertension, and diabetes mellitus. Using several spatial techniques, this study explored the relationship between SUD and greenspace. We adjudicated 396 SUD cases that occurred from March 2013 to February 2015 among reports from emergency medical services (EMS) that attended out-of-hospital deaths in Wake County (central North Carolina, USA). We measured multiple greenspace metrics in each census tract, including the percentages of forest, grassland, average tree canopy, tree canopy diversity, near-road tree canopy and greenway density. The associations between SUD incidence and these greenspace metrics were examined using Poisson regression (non-spatial) and Bayesian spatial models. The results from both models indicated that SUD incidence was inversely associated with both greenway density (adjusted risk ratio [RR] = 0.82, 95% credible/ confidence interval [CI]: 0.69-0.97) and the percentage of forest (adjusted RR = 0.90, 95% CI: 0.81-0.99). These results suggest that increases in greenway density by 1 km/km 2 and in forest by 10% were associated with a decrease in SUD risk of 18% and 10%, respectively. The inverse relationship was not observed between SUD incidence and other metrics, including grassland, average tree canopy, near-road tree canopy and tree canopy diversity. This study implies that greenspace, specifically greenways and forest, may have beneficial effects for people at risk of SUD. Further studies are needed to investigate potential causal relationships between greenspace and SUD, and potential mechanisms such as promoting physical activity and reducing stress. Copyright © 2018 Elsevier Ltd. All rights reserved.

Robust frequency diversity based algorithm for clutter noise reduction of ultrasonic signals using multiple sub-spectrum phase coherence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gongzhang, R.; Xiao, B.; Lardner, T.

2014-02-18

This paper presents a robust frequency diversity based algorithm for clutter reduction in ultrasonic A-scan waveforms. The performance of conventional spectral-temporal techniques like Split Spectrum Processing (SSP) is highly dependent on the parameter selection, especially when the signal to noise ratio (SNR) is low. Although spatial beamforming offers noise reduction with less sensitivity to parameter variation, phased array techniques are not always available. The proposed algorithm first selects an ascending series of frequency bands. A signal is reconstructed for each selected band in which a defect is present when all frequency components are in uniform sign. Combining all reconstructed signalsmore » through averaging gives a probability profile of potential defect position. To facilitate data collection and validate the proposed algorithm, Full Matrix Capture is applied on the austenitic steel and high nickel alloy (HNA) samples with 5MHz transducer arrays. When processing A-scan signals with unrefined parameters, the proposed algorithm enhances SNR by 20dB for both samples and consequently, defects are more visible in B-scan images created from the large amount of A-scan traces. Importantly, the proposed algorithm is considered robust, while SSP is shown to fail on the austenitic steel data and achieves less SNR enhancement on the HNA data.« less

Nonrandom community assembly and high temporal turnover promote regional coexistence in tropics but not temperate zone.

PubMed

Freestone, Amy L; Inouye, Brian D

2015-01-01

A persistent challenge for ecologists is understanding the ecological mechanisms that maintain global patterns of biodiversity, particularly the latitudinal diversity gradient of peak species richness in the tropics. Spatial and temporal variation in community composition contribute to these patterns of biodiversity, but how this variation and its underlying processes change across latitude remains unresolved. Using a model system of sessile marine invertebrates across 25 degrees of latitude, from the temperate zone to the tropics, we tested the prediction that spatial and temporal patterns of taxonomic richness and composition, and the community assembly processes underlying these patterns, will differ across latitude. Specifically, we predicted that high beta diversity (spatial variation in composition) and high temporal turnover contribute to the high species richness of the tropics. Using a standardized experimental approach that controls for several confounding factors that hinder interpretation of prior studies, we present results that support our predictions. In the temperate zone, communities were more similar across spatial scales from centimeters to tens of kilometers and temporal scales up to one year than at lower latitudes. Since the patterns at northern latitudes were congruent with a null model, stochastic assembly processes are implicated. In contrast, the communities in the tropics were a dynamic spatial and temporal mosaic, with low similarity even across small spatial scales and high temporal turnover at both local and regional scales. Unlike the temperate zone, deterministic community assembly processes such as predation likely contributed to the high beta diversity in the tropics. Our results suggest that community assembly processes and temporal dynamics vary across latitude and help structure and maintain latitudinal patterns of diversity.

The evolution of a Müllerian mimic in a spatially distributed community.

PubMed

Joron, Mathieu; Iwasa, Yoh

2005-11-07

Strong positive density-dependence should lead to a loss of diversity, but warning-colour and Müllerian mimicry systems show extraordinary levels of diversity. Here, we propose an analytical model to explore the dynamics of two forms of a Müllerian mimic in a heterogeneous environment with two alternative model species. Two connected populations of a dimorphic, chemically defended mimic are allowed to evolve and disperse. The proportions of the respective model species vary spatially. We use a nonlinear approximation of Müller's number-dependent equations to model a situation where the mortality for either form of the mimic decreases hyberbolically when its local density increases. A first non-spatial analysis confirms that the positive density-dependence makes coexistence of mimetic forms unstable in a single isolated patch, but shows that mimicry of the rarer model can be stable once established. The two-patch analysis shows that when models have different abundance in different places, local mimetic diversity in the mimic is maintained only if spatial heterogeneity is strong, or, more interestingly, if the mimic is not too strongly distasteful. Therefore, mildly toxic species can become polymorphic in a wider range of ecological settings. Spatial dynamics thus reveal a region of Müllerian polymorphism separating classical Batesian polymorphism and Müllerian monomorphism along the mimic's palatability spectrum. Such polymorphism-palatability relationship in a spatial environment provides a parsimonious hypothesis accounting for the observed Müllerian polymorphism that does not require quasi-Batesian dynamics. While the stability of coexistence depends on all factors, only the migration rate and strength of selection appear to affect the level of diversity at the polymorphic equilibrium. Local adaptation is predicted in most polymorphic cases. These results are in very good accordance with recent empirical findings on the polymorphic butterflies Heliconius numata and H. cydno.

Spatial heterogeneity of physicochemical properties explains differences in microbial composition in arid soils from Cuatro Cienegas, Mexico

PubMed Central

Pajares, Silvia; Noguez, Ana M.; García-Oliva, Felipe; Martínez-Piedragil, Celeste; Cram, Silke S.; Eguiarte, Luis Enrique; Souza, Valeria

2016-01-01

Arid ecosystems are characterized by high spatial heterogeneity, and the variation among vegetation patches is a clear example. Soil biotic and abiotic factors associated with these patches have also been well documented as highly heterogeneous in space. Given the low vegetation cover and little precipitation in arid ecosystems, soil microorganisms are the main drivers of nutrient cycling. Nonetheless, little is known about the spatial distribution of microorganisms and the relationship that their diversity holds with nutrients and other physicochemical gradients in arid soils. In this study, we evaluated the spatial variability of soil microbial diversity and chemical parameters (nutrients and ion content) at local scale (meters) occurring in a gypsum-based desert soil, to gain knowledge on what soil abiotic factors control the distribution of microbes in arid ecosystems. We analyzed 32 soil samples within a 64 m2 plot and: (a) characterized microbial diversity using T-RFLPs of the bacterial 16S rRNA gene, (b) determined soil chemical parameters, and (c) identified relationships between microbial diversity and chemical properties. Overall, we found a strong correlation between microbial composition heterogeneity and spatial variation of cations (Ca2, K+) and anions (HCO\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}${}_{3}^{-}$\\end{document}3−, Cl−, SO\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}${}_{4}^{2-}$\\end{document}42−) content in this small plot. Our results could be attributable to spatial differences of soil saline content, favoring the patchy emergence of salt and soil microbial communities. PMID:27652001

Regional variation in the hierarchical partitioning of diversity in coral-dwelling fishes.

PubMed

Belmaker, Jonathan; Ziv, Yaron; Shashar, Nadav; Connolly, Sean R

2008-10-01

The size of the regional species pool may influence local patterns of diversity. However, it is unclear whether certain spatial scales are less sensitive to regional influences than others. Additive partitioning was used to separate coral-dwelling fish diversity to its alpha and beta components, at multiple scales, in several regions across the Indo-Pacific. We then examined how the relative contribution of these components changes with increased regional diversity. By employing specific random-placement null models, we overcome methodological problems with local-regional regressions. We show that, although alpha and beta diversities within each region are consistently different from random-placement null models, the increase in beta diversities among regions was similar to that predicted once heterogeneity in coral habitat was accounted for. In contrast, alpha diversity within single coral heads was limited and increased less than predicted by the null models. This was correlated with increased intraspecific aggregation in more diverse regions and is consistent with ecological limitations on the number of coexisting species at the local scale. These results suggest that, apart from very small spatial scales, variation in the partitioning of fish diversity along regional species richness gradients is driven overwhelmingly by the corresponding gradients in coral assemblage structure.

Local loss and spatial homogenization of plant diversity reduce ecosystem multifunctionality.

PubMed

Hautier, Yann; Isbell, Forest; Borer, Elizabeth T; Seabloom, Eric W; Harpole, W Stanley; Lind, Eric M; MacDougall, Andrew S; Stevens, Carly J; Adler, Peter B; Alberti, Juan; Bakker, Jonathan D; Brudvig, Lars A; Buckley, Yvonne M; Cadotte, Marc; Caldeira, Maria C; Chaneton, Enrique J; Chu, Chengjin; Daleo, Pedro; Dickman, Christopher R; Dwyer, John M; Eskelinen, Anu; Fay, Philip A; Firn, Jennifer; Hagenah, Nicole; Hillebrand, Helmut; Iribarne, Oscar; Kirkman, Kevin P; Knops, Johannes M H; La Pierre, Kimberly J; McCulley, Rebecca L; Morgan, John W; Pärtel, Meelis; Pascual, Jesus; Price, Jodi N; Prober, Suzanne M; Risch, Anita C; Sankaran, Mahesh; Schuetz, Martin; Standish, Rachel J; Virtanen, Risto; Wardle, Glenda M; Yahdjian, Laura; Hector, Andy

2018-01-01

Biodiversity is declining in many local communities while also becoming increasingly homogenized across space. Experiments show that local plant species loss reduces ecosystem functioning and services, but the role of spatial homogenization of community composition and the potential interaction between diversity at different scales in maintaining ecosystem functioning remains unclear, especially when many functions are considered (ecosystem multifunctionality). We present an analysis of eight ecosystem functions measured in 65 grasslands worldwide. We find that more diverse grasslands-those with both species-rich local communities (α-diversity) and large compositional differences among localities (β-diversity)-had higher levels of multifunctionality. Moreover, α- and β-diversity synergistically affected multifunctionality, with higher levels of diversity at one scale amplifying the contribution to ecological functions at the other scale. The identity of species influencing ecosystem functioning differed among functions and across local communities, explaining why more diverse grasslands maintained greater functionality when more functions and localities were considered. These results were robust to variation in environmental drivers. Our findings reveal that plant diversity, at both local and landscape scales, contributes to the maintenance of multiple ecosystem services provided by grasslands. Preserving ecosystem functioning therefore requires conservation of biodiversity both within and among ecological communities.

Propagation phasor approach for holographic image reconstruction

PubMed Central

Luo, Wei; Zhang, Yibo; Göröcs, Zoltán; Feizi, Alborz; Ozcan, Aydogan

2016-01-01

To achieve high-resolution and wide field-of-view, digital holographic imaging techniques need to tackle two major challenges: phase recovery and spatial undersampling. Previously, these challenges were separately addressed using phase retrieval and pixel super-resolution algorithms, which utilize the diversity of different imaging parameters. Although existing holographic imaging methods can achieve large space-bandwidth-products by performing pixel super-resolution and phase retrieval sequentially, they require large amounts of data, which might be a limitation in high-speed or cost-effective imaging applications. Here we report a propagation phasor approach, which for the first time combines phase retrieval and pixel super-resolution into a unified mathematical framework and enables the synthesis of new holographic image reconstruction methods with significantly improved data efficiency. In this approach, twin image and spatial aliasing signals, along with other digital artifacts, are interpreted as noise terms that are modulated by phasors that analytically depend on the lateral displacement between hologram and sensor planes, sample-to-sensor distance, wavelength, and the illumination angle. Compared to previous holographic reconstruction techniques, this new framework results in five- to seven-fold reduced number of raw measurements, while still achieving a competitive resolution and space-bandwidth-product. We also demonstrated the success of this approach by imaging biological specimens including Papanicolaou and blood smears. PMID:26964671

Novel approach to real-time flash photolysis and confocal [Ca2+] imaging

PubMed Central

Sobie, Eric A.; Kao, Joseph P.Y.; Lederer, W. J.

2008-01-01

Flash photolysis of “caged” compounds using ultraviolet light is a powerful experimental technique for producing rapid changes in concentrations of bioactive signaling molecules. Studies that employ this technique have used diverse strategies for controlling the spatial and temporal application of light to the specimen. Here we describe a new system for flash photolysis that delivers light from a pulsed, adjustable intensity laser through an optical fiber coupled into the epifluorescence port of a commercial confocal microscope. Photolysis is achieved with extremely brief (5 ns) pulses of ultraviolet light (355 nm) that can be synchronized with respect to confocal laser scanning. The system described also localizes the UV intensity spatially so that uncaging only occurs in defined sub-cellular regions; moreover, since the microscope optics are used in localization, the photolysis volume can be easily adjusted. Experiments performed on rat ventricular myocytes loaded with the Ca2+ indicator fluo-3 and the Ca2+ cage NP-EGTA demonstrate the system's capabilities. Localized intracellular increases in [Ca2+] can trigger sarcoplasmic reticular Ca2+ release events such as Ca2+ sparks and, under certain conditions, regenerative Ca2+ waves. This relatively simple and inexpensive system is therefore a useful tool for examining local signaling in heart and other tissues. PMID:17323075

Hyperspectral range imaging for transportation systems evaluation

NASA Astrophysics Data System (ADS)

Bridgelall, Raj; Rafert, J. B.; Atwood, Don; Tolliver, Denver D.

2016-04-01

Transportation agencies expend significant resources to inspect critical infrastructure such as roadways, railways, and pipelines. Regular inspections identify important defects and generate data to forecast maintenance needs. However, cost and practical limitations prevent the scaling of current inspection methods beyond relatively small portions of the network. Consequently, existing approaches fail to discover many high-risk defect formations. Remote sensing techniques offer the potential for more rapid and extensive non-destructive evaluations of the multimodal transportation infrastructure. However, optical occlusions and limitations in the spatial resolution of typical airborne and space-borne platforms limit their applicability. This research proposes hyperspectral image classification to isolate transportation infrastructure targets for high-resolution photogrammetric analysis. A plenoptic swarm of unmanned aircraft systems will capture images with centimeter-scale spatial resolution, large swaths, and polarization diversity. The light field solution will incorporate structure-from-motion techniques to reconstruct three-dimensional details of the isolated targets from sequences of two-dimensional images. A comparative analysis of existing low-power wireless communications standards suggests an application dependent tradeoff in selecting the best-suited link to coordinate swarming operations. This study further produced a taxonomy of specific roadway and railway defects, distress symptoms, and other anomalies that the proposed plenoptic swarm sensing system would identify and characterize to estimate risk levels.

Insights into metals in individual fine particles from municipal solid waste using synchrotron radiation-based micro-analytical techniques.

PubMed

Zhu, Yumin; Zhang, Hua; Shao, Liming; He, Pinjing

2015-01-01

Excessive inter-contamination with heavy metals hampers the application of biological treatment products derived from mixed or mechanically-sorted municipal solid waste (MSW). In this study, we investigated fine particles of <2mm, which are small fractions in MSW but constitute a significant component of the total heavy metal content, using bulk detection techniques. A total of 17 individual fine particles were evaluated using synchrotron radiation-based micro-X-ray fluorescence and micro-X-ray diffraction. We also discussed the association, speciation and source apportionment of heavy metals. Metals were found to exist in a diffuse distribution with heterogeneous intensities and intense hot-spots of <10 μm within the fine particles. Zn-Cu, Pb-Fe and Fe-Mn-Cr had significant correlations in terms of spatial distribution. The overlapped enrichment, spatial association, and the mineral phases of metals revealed the potential sources of fine particles from size-reduced waste fractions (such as scraps of organic wastes or ceramics) or from the importation of other particles. The diverse sources of heavy metal pollutants within the fine particles suggested that separate collection and treatment of the biodegradable waste fraction (such as food waste) is a preferable means of facilitating the beneficial utilization of the stabilized products. Copyright © 2014. Published by Elsevier B.V.

International Watershed Technology: Improving Water Quality and Quantity at the Local, Basin, and Regional Scales

USGS Publications Warehouse

Tollner, Ernest W.; Douglas-Mankin, Kyle R.

2017-01-01

This article introduces the five papers in the “International Watershed Technology” collection. These papers were selected from 60 technical presentations at the fifth biennial ASABE 21st Century Watershed Technology Conference and Workshop: Improving the Quality of Water Resources at Local, Basin, and Regional Scales, held in Quito, Ecuador, on 3-9 December 2016. The conference focused on solving spatial and temporal water quality and quantity problems and addressed topics such as watershed management in developing countries, aquatic ecology and ecohydrology, ecosystem services, climate change mitigation strategies, flood forecasting, remote sensing, and water resource policy and management. While diverse, the presentation topics reflected the continuing evolution of the “data mining” and “big data” themes of past conferences related to geospatial data applications, with increasing emphasis on practical solutions. The papers selected for this collection represent applications of spatial data analyses toward practical ends with a theme of “tools and techniques for sustainability.” The papers address a range of topics, including the matching of crops with water availability, and assessing the environmental impacts of agricultural production. The papers identify some of the latest tools and techniques for improving sustainability in watershed resource management that are relevant to both developing and developed countries.

Applicability of Montreal Process Criterion 1 - conservation of biological diversity - to rangeland sustainability

Treesearch

Curtis H. Flather; Carolyn Hull Sieg

2000-01-01

Nine indicators of biodiversity conservation have been defined by the nations participating in the Montreal Process for assessing sustainability of temperate and boreal forests. Five of these indicators address compositional and spatial diversity of ecosystems; two address species diversity; and two are indirect measures of genetic diversity. Our objective was to...

Monitoring tree secies diversity over large spatial and temporal scales

Treesearch

James F. Rosson; Clifford C. Amundsen

2004-01-01

The prospect of decline in biological diversity has become a central concern in the life sciences, both around the world and across the United States. Anthropogenic disturbance has been identified as a major factor affecting species diversity trends. An increase in the harvesting of naturally diverse timber stands in the South has become an important issue. The...

Predicting temporal variation in zooplankton beta diversity is challenging

PubMed Central

Castelo Branco, Christina W.; Kozlowsky-Suzuki, Betina; Sousa-Filho, Izidro F.; Souza, Leonardo Coimbra e; Bini, Luis Mauricio

2017-01-01

Beta diversity, the spatial variation in species composition, has been related to different explanatory variables, including environmental heterogeneity, productivity and connectivity. Using a long-term time series of zooplankton data collected over 62 months in a tropical reservoir (Ribeirão das Lajes Reservoir, Rio de Janeiro State, Brazil), we tested whether beta diversity (as measured across six sites distributed along the main axis of the reservoir) was correlated with environmental heterogeneity (spatial environmental variation in a given month), chlorophyll-a concentration (a surrogate for productivity) and water level. We did not found evidence for the role of these predictors, suggesting the need to reevaluate predictions or at least to search for better surrogates of the processes that hypothetically control beta diversity variation. However, beta diversity declined over time, which is consistent with the process of biotic homogenization, a worldwide cause of concern. PMID:29095892

Predicting temporal variation in zooplankton beta diversity is challenging.

PubMed

Lopes, Vanessa Guimarães; Castelo Branco, Christina W; Kozlowsky-Suzuki, Betina; Sousa-Filho, Izidro F; Souza, Leonardo Coimbra E; Bini, Luis Mauricio

2017-01-01

Beta diversity, the spatial variation in species composition, has been related to different explanatory variables, including environmental heterogeneity, productivity and connectivity. Using a long-term time series of zooplankton data collected over 62 months in a tropical reservoir (Ribeirão das Lajes Reservoir, Rio de Janeiro State, Brazil), we tested whether beta diversity (as measured across six sites distributed along the main axis of the reservoir) was correlated with environmental heterogeneity (spatial environmental variation in a given month), chlorophyll-a concentration (a surrogate for productivity) and water level. We did not found evidence for the role of these predictors, suggesting the need to reevaluate predictions or at least to search for better surrogates of the processes that hypothetically control beta diversity variation. However, beta diversity declined over time, which is consistent with the process of biotic homogenization, a worldwide cause of concern.

Mapping and determinism of soil microbial community distribution across an agricultural landscape.

PubMed

Constancias, Florentin; Terrat, Sébastien; Saby, Nicolas P A; Horrigue, Walid; Villerd, Jean; Guillemin, Jean-Philippe; Biju-Duval, Luc; Nowak, Virginie; Dequiedt, Samuel; Ranjard, Lionel; Chemidlin Prévost-Bouré, Nicolas

2015-06-01

Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

The influence of linear elements on plant species diversity of Mediterranean rural landscapes: assessment of different indices and statistical approaches.

PubMed

García del Barrio, J M; Ortega, M; Vázquez De la Cueva, A; Elena-Rosselló, R

2006-08-01

This paper mainly aims to study the linear element influence on the estimation of vascular plant species diversity in five Mediterranean landscapes modeled as land cover patch mosaics. These landscapes have several core habitats and a different set of linear elements--habitat edges or ecotones, roads or railways, rivers, streams and hedgerows on farm land--whose plant composition were examined. Secondly, it aims to check plant diversity estimation in Mediterranean landscapes using parametric and non-parametric procedures, with two indices: Species richness and Shannon index. Land cover types and landscape linear elements were identified from aerial photographs. Their spatial information was processed using GIS techniques. Field plots were selected using a stratified sampling design according to relieve and tree density of each habitat type. A 50x20 m2 multi-scale sampling plot was designed for the core habitats and across the main landscape linear elements. Richness and diversity of plant species were estimated by comparing the observed field data to ICE (Incidence-based Coverage Estimator) and ACE (Abundance-based Coverage Estimator) non-parametric estimators. The species density, percentage of unique species, and alpha diversity per plot were significantly higher (p < 0.05) in linear elements than in core habitats. ICE estimate of number of species was 32% higher than of ACE estimate, which did not differ significantly from the observed values. Accumulated species richness in core habitats together with linear elements, were significantly higher than those recorded only in the core habitats in all the landscapes. Conversely, Shannon diversity index did not show significant differences.

Processing of spatial and non-spatial information in rats with lesions of the medial and lateral entorhinal cortex: Environmental complexity matters.

PubMed

Rodo, Christophe; Sargolini, Francesca; Save, Etienne

2017-03-01

The entorhinal-hippocampal circuitry has been suggested to play an important role in episodic memory but the contribution of the entorhinal cortex remains elusive. Predominant theories propose that the medial entorhinal cortex (MEC) processes spatial information whereas the lateral entorhinal cortex (LEC) processes non spatial information. A recent study using an object exploration task has suggested that the involvement of the MEC and LEC spatial and non-spatial information processing could be modulated by the amount of information to be processed, i.e. environmental complexity. To address this hypothesis we used an object exploration task in which rats with excitotoxic lesions of the MEC and LEC had to detect spatial and non-spatial novelty among a set of objects and we varied environmental complexity by decreasing the number of objects or amount of object diversity. Reducing diversity resulted in restored ability to process spatial and non-spatial information in MEC and LEC groups, respectively. Reducing the number of objects yielded restored ability to process non-spatial information in the LEC group but not the ability to process spatial information in the MEC group. The findings indicate that the MEC and LEC are not strictly necessary for spatial and non-spatial processing but that their involvement depends on the complexity of the information to be processed. Copyright © 2016 Elsevier B.V. All rights reserved.

Calcium-dependent molecular fMRI using a magnetic nanosensor.

PubMed

Okada, Satoshi; Bartelle, Benjamin B; Li, Nan; Breton-Provencher, Vincent; Lee, Jiyoung J; Rodriguez, Elisenda; Melican, James; Sur, Mriganka; Jasanoff, Alan

2018-06-01

Calcium ions are ubiquitous signalling molecules in all multicellular organisms, where they mediate diverse aspects of intracellular and extracellular communication over widely varying temporal and spatial scales 1 . Though techniques to map calcium-related activity at a high resolution by optical means are well established, there is currently no reliable method to measure calcium dynamics over large volumes in intact tissue 2 . Here, we address this need by introducing a family of magnetic calcium-responsive nanoparticles (MaCaReNas) that can be detected by magnetic resonance imaging (MRI). MaCaReNas respond within seconds to [Ca 2+ ] changes in the 0.1-1.0 mM range, suitable for monitoring extracellular calcium signalling processes in the brain. We show that the probes permit the repeated detection of brain activation in response to diverse stimuli in vivo. MaCaReNas thus provide a tool for calcium-activity mapping in deep tissue and offer a precedent for the development of further nanoparticle-based sensors for dynamic molecular imaging with MRI.

Lipid Cell Biology: A Focus on Lipids in Cell Division.

PubMed

Storck, Elisabeth M; Özbalci, Cagakan; Eggert, Ulrike S

2018-06-20

Cells depend on hugely diverse lipidomes for many functions. The actions and structural integrity of the plasma membrane and most organelles also critically depend on membranes and their lipid components. Despite the biological importance of lipids, our understanding of lipid engagement, especially the roles of lipid hydrophobic alkyl side chains, in key cellular processes is still developing. Emerging research has begun to dissect the importance of lipids in intricate events such as cell division. This review discusses how these structurally diverse biomolecules are spatially and temporally regulated during cell division, with a focus on cytokinesis. We analyze how lipids facilitate changes in cellular morphology during division and how they participate in key signaling events. We identify which cytokinesis proteins are associated with membranes, suggesting lipid interactions. More broadly, we highlight key unaddressed questions in lipid cell biology and techniques, including mass spectrometry, advanced imaging, and chemical biology, which will help us gain insights into the functional roles of lipids.

Calcium-dependent molecular fMRI using a magnetic nanosensor

NASA Astrophysics Data System (ADS)

Okada, Satoshi; Bartelle, Benjamin B.; Li, Nan; Breton-Provencher, Vincent; Lee, Jiyoung J.; Rodriguez, Elisenda; Melican, James; Sur, Mriganka; Jasanoff, Alan

2018-06-01

Calcium ions are ubiquitous signalling molecules in all multicellular organisms, where they mediate diverse aspects of intracellular and extracellular communication over widely varying temporal and spatial scales1. Though techniques to map calcium-related activity at a high resolution by optical means are well established, there is currently no reliable method to measure calcium dynamics over large volumes in intact tissue2. Here, we address this need by introducing a family of magnetic calcium-responsive nanoparticles (MaCaReNas) that can be detected by magnetic resonance imaging (MRI). MaCaReNas respond within seconds to [Ca2+] changes in the 0.1-1.0 mM range, suitable for monitoring extracellular calcium signalling processes in the brain. We show that the probes permit the repeated detection of brain activation in response to diverse stimuli in vivo. MaCaReNas thus provide a tool for calcium-activity mapping in deep tissue and offer a precedent for the development of further nanoparticle-based sensors for dynamic molecular imaging with MRI.

A robot sets a table: a case for hybrid reasoning with different types of knowledge

NASA Astrophysics Data System (ADS)

Mansouri, Masoumeh; Pecora, Federico

2016-09-01

An important contribution of AI to Robotics is the model-centred approach, whereby competent robot behaviour stems from automated reasoning in models of the world which can be changed to suit different environments, physical capabilities and tasks. However models need to capture diverse (and often application-dependent) aspects of the robot's environment and capabilities. They must also have good computational properties, as robots need to reason while they act in response to perceived context. In this article, we investigate the use of a meta-CSP-based technique to interleave reasoning in diverse knowledge types. We reify the approach through a robotic waiter case study, for which a particular selection of spatial, temporal, resource and action KR formalisms is made. Using this case study, we discuss general principles pertaining to the selection of appropriate KR formalisms and jointly reasoning about them. The resulting integration is evaluated both formally and experimentally on real and simulated robotic platforms.

Seed dispersal increases local species richness and reduces spatial turnover of tropical tree seedlings

PubMed Central

Dunham, Amy E.; Duncan, Richard P.; Rogers, Haldre S.

2017-01-01

Dispersal is thought to be a key process underlying the high spatial diversity of tropical forests. Just how important dispersal is in structuring plant communities is nevertheless an open question because it is very difficult to isolate dispersal from other processes, and thereby measure its effect. Using a unique situation, the loss of vertebrate seed dispersers on the island of Guam and their presence on the neighboring islands of Saipan and Rota, we quantify the contribution of vertebrate seed dispersal to spatial patterns of diversity of tree seedlings in treefall gaps. The presence of vertebrate seed dispersers approximately doubled seedling species richness within canopy gaps and halved species turnover among gaps. Our study demonstrates that dispersal plays a key role in maintaining local and regional patterns of diversity, and highlights the potential for ongoing declines in vertebrate seed dispersers to profoundly alter tropical forest composition. PMID:28847937

Seed dispersal increases local species richness and reduces spatial turnover of tropical tree seedlings.

PubMed

Wandrag, Elizabeth M; Dunham, Amy E; Duncan, Richard P; Rogers, Haldre S

2017-10-03

Dispersal is thought to be a key process underlying the high spatial diversity of tropical forests. Just how important dispersal is in structuring plant communities is nevertheless an open question because it is very difficult to isolate dispersal from other processes, and thereby measure its effect. Using a unique situation, the loss of vertebrate seed dispersers on the island of Guam and their presence on the neighboring islands of Saipan and Rota, we quantify the contribution of vertebrate seed dispersal to spatial patterns of diversity of tree seedlings in treefall gaps. The presence of vertebrate seed dispersers approximately doubled seedling species richness within canopy gaps and halved species turnover among gaps. Our study demonstrates that dispersal plays a key role in maintaining local and regional patterns of diversity, and highlights the potential for ongoing declines in vertebrate seed dispersers to profoundly alter tropical forest composition.

Population genomic analysis suggests strong influence of river network on spatial distribution of genetic variation in invasive saltcedar across the southwestern United States

USGS Publications Warehouse

Lee, Soo-Rang; Jo, Yeong-Seok; Park, Chan-Ho; Friedman, Jonathan M.; Olson, Matthew S.

2018-01-01

Understanding the complex influences of landscape and anthropogenic elements that shape the population genetic structure of invasive species provides insight into patterns of colonization and spread. The application of landscape genomics techniques to these questions may offer detailed, previously undocumented insights into factors influencing species invasions. We investigated the spatial pattern of genetic variation and the influences of landscape factors on population similarity in an invasive riparian shrub, saltcedar (Tamarix L.) by analysing 1,997 genomewide SNP markers for 259 individuals from 25 populations collected throughout the southwestern United States. Our results revealed a broad-scale spatial genetic differentiation of saltcedar populations between the Colorado and Rio Grande river basins and identified potential barriers to population similarity along both river systems. River pathways most strongly contributed to population similarity. In contrast, low temperature and dams likely served as barriers to population similarity. We hypothesize that large-scale geographic patterns in genetic diversity resulted from a combination of early introductions from distinct populations, the subsequent influence of natural selection, dispersal barriers and founder effects during range expansion.

Moving GIS Research Indoors: Spatiotemporal Analysis of Agricultural Animals

PubMed Central

Daigle, Courtney L.; Banerjee, Debasmit; Montgomery, Robert A.; Biswas, Subir; Siegford, Janice M.

2014-01-01

A proof of concept applying wildlife ecology techniques to animal welfare science in intensive agricultural environments was conducted using non-cage laying hens. Studies of wildlife ecology regularly use Geographic Information Systems (GIS) to assess wild animal movement and behavior within environments with relatively unlimited space and finite resources. However, rather than depicting landscapes, a GIS could be developed in animal production environments to provide insight into animal behavior as an indicator of animal welfare. We developed a GIS-based approach for studying agricultural animal behavior in an environment with finite space and unlimited resources. Concurrent data from wireless body-worn location tracking sensor and video-recording systems, which depicted spatially-explicit behavior of hens (135 hens/room) in two identical indoor enclosures, were collected. The spatial configuration of specific hen behaviors, variation in home range patterns, and variation in home range overlap show that individual hens respond to the same environment differently. Such information could catalyze management practice adjustments (e.g., modifying feeder design and/or location). Genetically-similar hens exhibited diverse behavioral and spatial patterns via a proof of concept approach enabling detailed examinations of individual non-cage laying hen behavior and welfare. PMID:25098421

Design and implementation of visualization methods for the CHANGES Spatial Decision Support System

NASA Astrophysics Data System (ADS)

Cristal, Irina; van Westen, Cees; Bakker, Wim; Greiving, Stefan

2014-05-01

The CHANGES Spatial Decision Support System (SDSS) is a web-based system aimed for risk assessment and the evaluation of optimal risk reduction alternatives at local level as a decision support tool in long-term natural risk management. The SDSS use multidimensional information, integrating thematic, spatial, temporal and documentary data. The role of visualization in this context becomes of vital importance for efficiently representing each dimension. This multidimensional aspect of the required for the system risk information, combined with the diversity of the end-users imposes the use of sophisticated visualization methods and tools. The key goal of the present work is to exploit efficiently the large amount of data in relation to the needs of the end-user, utilizing proper visualization techniques. Three main tasks have been accomplished for this purpose: categorization of the end-users, the definition of system's modules and the data definition. The graphical representation of the data and the visualization tools were designed to be relevant to the data type and the purpose of the analysis. Depending on the end-users category, each user should have access to different modules of the system and thus, to the proper visualization environment. The technologies used for the development of the visualization component combine the latest and most innovative open source JavaScript frameworks, such as OpenLayers 2.13.1, ExtJS 4 and GeoExt 2. Moreover, the model-view-controller (MVC) pattern is used in order to ensure flexibility of the system at the implementation level. Using the above technologies, the visualization techniques implemented so far offer interactive map navigation, querying and comparison tools. The map comparison tools are of great importance within the SDSS and include the following: swiping tool for comparison of different data of the same location; raster subtraction for comparison of the same phenomena varying in time; linked views for comparison of data from different locations and a time slider tool for monitoring changes in spatio-temporal data. All these techniques are part of the interactive interface of the system and make use of spatial and spatio-temporal data. Further significant aspects of the visualization component include conventional cartographic techniques and visualization of non-spatial data. The main expectation from the present work is to offer efficient visualization of risk-related data in order to facilitate the decision making process, which is the final purpose of the CHANGES SDSS. This work is part of the "CHANGES" project, funded by the European Community's 7th Framework Programme.

Temporal and Spatial Variation of Soil Bacteria Richness, Composition, and Function in a Neotropical Rainforest

PubMed Central

Kivlin, Stephanie N; Hawkes, Christine V

2016-01-01

The high diversity of tree species has traditionally been considered an important controller of belowground processes in tropical rainforests. However, soil water availability and resources are also primary regulators of soil bacteria in many ecosystems. Separating the effects of these biotic and abiotic factors in the tropics is challenging because of their high spatial and temporal heterogeneity. To determine the drivers of tropical soil bacteria, we examined tree species effects using experimental tree monocultures and secondary forests at La Selva Biological Station in Costa Rica. A randomized block design captured spatial variation and we sampled at four dates across two years to assess temporal variation. We measured bacteria richness, phylogenetic diversity, community composition, biomass, and functional potential. All bacteria parameters varied significantly across dates. In addition, bacteria richness and phylogenetic diversity were affected by the interaction of vegetation type and date, whereas bacteria community composition was affected by the interaction of vegetation type and block. Shifts in bacteria community richness and composition were unrelated to shifts in enzyme function, suggesting physiological overlap among taxa. Based on the observed temporal and spatial heterogeneity, our understanding of tropical soil bacteria will benefit from additional work to determine the optimal temporal and spatial scales for sampling. Understanding spatial and temporal variation will facilitate prediction of how tropical soil microbes will respond to future environmental change. PMID:27391450

Temporal and Spatial Variation of Soil Bacteria Richness, Composition, and Function in a Neotropical Rainforest.

PubMed

Kivlin, Stephanie N; Hawkes, Christine V

2016-01-01

The high diversity of tree species has traditionally been considered an important controller of belowground processes in tropical rainforests. However, soil water availability and resources are also primary regulators of soil bacteria in many ecosystems. Separating the effects of these biotic and abiotic factors in the tropics is challenging because of their high spatial and temporal heterogeneity. To determine the drivers of tropical soil bacteria, we examined tree species effects using experimental tree monocultures and secondary forests at La Selva Biological Station in Costa Rica. A randomized block design captured spatial variation and we sampled at four dates across two years to assess temporal variation. We measured bacteria richness, phylogenetic diversity, community composition, biomass, and functional potential. All bacteria parameters varied significantly across dates. In addition, bacteria richness and phylogenetic diversity were affected by the interaction of vegetation type and date, whereas bacteria community composition was affected by the interaction of vegetation type and block. Shifts in bacteria community richness and composition were unrelated to shifts in enzyme function, suggesting physiological overlap among taxa. Based on the observed temporal and spatial heterogeneity, our understanding of tropical soil bacteria will benefit from additional work to determine the optimal temporal and spatial scales for sampling. Understanding spatial and temporal variation will facilitate prediction of how tropical soil microbes will respond to future environmental change.

β-Diversity of Functional Groups of Woody Plants in a Tropical Dry Forest in Yucatan

PubMed Central

López-Martínez, Jorge Omar; Sanaphre-Villanueva, Lucía; Dupuy, Juan Manuel; Hernández-Stefanoni, José Luis; Meave, Jorge Arturo; Gallardo-Cruz, José Alberto

2013-01-01

Two main theories have attempted to explain variation in plant species composition (β-diversity). Niche theory proposes that most of the variation is related to environment (environmental filtering), whereas neutral theory posits that dispersal limitation is the main driver of β-diversity. In this study, we first explored how α- and β-diversity of plant functional groups defined by growth form (trees, shrubs and lianas, which represent different strategies of resource partitioning), and dispersal syndrome (autochory, anemochory and zoochory, which represent differences in dispersal limitation) vary with successional age and topographic position in a tropical dry forest. Second, we examined the effects of environmental, spatial, and spatially-structured environmental factors on β-diversity of functional groups; we used the spatial structure of sampling sites as a proxy for dispersal limitation, and elevation, soil properties and forest stand age as indicators of environmental filtering. We recorded 200 species and 22,245 individuals in 276 plots; 120 species were trees, 41 shrubs and 39 lianas. We found that β-diversity was highest for shrubs, intermediate for lianas and lowest for trees, and was slightly higher for zoochorous than for autochorous and anemochorous species. All three dispersal syndromes, trees and shrubs varied in composition among vegetation classes (successional age and topographic position), whilst lianas did not. β-diversity was influenced mostly by proxies of environmental filtering, except for shrubs, for which the influence of dispersal limitation was more important. Stand age and topography significantly influenced α-diversity across functional groups, but showed a low influence on β-diversity –possibly due to the counterbalancing effect of resprouting on plant distribution and composition. Our results show that considering different plant functional groups reveals important differences in both α- and β-diversity patterns and correlates that are not apparent when focusing on overall woody plant diversity, and that have important implications for ecological theory and biodiversity conservation. PMID:24040014

Genetic Diversity and Structure of Managed and Semi-natural Populations of Cocoa (Theobroma cacao) in the Huallaga and Ucayali Valleys of Peru

PubMed Central

ZHANG, DAPENG; AREVALO-GARDINI, ENRIQUE; MISCHKE, SUE; ZÚÑIGA-CERNADES, LUIS; BARRETO-CHAVEZ, ALEJANDRO; AGUILA, JORGE ADRIAZOLA DEL

2006-01-01

• Background and Aims Cocoa (Theobroma cacao) is indigenous to the Amazon region of South America, and it is well known that the Peruvian Amazon harbours a large number of diverse cocoa populations. A small fraction of the diversity has been collected and maintained as an ex-situ germplasm repository in Peru. However, incorrect labelling of accessions and lack of information on genetic diversity have hindered efficient conservation and use of this germplasm. This study targeted assessment of genetic diversity and population structure in a managed and a semi-natural population. •Methods Using a capillary electrophoresis genotyping system, 105 cocoa accessions collected from the Huallaga and Ucayali valleys of Peru were fingerprinted. Based on 15 loci SSR profiles, genetic identity was examined for each accession and duplicates identified, population structure assessed and genetic diversity analysed in these two populations. •Key Results Ten synonymous mislabelled groups were identified among the 105 accessions. The germplasm group in the Huallaga valley was clearly separated from the group in Ucayali valley by the Bayesian assignment test. The Huallaga group has lower genetic diversity, both in terms of allelic richness and of gene diversity, than the Ucayali group. Analysis of molecular variance suggested genetic substructure in the Ucayali group. Significant spatial correlation between genetic distance and geographical distances was detected in the Ucayali group by Mantel tests. •Conclusions These results substantiate the hypothesis that the Peruvian Amazon hosts a high level of cocoa genetic diversity, and the diversity has a spatial structure. The introduction of exotic seed populations into the Peruvian Amazon is changing the cocoa germplasm spectrum in this region. The spatial structure of cocoa diversity recorded here highlights the need for additional collecting and conservation measures for natural and semi-natural cocoa populations. PMID:16845139

Genetic Diversity and Spatial Genetic Structure of the Grassland Perennial Saxifraga granulata along Two River Systems

PubMed Central

van der Meer, Sascha; Jacquemyn, Hans

2015-01-01

Due to changes in land use, the natural habitats of an increasing number of plant species have become more and more fragmented. In landscapes that consist of patches of suitable habitat, the frequency and extent of long-distance seed dispersal can be expected to be an important factor determining local genetic diversity and regional population structure of the remaining populations. In plant species that are restricted to riparian habitats, rivers can be expected to have a strong impact on the dynamics and spatial genetic structure of populations as they may enable long-distance seed dispersal and thus maintain gene flow between fragmented populations. In this study, we used polymorphic microsatellite markers to investigate the genetic diversity and the spatial genetic structure of 28 populations of Saxifraga granulata along two rivers in central Belgium. We hypothesized that rivers might be essential for gene flow among increasingly isolated populations of this species. Genetic diversity was high (HS = 0.68), which to a certain extent can be explained by the octoploid nature of S. granulata in the study area. Populations along the Dijle and Demer rivers were also highly differentiated (G” ST = 0.269 and 0.164 and D EST = 0.190 and 0.124, respectively) and showed significant isolation-by-distance, indicating moderate levels of gene flow primarily between populations that are geographically close to each other. Along the river Demer population genetic diversity was higher upstream than downstream, suggesting that seed dispersal via the water was not the primary mode of dispersal. Overall, these results indicate that despite increasing fragmentation populations along both rivers were highly genetically diverse. The high ploidy level and longevity of S. granulata have most likely buffered negative effects of fragmentation on genetic diversity and the spatial genetic structure of populations in riparian grasslands. PMID:26079603

Examination of time-reversal acoustics in shallow water and applications to noncoherent underwater communications.

PubMed

Smith, Kevin B; Abrantes, Antonio A M; Larraza, Andres

2003-06-01

The shallow water acoustic communication channel is characterized by strong signal degradation caused by multipath propagation and high spatial and temporal variability of the channel conditions. At the receiver, multipath propagation causes intersymbol interference and is considered the most important of the channel distortions. This paper examines the application of time-reversal acoustic (TRA) arrays, i.e., phase-conjugated arrays (PCAs), that generate a spatio-temporal focus of acoustic energy at the receiver location, eliminating distortions introduced by channel propagation. This technique is self-adaptive and automatically compensates for environmental effects and array imperfections without the need to explicitly characterize the environment. An attempt is made to characterize the influences of a PCA design on its focusing properties with particular attention given to applications in noncoherent underwater acoustic communication systems. Due to the PCA spatial diversity focusing properties, PC arrays may have an important role in an acoustic local area network. Each array is able to simultaneously transmit different messages that will focus only at the destination receiver node.

Factors affecting plant diversity during post-fire recovery and succession of mediterranean-climate shrublands in California, USA

USGS Publications Warehouse

Keeley, J.E.; Fotheringham, C.J.; Baer-Keeley, M.

2005-01-01

Plant community diversity, measured as species richness, is typically highest in the early post-fire years in California shrublands. However, this generalization is overly simplistic and the present study demonstrates that diversity is determined by a complex of temporal and spatial effects. Ninety sites distributed across southern California were studied for 5 years after a series of fires. Characteristics of the disturbance event, in this case fire severity, can alter post-fire diversity, both decreasing and increasing diversity, depending on life form. Spatial variability in resource availability is an important factor explaining patterns of diversity, and there is a complex interaction between landscape features and life form. Temporal variability in resource availability affects diversity, and the diversity peak in the immediate post-fire year (or two) appears to be driven by factors different from subsequent diversity peaks. Early post-fire diversity is influenced by life-history specialization, illustrated by species that spend the bulk of their life cycle as a dormant seed bank, which is then triggered to germinate by fire. Resource fluctuations, precipitation in particular, may be associated with subsequent post-fire diversity peaks. These later peaks in diversity comprise a flora that is compositionally different from the immediate post-fire flora, and their presence may be due to mass effects from population expansion of local populations in adjacent burned areas. ?? 2005 Blackwell Publishing Ltd.

Statistical Analysis of 3D Images Detects Regular Spatial Distributions of Centromeres and Chromocenters in Animal and Plant Nuclei

PubMed Central

Biot, Eric; Adenot, Pierre-Gaël; Hue-Beauvais, Cathy; Houba-Hérin, Nicole; Duranthon, Véronique; Devinoy, Eve; Beaujean, Nathalie; Gaudin, Valérie; Maurin, Yves; Debey, Pascale

2010-01-01

In eukaryotes, the interphase nucleus is organized in morphologically and/or functionally distinct nuclear “compartments”. Numerous studies highlight functional relationships between the spatial organization of the nucleus and gene regulation. This raises the question of whether nuclear organization principles exist and, if so, whether they are identical in the animal and plant kingdoms. We addressed this issue through the investigation of the three-dimensional distribution of the centromeres and chromocenters. We investigated five very diverse populations of interphase nuclei at different differentiation stages in their physiological environment, belonging to rabbit embryos at the 8-cell and blastocyst stages, differentiated rabbit mammary epithelial cells during lactation, and differentiated cells of Arabidopsis thaliana plantlets. We developed new tools based on the processing of confocal images and a new statistical approach based on G- and F- distance functions used in spatial statistics. Our original computational scheme takes into account both size and shape variability by comparing, for each nucleus, the observed distribution against a reference distribution estimated by Monte-Carlo sampling over the same nucleus. This implicit normalization allowed similar data processing and extraction of rules in the five differentiated nuclei populations of the three studied biological systems, despite differences in chromosome number, genome organization and heterochromatin content. We showed that centromeres/chromocenters form significantly more regularly spaced patterns than expected under a completely random situation, suggesting that repulsive constraints or spatial inhomogeneities underlay the spatial organization of heterochromatic compartments. The proposed technique should be useful for identifying further spatial features in a wide range of cell types. PMID:20628576

Image sharpening for mixed spatial and spectral resolution satellite systems

NASA Technical Reports Server (NTRS)

Hallada, W. A.; Cox, S.

1983-01-01

Two methods of image sharpening (reconstruction) are compared. The first, a spatial filtering technique, extrapolates edge information from a high spatial resolution panchromatic band at 10 meters and adds it to the low spatial resolution narrow spectral bands. The second method, a color normalizing technique, is based on the ability to separate image hue and brightness components in spectral data. Using both techniques, multispectral images are sharpened from 30, 50, 70, and 90 meter resolutions. Error rates are calculated for the two methods and all sharpened resolutions. The results indicate that the color normalizing method is superior to the spatial filtering technique.

How large is large enough for insects? Forest fragmentation effects at three spatial scales

NASA Astrophysics Data System (ADS)

Ribas, C. R.; Sobrinho, T. G.; Schoereder, J. H.; Sperber, C. F.; Lopes-Andrade, C.; Soares, S. M.

2005-02-01

Several mechanisms may lead to species loss in fragmented habitats, such as edge and shape effects, loss of habitat and heterogeneity. Ants and crickets were sampled in 18 forest remnants in south-eastern Brazil, to test whether a group of small remnants maintains the same insect species richness as similar sized large remnants, at three spatial scales. We tested hypotheses about alpha and gamma diversity to explain the results. Groups of remnants conserve as many species of ants as a single one. Crickets, however, showed a scale-dependent pattern: at small scales there was no significant or important difference between groups of remnants and a single one, while at the larger scale the group of remnants maintained more species. Alpha diversity (local species richness) was similar in a group of remnants and in a single one, at the three spatial scales, both for ants and crickets. Gamma diversity, however, varied both with taxa (ants and crickets) and spatial scale, which may be linked to insect mobility, remnant isolation, and habitat heterogeneity. Biological characteristics of the organisms involved have to be considered when studying fragmentation effects, as well as spatial scale at which it operates. Mobility of the organisms influences fragmentation effects, and consequently conservation strategies.

DNA Barcoding Reveals Hidden Diversity of Sand Flies (Diptera: Psychodidae) at Fine and Broad Spatial Scales in Brazilian Endemic Regions for Leishmaniasis.

PubMed

Rodrigues, Bruno Leite; Carvalho-Costa, Luís Fernando; Pinto, Israel de Souza; Rebêlo, José Manuel Macário

2018-03-17

Sand fly (Diptera: Psychodidae) taxonomy is complex and time-consuming, which hampers epidemiological efforts directed toward controlling leishmaniasis in endemic regions such as northeastern Brazil. Here, we used a fragment of the mitochondrial cytochrome c oxidase I (COI) gene to identify sand fly species in Maranhão State (northeastern Brazil) and to assess cryptic diversity occurring at different spatial scales. For this, we obtained 148 COI sequences of 15 sand fly species (10 genera) from Maranhão (fine spatial scale), and joined them to COI sequences from other Brazilian localities (distant about 2,000 km from Maranhão, broad spatial scale) available in GenBank. We revealed cases of cryptic diversity in sand flies both at fine (Lutzomyia longipalpis (Lutz and Neiva) and Evandromyia termitophila (Martins, Falcão and Silva)) and broad spatial scales (Migonemyia migonei (França), Pressatia choti (Floch and Abonnenc), Psychodopygus davisi (Root), Sciopemyia sordellii (Shannon and Del Ponte), and Bichromomyia flaviscutellata (Mangabeira)). We argue that in the case of Bi. flaviscutellata, the cryptic diversity is associated with a putative new species. Cases in which DNA taxonomy was not as effective as morphological identification possibly involved recent speciation and/or introgressive hybridization, highlighting the need for integrative approaches to identify some sand fly species. Finally, we provide the first barcode sequences for four species (Brumptomyia avellari (Costa Lima), Evandromyia infraspinosa (Mangabeira), Evandromyia evandroi (Costa Lima and Antunes), and Psychodopygus complexus (Mangabeira)), which will be useful for further molecular identification of neotropical species.

A pigment analysis tool for hyperspectral images of cultural heritage artifacts

NASA Astrophysics Data System (ADS)

Bai, Di; Messinger, David W.; Howell, David

2017-05-01

The Gough Map, in the collection at the Bodleian Library, Oxford University, is one of the earliest surviving maps of Britain. Previous research deemed that it was likely created over the 15th century and afterwards it was extensively revised more than once. In 2015, the Gough Map was imaged using a hyperspectral imaging system at the Bodleian Library. The collection of the hyperspectral image (HSI) data was aimed at faded text enhancement for reading and pigment analysis for the material diversity of its composition and potentially the timeline of its creation. In this research, we introduce several methods to analyze the green pigments in the Gough Map, especially the number and spatial distribution of distinct green pigments. One approach, called the Gram Matrix, has been used to estimate the material diversity in a scene (i.e., endmember selection and dimensionality estimation). Here, we use the Gram Matrix technique to study the within-material differences of pigments in the Gough map with common visual color. We develop a pigment analysis tool that extracts visually common pixels, green pigments in this case, from the Gough Map and estimates its material diversity. It reveals that the Gough Map consists of at least six kinds of dominant green pigments. Both historical geographers and cartographic historians will benefit from this work to analyze the pigment diversity using HSI of cultural heritage artifacts.

A dynamic fuzzy genetic algorithm for natural image segmentation using adaptive mean shift

NASA Astrophysics Data System (ADS)

Arfan Jaffar, M.

2017-01-01

In this paper, a colour image segmentation approach based on hybridisation of adaptive mean shift (AMS), fuzzy c-mean and genetic algorithms (GAs) is presented. Image segmentation is the perceptual faction of pixels based on some likeness measure. GA with fuzzy behaviour is adapted to maximise the fuzzy separation and minimise the global compactness among the clusters or segments in spatial fuzzy c-mean (sFCM). It adds diversity to the search process to find the global optima. A simple fusion method has been used to combine the clusters to overcome the problem of over segmentation. The results show that our technique outperforms state-of-the-art methods.

GIS-based analysis and modelling with empirical and remotely-sensed data on coastline advance and retreat

NASA Astrophysics Data System (ADS)

Ahmad, Sajid Rashid

With the understanding that far more research remains to be done on the development and use of innovative and functional geospatial techniques and procedures to investigate coastline changes this thesis focussed on the integration of remote sensing, geographical information systems (GIS) and modelling techniques to provide meaningful insights on the spatial and temporal dynamics of coastline changes. One of the unique strengths of this research was the parameterization of the GIS with long-term empirical and remote sensing data. Annual empirical data from 1941--2007 were analyzed by the GIS, and then modelled with statistical techniques. Data were also extracted from Landsat TM and ETM+ images. The band ratio method was used to extract the coastlines. Topographic maps were also used to extract digital map data. All data incorporated into ArcGIS 9.2 were analyzed with various modules, including Spatial Analyst, 3D Analyst, and Triangulated Irregular Networks. The Digital Shoreline Analysis System was used to analyze and predict rates of coastline change. GIS results showed the spatial locations along the coast that will either advance or retreat over time. The linear regression results highlighted temporal changes which are likely to occur along the coastline. Box-Jenkins modelling procedures were utilized to determine statistical models which best described the time series (1941--2007) of coastline change data. After several iterations and goodness-of-fit tests, second-order spatial cyclic autoregressive models, first-order autoregressive models and autoregressive moving average models were identified as being appropriate for describing the deterministic and random processes operating in Guyana's coastal system. The models highlighted not only cyclical patterns in advance and retreat of the coastline, but also the existence of short and long-term memory processes. Long-term memory processes could be associated with mudshoal propagation and stabilization while short-term memory processes were indicative of transitory hydrodynamic and other processes. An innovative framework for a spatio-temporal information-based system (STIBS) was developed. STIBS incorporated diverse datasets within a GIS, dynamic computer-based simulation models, and a spatial information query and graphical subsystem. Tests of the STIBS proved that it could be used to simulate and visualize temporal variability in shifting morphological states of the coastline.

Spatial scaling of bacterial community diversity at shallow hydrothermal vents: a global comparison

NASA Astrophysics Data System (ADS)

Pop Ristova, P.; Hassenrueck, C.; Molari, M.; Fink, A.; Bühring, S. I.

2016-02-01

Marine shallow hydrothermal vents are extreme environments, often characterized by discharge of fluids with e.g. high temperatures, low pH, and laden with elements toxic to higher organisms. They occur at continental margins around the world's oceans, but represent fragmented, isolated habitats of locally small areal coverage. Microorganisms contribute the main biomass at shallow hydrothermal vent ecosystems and build the basis of the food chain by autotrophic fixation of carbon both via chemosynthesis and photosynthesis, occurring simultaneously. Despite their importance and unique capacity to adapt to these extreme environments, little is known about the spatial scales on which the alpha- and beta-diversity of microbial communities vary at shallow vents, and how the geochemical habitat heterogeneity influences shallow vent biodiversity. Here for the first time we investigated the spatial scaling of microbial biodiversity patterns and their interconnectivity at geochemically diverse shallow vents on a global scale. This study presents data on the comparison of bacterial community structures on large (> 1000 km) and small (0.1 - 100 m) spatial scales as derived from ARISA and Illumina sequencing. Despite the fragmented global distribution of shallow hydrothermal vents, similarity of vent bacterial communities decreased with geographic distance, confirming the ubiquity of distance-decay relationship. Moreover, at all investigated vents, pH was the main factor locally structuring these communities, while temperature influenced both the alpha- and beta-diversity.

Integrating the effects of latitude and altitude on the spatial differentiation of plant community diversity in a mountainous ecosystem in China

PubMed Central

Xu, Manhou; Ma, Li; Jia, Yanyan; Liu, Min

2017-01-01

Varying patterns of plant community diversity along geographical gradients are a significant topic in biodiversity research. Here, to explore the integrated effects of latitude and altitude on the plant community diversity in a mountainous ecosystem, we set Guancen Mountain in the northern section, Guandi Mountain in the middle section, and Wulu Mountain in the southern section of the Lvliang Mountains as study areas, and the plant community diversity (basal diameter and height of tree and species diversity indices of shrub and herb) was measured horizontally at different latitude gradients and vertically at different altitude gradients in late July 2015. The results showed that (1) the trees were taller and wider at the middle latitude and higher altitude with a stronger spatial heterogeneity in the structures along the latitudinal and altitudinal gradients. The evergreen tree growth preceded that of the deciduous trees in the higher latitude and lower altitude regions, whereas the deciduous tree growth preceded that of the evergreen trees in the middle latitude and higher altitude regions. (2) Shrubs and herbs tended to grow well in the lower latitude and middle-lower altitude regions. The shrubs had a larger species diversity at lower latitude and lower altitude, but the species diversity of the herbs was not sensitive to the influences of the latitudinal and altitudinal gradients. With the latitude and altitude increasing, perennial herbs tended to grow well at higher latitude and higher altitude, while annual herbs tended to thrive at the middle latitude and lower altitude. In conclusion, environmental deviations caused by latitudinal and altitudinal gradients had great influences on the spatial distributions of the plant community diversity in the Lvliang Mountains. PMID:28323909

Scale dependency of forest functional diversity assessed using imaging spectroscopy and airborne laser scanning

NASA Astrophysics Data System (ADS)

Schneider, F. D.; Morsdorf, F.; Schmid, B.; Petchey, O. L.; Hueni, A.; Schimel, D.; Schaepman, M. E.

2016-12-01

Forest functional traits offer a mechanistic link between ecological processes and community structure and assembly rules. However, measuring functional traits of forests in a continuous and consistent way is particularly difficult due to the complexity of in-situ measurements and geo-referencing. New imaging spectroscopy measurements overcome these limitations allowing to map physiological traits on broad spatial scales. We mapped leaf chlorophyll, carotenoids and leaf water content over 900 ha of temperate mixed forest (Fig. 1a). The selected traits are functionally important because they are indicating the photosynthetic potential of trees, leaf longevity and protection, as well as tree water and drought stress. Spatially continuous measurements on the scale of individual tree crowns allowed to assess functional diversity patterns on a range of ecological extents. We used indexes of functional richness, divergence and evenness to map different aspects of diversity. Fig. 1b shows an example of physiological richness at an extent of 240 m radius. We compared physiological to morphological diversity patterns, derived based on plant area index, canopy height and foliage height diversity. Our results show that patterns of physiological and morphological diversity generally agree, independently measured by airborne imaging spectroscopy and airborne laser scanning, respectively. The occurrence of disturbance areas and mixtures of broadleaf and needle trees were the main drivers of the observed diversity patterns. Spatial patterns at varying extents and richness-area relationships indicated that environmental filtering is the predominant community assembly process. Our results demonstrate the potential for mapping physiological and morphological diversity in a temperate mixed forest between and within species on scales relevant to study community assembly and structure from space and test the corresponding measurement schemes.

Integrating the effects of latitude and altitude on the spatial differentiation of plant community diversity in a mountainous ecosystem in China.

PubMed

Xu, Manhou; Ma, Li; Jia, Yanyan; Liu, Min

2017-01-01

Varying patterns of plant community diversity along geographical gradients are a significant topic in biodiversity research. Here, to explore the integrated effects of latitude and altitude on the plant community diversity in a mountainous ecosystem, we set Guancen Mountain in the northern section, Guandi Mountain in the middle section, and Wulu Mountain in the southern section of the Lvliang Mountains as study areas, and the plant community diversity (basal diameter and height of tree and species diversity indices of shrub and herb) was measured horizontally at different latitude gradients and vertically at different altitude gradients in late July 2015. The results showed that (1) the trees were taller and wider at the middle latitude and higher altitude with a stronger spatial heterogeneity in the structures along the latitudinal and altitudinal gradients. The evergreen tree growth preceded that of the deciduous trees in the higher latitude and lower altitude regions, whereas the deciduous tree growth preceded that of the evergreen trees in the middle latitude and higher altitude regions. (2) Shrubs and herbs tended to grow well in the lower latitude and middle-lower altitude regions. The shrubs had a larger species diversity at lower latitude and lower altitude, but the species diversity of the herbs was not sensitive to the influences of the latitudinal and altitudinal gradients. With the latitude and altitude increasing, perennial herbs tended to grow well at higher latitude and higher altitude, while annual herbs tended to thrive at the middle latitude and lower altitude. In conclusion, environmental deviations caused by latitudinal and altitudinal gradients had great influences on the spatial distributions of the plant community diversity in the Lvliang Mountains.

Large Spatial Scale Variability in Bathyal Macrobenthos Abundance, Biomass, α- and β-Diversity along the Mediterranean Continental Margin

PubMed Central

Baldrighi, Elisa; Lavaleye, Marc; Aliani, Stefano; Conversi, Alessandra; Manini, Elena

2014-01-01

The large-scale deep-sea biodiversity distribution of the benthic fauna was explored in the Mediterranean Sea, which can be seen as a miniature model of the oceans of the world. Within the framework of the BIOFUN project (“Biodiversity and Ecosystem Functioning in Contrasting Southern European Deep-sea Environments: from viruses to megafauna”), we investigated the large spatial scale variability (over >1,000 km) of the bathyal macrofauna communities that inhabit the Mediterranean basin, and their relationships with the environmental variables. The macrofauna abundance, biomass, community structure and functional diversity were analysed and the α-diversity and β-diversity were estimated across six selected slope areas at different longitudes and along three main depths. The macrobenthic standing stock and α-diversity were lower in the deep-sea sediments of the eastern Mediterranean basin, compared to the western and central basins. The macrofaunal standing stock and diversity decreased significantly from the upper bathyal to the lower bathyal slope stations. The major changes in the community composition of the higher taxa and in the trophic (functional) structure occurred at different longitudes, rather than at increasing water depth. For the β-diversity, very high dissimilarities emerged at all levels: (i) between basins; (ii) between slopes within the same basin; and (iii) between stations at different depths; this therefore demonstrates the high macrofaunal diversity of the Mediterranean basins at large spatial scales. Overall, the food sources (i.e., quantity and quality) that characterised the west, central and eastern Mediterranean basins, as well as sediment grain size, appear to influence the macrobenthic standing stock and the biodiversity along the different slope areas. PMID:25225909

Revealing Beta-Diversity Patterns of Breeding Bird and Lizard Communities on Inundated Land-Bridge Islands by Separating the Turnover and Nestedness Components

PubMed Central

Si, Xingfeng; Baselga, Andrés; Ding, Ping

2015-01-01

Beta diversity describes changes in species composition among sites in a region and has particular relevance for explaining ecological patterns in fragmented habitats. However, it is difficult to reveal the mechanisms if broad sense beta-diversity indices (i.e. yielding identical values under nestedness and species replacement) are used. Partitioning beta diversity into turnover (caused by species replacement from site to site) and nestedness-resultant components (caused by nested species losses) could provide a unique way to understand the variation of species composition in fragmented habitats. Here, we collected occupancy data of breeding birds and lizards on land-bridge islands in an inundated lake in eastern China. We decomposed beta diversity of breeding bird and lizard communities into spatial turnover and nestedness-resultant components to assess their relative contributions and respective relationships to differences in island area, isolation, and habitat richness. Our results showed that spatial turnover contributed more to beta diversity than the nestedness-resultant component. The degree of isolation had no significant effect on overall beta diversity or its components, neither for breeding birds nor for lizards. In turn, in both groups the nestedness-resultant component increased with larger differences in island area and habitat richness, respectively, while turnover component decreased with them. The major difference among birds and lizards was a higher relevance of nestedness-resultant dissimilarity in lizards, suggesting that they are more prone to local extinctions derived from habitat fragmentation. The dominance of the spatial turnover component of beta diversity suggests that all islands have potential conservation value for breeding bird and lizard communities. PMID:25992559

Large spatial scale variability in bathyal macrobenthos abundance, biomass, α- and β-diversity along the Mediterranean continental margin.

PubMed

Baldrighi, Elisa; Lavaleye, Marc; Aliani, Stefano; Conversi, Alessandra; Manini, Elena

2014-01-01

The large-scale deep-sea biodiversity distribution of the benthic fauna was explored in the Mediterranean Sea, which can be seen as a miniature model of the oceans of the world. Within the framework of the BIOFUN project ("Biodiversity and Ecosystem Functioning in Contrasting Southern European Deep-sea Environments: from viruses to megafauna"), we investigated the large spatial scale variability (over >1,000 km) of the bathyal macrofauna communities that inhabit the Mediterranean basin, and their relationships with the environmental variables. The macrofauna abundance, biomass, community structure and functional diversity were analysed and the α-diversity and β-diversity were estimated across six selected slope areas at different longitudes and along three main depths. The macrobenthic standing stock and α-diversity were lower in the deep-sea sediments of the eastern Mediterranean basin, compared to the western and central basins. The macrofaunal standing stock and diversity decreased significantly from the upper bathyal to the lower bathyal slope stations. The major changes in the community composition of the higher taxa and in the trophic (functional) structure occurred at different longitudes, rather than at increasing water depth. For the β-diversity, very high dissimilarities emerged at all levels: (i) between basins; (ii) between slopes within the same basin; and (iii) between stations at different depths; this therefore demonstrates the high macrofaunal diversity of the Mediterranean basins at large spatial scales. Overall, the food sources (i.e., quantity and quality) that characterised the west, central and eastern Mediterranean basins, as well as sediment grain size, appear to influence the macrobenthic standing stock and the biodiversity along the different slope areas.

Incorporating historical ecosystem diversity into conservation planning efforts in grass and shrub ecosystems

Treesearch

Amy C. Ganguli; Johathan B. Haufler; Carolyn A. Mehl; Jimmie D. Chew

2011-01-01

Understanding historical ecosystem diversity and wildlife habitat quality can provide a useful reference for managing and restoring rangeland ecosystems. We characterized historical ecosystem diversity using available empirical data, expert opinion, and the spatially explicit vegetation dynamics model SIMPPLLE (SIMulating Vegetative Patterns and Processes at Landscape...

Modeling the impacts of phenological and inter-annual changes in landscape metrics on local biodiversity of agricultural lands of Eastern Ontario using multi-spatial and multi-temporal remote sensing data

NASA Astrophysics Data System (ADS)

Alavi-Shoushtari, N.; King, D.

2017-12-01

Agricultural landscapes are highly variable ecosystems and are home to many local farmland species. Seasonal, phenological and inter-annual agricultural landscape dynamics have potential to affect the richness and abundance of farmland species. Remote sensing provides data and techniques which enable monitoring landscape changes in multiple temporal and spatial scales. MODIS high temporal resolution remote sensing images enable detection of seasonal and phenological trends, while Landsat higher spatial resolution images, with its long term archive enables inter-annual trend analysis over several decades. The objective of this study to use multi-spatial and multi-temporal remote sensing data to model the response of farmland species to landscape metrics. The study area is the predominantly agricultural region of eastern Ontario. 92 sample landscapes were selected within this region using a protocol designed to maximize variance in composition and configuration heterogeneity while controlling for amount of forest and spatial autocorrelation. Two sample landscape extents (1×1km and 3×3km) were selected to analyze the impacts of spatial scale on biodiversity response. Gamma diversity index data for four taxa groups (birds, butterflies, plants, and beetles) were collected during the summers of 2011 and 2012 within the cropped area of each landscape. To extract the seasonal and phenological metrics a 2000-2012 MODIS NDVI time-series was used, while a 1985-2012 Landsat time-series was used to model the inter-annual trends of change in the sample landscapes. The results of statistical modeling showed significant relationships between farmland biodiversity for several taxa and the phenological and inter-annual variables. The following general results were obtained: 1) Among the taxa groups, plant and beetles diversity was most significantly correlated with the phenological variables; 2) Those phenological variables which are associated with the variability in the start of season date across the sample landscapes and the variability in the corresponding NDVI values at that date showed the strongest correlation with the biodiversity indices; 3) The significance of the models improved when using 3×3km site extent both for MODIS and Landsat based models due most likely to the larger sample size over 3x3km.

Large-scale spatio-temporal monitoring highlights hotspots of demersal fish diversity in the Mediterranean Sea

NASA Astrophysics Data System (ADS)

Granger, Victoria; Fromentin, Jean-Marc; Bez, Nicolas; Relini, Giulio; Meynard, Christine N.; Gaertner, Jean-Claude; Maiorano, Porzia; Garcia Ruiz, Cristina; Follesa, Cristina; Gristina, Michele; Peristeraki, Panagiota; Brind'Amour, Anik; Carbonara, Pierluigi; Charilaou, Charis; Esteban, Antonio; Jadaud, Angélique; Joksimovic, Aleksandar; Kallianiotis, Argyris; Kolitari, Jerina; Manfredi, Chiara; Massuti, Enric; Mifsud, Roberta; Quetglas, Antoni; Refes, Wahid; Sbrana, Mario; Vrgoc, Nedo; Spedicato, Maria Teresa; Mérigot, Bastien

2015-01-01

Increasing human pressures and global environmental change may severely affect the diversity of species assemblages and associated ecosystem services. Despite the recent interest in phylogenetic and functional diversity, our knowledge on large spatio-temporal patterns of demersal fish diversity sampled by trawling remains still incomplete, notably in the Mediterranean Sea, one of the most threatened marine regions of the world. We investigated large spatio-temporal diversity patterns by analysing a dataset of 19,886 hauls from 10 to 800 m depth performed annually during the last two decades by standardised scientific bottom trawl field surveys across the Mediterranean Sea, within the MEDITS program. A multi-component (eight diversity indices) and multi-scale (local assemblages, biogeographic regions to basins) approach indicates that only the two most traditional components (species richness and evenness) were sufficient to reflect patterns in taxonomic, phylogenetic or functional richness and divergence. We also put into question the use of widely computed indices that allow comparing directly taxonomic, phylogenetic and functional diversity within a unique mathematical framework. In addition, demersal fish assemblages sampled by trawl do not follow a continuous decreasing longitudinal/latitudinal diversity gradients (spatial effects explained up to 70.6% of deviance in regression tree and generalised linear models), for any of the indices and spatial scales analysed. Indeed, at both local and regional scales species richness was relatively high in the Iberian region, Malta, the Eastern Ionian and Aegean seas, meanwhile the Adriatic Sea and Cyprus showed a relatively low level. In contrast, evenness as well as taxonomic, phylogenetic and functional divergences did not show regional hotspots. All studied diversity components remained stable over the last two decades. Overall, our results highlight the need to use complementary diversity indices through different spatial scales when developing conservation strategies and defining delimitations for protected areas.

Methods of alleviation of ionospheric scintillation effects on digital communications

NASA Technical Reports Server (NTRS)

Massey, J. L.

1974-01-01

The degradation of the performance of digital communication systems because of ionospheric scintillation effects can be reduced either by diversity techniques or by coding. The effectiveness of traditional space-diversity, frequency-diversity and time-diversity techniques is reviewed and design considerations isolated. Time-diversity signaling is then treated as an extremely simple form of coding. More advanced coding methods, such as diffuse threshold decoding and burst-trapping decoding, which appear attractive in combatting scintillation effects are discussed and design considerations noted. Finally, adaptive coding techniques appropriate when the general state of the channel is known are discussed.

Explaining variation in tropical plant community composition: influence of environmental and spatial data quality.

PubMed

Jones, Mirkka M; Tuomisto, Hanna; Borcard, Daniel; Legendre, Pierre; Clark, David B; Olivas, Paulo C

2008-03-01

The degree to which variation in plant community composition (beta-diversity) is predictable from environmental variation, relative to other spatial processes, is of considerable current interest. We addressed this question in Costa Rican rain forest pteridophytes (1,045 plots, 127 species). We also tested the effect of data quality on the results, which has largely been overlooked in earlier studies. To do so, we compared two alternative spatial models [polynomial vs. principal coordinates of neighbour matrices (PCNM)] and ten alternative environmental models (all available environmental variables vs. four subsets, and including their polynomials vs. not). Of the environmental data types, soil chemistry contributed most to explaining pteridophyte community variation, followed in decreasing order of contribution by topography, soil type and forest structure. Environmentally explained variation increased moderately when polynomials of the environmental variables were included. Spatially explained variation increased substantially when the multi-scale PCNM spatial model was used instead of the traditional, broad-scale polynomial spatial model. The best model combination (PCNM spatial model and full environmental model including polynomials) explained 32% of pteridophyte community variation, after correcting for the number of sampling sites and explanatory variables. Overall evidence for environmental control of beta-diversity was strong, and the main floristic gradients detected were correlated with environmental variation at all scales encompassed by the study (c. 100-2,000 m). Depending on model choice, however, total explained variation differed more than fourfold, and the apparent relative importance of space and environment could be reversed. Therefore, we advocate a broader recognition of the impacts that data quality has on analysis results. A general understanding of the relative contributions of spatial and environmental processes to species distributions and beta-diversity requires that methodological artefacts are separated from real ecological differences.

Disentangling how landscape spatial and temporal heterogeneity affects Savanna birds.

PubMed

Price, Bronwyn; McAlpine, Clive A; Kutt, Alex S; Ward, Doug; Phinn, Stuart R; Ludwig, John A

2013-01-01

In highly seasonal tropical environments, temporal changes in habitat and resources are a significant determinant of the spatial distribution of species. This study disentangles the effects of spatial and mid to long-term temporal heterogeneity in habitat on the diversity and abundance of savanna birds by testing four competing conceptual models of varying complexity. Focussing on sites in northeast Australia over a 20 year time period, we used ground cover and foliage projected cover surfaces derived from a time series of Landsat Thematic Mapper imagery, rainfall data and site-level vegetation surveys to derive measures of habitat structure at local (1-100 ha) and landscape (100-1000s ha) scales. We used generalised linear models and an information theoretic approach to test the independent effects of spatial and temporal influences on savanna bird diversity and the abundance of eight species with different life-history behaviours. Of four competing models defining influences on assemblages of savanna birds, the most parsimonious included temporal and spatial variability in vegetation cover and site-scale vegetation structure, suggesting savanna bird species respond to spatial and temporal habitat heterogeneity at both the broader landscape scale and at the fine-scale. The relative weight, strength and direction of the explanatory variables changed with each of the eight species, reflecting their different ecology and behavioural traits. This study demonstrates that variations in the spatial pattern of savanna vegetation over periods of 10 to 20 years at the local and landscape scale strongly affect bird diversity and abundance. Thus, it is essential to monitor and manage both spatial and temporal variability in avian habitat to achieve long-term biodiversity outcomes.

Disentangling How Landscape Spatial and Temporal Heterogeneity Affects Savanna Birds

PubMed Central

Price, Bronwyn; McAlpine, Clive A.; Kutt, Alex S.; Ward, Doug; Phinn, Stuart R.; Ludwig, John A.

2013-01-01

In highly seasonal tropical environments, temporal changes in habitat and resources are a significant determinant of the spatial distribution of species. This study disentangles the effects of spatial and mid to long-term temporal heterogeneity in habitat on the diversity and abundance of savanna birds by testing four competing conceptual models of varying complexity. Focussing on sites in northeast Australia over a 20 year time period, we used ground cover and foliage projected cover surfaces derived from a time series of Landsat Thematic Mapper imagery, rainfall data and site-level vegetation surveys to derive measures of habitat structure at local (1–100 ha) and landscape (100–1000s ha) scales. We used generalised linear models and an information theoretic approach to test the independent effects of spatial and temporal influences on savanna bird diversity and the abundance of eight species with different life-history behaviours. Of four competing models defining influences on assemblages of savanna birds, the most parsimonious included temporal and spatial variability in vegetation cover and site-scale vegetation structure, suggesting savanna bird species respond to spatial and temporal habitat heterogeneity at both the broader landscape scale and at the fine-scale. The relative weight, strength and direction of the explanatory variables changed with each of the eight species, reflecting their different ecology and behavioural traits. This study demonstrates that variations in the spatial pattern of savanna vegetation over periods of 10 to 20 years at the local and landscape scale strongly affect bird diversity and abundance. Thus, it is essential to monitor and manage both spatial and temporal variability in avian habitat to achieve long-term biodiversity outcomes. PMID:24066138

Advanced microscopy of star-shaped gold nanoparticles and their adsorption-uptake by macrophages

PubMed Central

Plascencia-Villa, Germán; Bahena, Daniel; Rodríguez, Annette R.; Ponce, Arturo; José-Yacamán, Miguel

2013-01-01

Metallic nanoparticles have diverse applications in biomedicine, as diagnostics, image contrast agents, nanosensors and drug delivery systems. Anisotropic metallic nanoparticles possess potential applications in cell imaging and therapy+diagnostics (theranostics), but controlled synthesis and growth of these anisotropic or branched nanostructures has been challenging and usually require use of high concentrations of surfactants. Star-shaped gold nanoparticles were synthesized in high yield through a seed mediated route using HEPES as a precise shape-directing capping agent. Characterization was performed using advanced electron microscopy techniques including atomic resolution TEM, obtaining a detailed characterization of nanostructure and atomic arrangement. Spectroscopy techniques showed that particles have narrow size distribution, monodispersity and high colloidal stability, with absorbance into NIR region and high efficiency for SERS applications. Gold nanostars showed to be biocompatible and efficiently adsorbed and internalized by macrophages, as revealed by advanced FE-SEM and backscattered electron imaging techniques of complete unstained uncoated cells. Additionally, low voltage STEM and X-ray microanalysis revealed the ultra-structural location and confirmed stability of nanoparticles after endocytosis with high spatial resolution. PMID:23443314

Image Improvement Techniques

NASA Astrophysics Data System (ADS)

Shine, R. A.

1997-05-01

Over the last decade, a repertoire of techniques have been developed and/or refined to improve the quality of high spatial resolution solar movies taken from ground based observatories. These include real time image motion corrections, frame selection, phase diversity measurements of the wavefront, and extensive post processing to partially remove atmospheric distortion. Their practical application has been made possible by the increasing availability and decreasing cost of large CCD's with fast digital readouts and high speed computer workstations with large memories. Most successful have been broad band (0.3 to 10 nm) filtergram movies which can use exposure times of 10 to 30 ms, short enough to ``freeze'' atmospheric motions. Even so, only a handful of movies with excellent image quality for more than a hour have been obtained to date. Narrowband filtergrams (about 0.01 nm), such as those required for constructing magnetograms and Dopplergrams, have been more challenging although some single images approach the quality of the best continuum images. Some promising new techniques and instruments, together with persistence and good luck, should continue the progress made in the last several years.

Operational monitoring of land-cover change using multitemporal remote sensing data

NASA Astrophysics Data System (ADS)

Rogan, John

2005-11-01

Land-cover change, manifested as either land-cover modification and/or conversion, can occur at all spatial scales, and changes at local scales can have profound, cumulative impacts at broader scales. The implication of operational land-cover monitoring is that researchers have access to a continuous stream of remote sensing data, with the long term goal of providing for consistent and repetitive mapping. Effective large area monitoring of land-cover (i.e., >1000 km2) can only be accomplished by using remotely sensed images as an indirect data source in land-cover change mapping and as a source for land-cover change model projections. Large area monitoring programs face several challenges: (1) choice of appropriate classification scheme/map legend over large, topographically and phenologically diverse areas; (2) issues concerning data consistency and map accuracy (i.e., calibration and validation); (3) very large data volumes; (4) time consuming data processing and interpretation. Therefore, this dissertation research broadly addresses these challenges in the context of examining state-of-the-art image pre-processing, spectral enhancement, classification, and accuracy assessment techniques to assist the California Land-cover Mapping and Monitoring Program (LCMMP). The results of this dissertation revealed that spatially varying haze can be effectively corrected from Landsat data for the purposes of change detection. The Multitemporal Spectral Mixture Analysis (MSMA) spectral enhancement technique produced more accurate land-cover maps than those derived from the Multitemporal Kauth Thomas (MKT) transformation in northern and southern California study areas. A comparison of machine learning classifiers showed that Fuzzy ARTMAP outperformed two classification tree algorithms, based on map accuracy and algorithm robustness. Variation in spatial data error (positional and thematic) was explored in relation to environmental variables using geostatistical interpolation techniques. Finally, the land-cover modification maps generated for three time intervals (1985--1990--1996--2000), with nine change-classes revealed important variations in land-cover gain and loss between northern and southern California study areas.

sGD software for estimating spatially explicit indices of genetic diversity

Treesearch

A. J. Shirk; Samuel Cushman

2011-01-01

Anthropogenic landscape changes have greatly reduced the population size, range and migration rates of many terrestrial species. The small local effective population size of remnant populations favours loss of genetic diversity leading to reduced fitness and adaptive potential, and thus ultimately greater extinction risk. Accurately quantifying genetic diversity is...

Diversity and Community Can Coexist.

PubMed

Stivala, Alex; Robins, Garry; Kashima, Yoshihisa; Kirley, Michael

2016-03-01

We examine the (in)compatibility of diversity and sense of community by means of agent-based models based on the well-known Schelling model of residential segregation and Axelrod model of cultural dissemination. We find that diversity and highly clustered social networks, on the assumptions of social tie formation based on spatial proximity and homophily, are incompatible when agent features are immutable, and this holds even for multiple independent features. We include both mutable and immutable features into a model that integrates Schelling and Axelrod models, and we find that even for multiple independent features, diversity and highly clustered social networks can be incompatible on the assumptions of social tie formation based on spatial proximity and homophily. However, this incompatibility breaks down when cultural diversity can be sufficiently large, at which point diversity and clustering need not be negatively correlated. This implies that segregation based on immutable characteristics such as race can possibly be overcome by sufficient similarity on mutable characteristics based on culture, which are subject to a process of social influence, provided a sufficiently large "scope of cultural possibilities" exists. © Society for Community Research and Action 2016.

spads 1.0: a toolbox to perform spatial analyses on DNA sequence data sets.

PubMed

Dellicour, Simon; Mardulyn, Patrick

2014-05-01

SPADS 1.0 (for 'Spatial and Population Analysis of DNA Sequences') is a population genetic toolbox for characterizing genetic variability within and among populations from DNA sequences. In view of the drastic increase in genetic information available through sequencing methods, spads was specifically designed to deal with multilocus data sets of DNA sequences. It computes several summary statistics from populations or groups of populations, performs input file conversions for other population genetic programs and implements locus-by-locus and multilocus versions of two clustering algorithms to study the genetic structure of populations. The toolbox also includes two MATLAB and r functions, GDISPAL and GDIVPAL, to display differentiation and diversity patterns across landscapes. These functions aim to generate interpolating surfaces based on multilocus distance and diversity indices. In the case of multiple loci, such surfaces can represent a useful alternative to multiple pie charts maps traditionally used in phylogeography to represent the spatial distribution of genetic diversity. These coloured surfaces can also be used to compare different data sets or different diversity and/or distance measures estimated on the same data set. © 2013 John Wiley & Sons Ltd.

Demographic mechanisms underpinning genetic assimilation of remnant groups of a large carnivore

USGS Publications Warehouse

Mikle, Nathaniel; Graves, Tabitha A.; Kovach, Ryan P.; Kendall, Katherine C.; Macleod, Amy C.

2016-01-01

Current range expansions of large terrestrial carnivores are occurring following human-induced range contraction. Contractions are often incomplete, leaving small remnant groups in refugia throughout the former range. Little is known about the underlying ecological and evolutionary processes that influence how remnant groups are affected during range expansion. We used data from a spatially explicit, long-term genetic sampling effort of grizzly bears (Ursus arctos) in the Northern Continental Divide Ecosystem (NCDE), USA, to identify the demographic processes underlying spatial and temporal patterns of genetic diversity. We conducted parentage analysis to evaluate how reproductive success and dispersal contribute to spatio-temporal patterns of genetic diversity in remnant groups of grizzly bears existing in the southwestern (SW), southeastern (SE) and east-central (EC) regions of the NCDE. A few reproductively dominant individuals and local inbreeding caused low genetic diversity in peripheral regions that may have persisted for multiple generations before eroding rapidly (approx. one generation) during population expansion. Our results highlight that individual-level genetic and reproductive dynamics play critical roles during genetic assimilation, and show that spatial patterns of genetic diversity on the leading edge of an expansion may result from historical demographic patterns that are highly ephemeral.

Tree species, spatial heterogeneity, and seasonality drive soil fungal abundance, richness, and composition in Neotropical rainforests.

PubMed

Kivlin, Stephanie N; Hawkes, Christine V

2016-12-01

Tropical ecosystems remain poorly understood and this is particularly true for belowground soil fungi. Soil fungi may respond to plant identity when, for example, plants differentially allocate resources belowground. However, spatial and temporal heterogeneity in factors such as plant inputs, moisture, or nutrients can also affect fungal communities and obscure our ability to detect plant effects in single time point studies or within diverse forests. To address this, we sampled replicated monocultures of four tree species and secondary forest controls sampled in the drier and wetter seasons over 2 years. Fungal community composition was primarily related to vegetation type and spatial heterogeneity in the effects of vegetation type, with increasing divergence partly reflecting greater differences in soil pH and soil moisture. Across wetter versus drier dates, fungi were 7% less diverse, but up to four-fold more abundant. The combined effects of tree species and seasonality suggest that predicted losses of tropical tree diversity and intensification of drought have the potential to cascade belowground to affect both diversity and abundance of tropical soil fungi. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Demographic mechanisms underpinning genetic assimilation of remnant groups of a large carnivore

PubMed Central

Kovach, Ryan; Kendall, Katherine C.; Macleod, Amy C.

2016-01-01

Current range expansions of large terrestrial carnivores are occurring following human-induced range contraction. Contractions are often incomplete, leaving small remnant groups in refugia throughout the former range. Little is known about the underlying ecological and evolutionary processes that influence how remnant groups are affected during range expansion. We used data from a spatially explicit, long-term genetic sampling effort of grizzly bears (Ursus arctos) in the Northern Continental Divide Ecosystem (NCDE), USA, to identify the demographic processes underlying spatial and temporal patterns of genetic diversity. We conducted parentage analysis to evaluate how reproductive success and dispersal contribute to spatio-temporal patterns of genetic diversity in remnant groups of grizzly bears existing in the southwestern (SW), southeastern (SE) and east-central (EC) regions of the NCDE. A few reproductively dominant individuals and local inbreeding caused low genetic diversity in peripheral regions that may have persisted for multiple generations before eroding rapidly (approx. one generation) during population expansion. Our results highlight that individual-level genetic and reproductive dynamics play critical roles during genetic assimilation, and show that spatial patterns of genetic diversity on the leading edge of an expansion may result from historical demographic patterns that are highly ephemeral. PMID:27655768

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bernstein, Hans C.; Brislawn, Colin; Renslow, Ryan S.

Productivity is a major determinant of ecosystem diversity. Microbial ecosystems are the most diverse on the planet yet very few relationships between diversity and productivity have been reported as compared to macro-ecological studies. Here we evaluated the spatial relationships of productivity and microbiome diversity in a laboratory-cultivated photosynthetic mat. The goal was to determine how spatial diversification of microorganisms drives localized carbon and energy acquisition rates. We measured sub-millimeter depth profiles of net primary-productivity and gross oxygenic photosynthesis in the context of the localized microenvironment and community structure and observed negative correlations between species richness and productivity within the energy-replete,more » photic zone. Variations between localized community structures were associated with distinct taxa as well as environmental profiles describing a continuum of biological niches. Spatial regions corresponding to high primary productivity and photosynthesis rates had relatively low species richness and high evenness. Hence, this system exhibited negative species-productivity and species–energy relationships. These negative relationships may be indicative of photosynthetically-driven, light-controlled mat ecosystems that are able to be the most productive with a relatively smaller, even distributions of species that specialize within the highly-oxic, photic zones.« less

Integrating vegetation index time series and meteorological data to understand the effect of the land use/land cover (LULC) in the climatic seasonality of the Brazilian Cerrado

NASA Astrophysics Data System (ADS)

Lins, D. B.; Zullo, J.; Friedel, M. J.

2013-12-01

The Cerrado (savanna ecosystem) of São Paulo state (Brazil) represent a complex mosaic of different typologies of uses, actors and biophysical and social restrictions. Originally, 14% of the state of São Paulo area was covered by the diversity of Cerrado phytophysiognomies. Currently, only 1% of this original composition remains fragmented into numerous relicts of biodiversity, mainly concentrated in the central-eastern of the state. A relevant part of the fragments are found in areas of intense coverage change by human activities, whereas the greatest pressure comes from sugar cane cultivation, either by direct replacement of Cerrado vegetation or occupying pasture areas in the fragments edges. As a result, new local level dynamics has been introduced, directly or indirectly, affecting the established of processes in climate systems. In this study, the main goal is analyzing the relationship between the Cerrado landscape changing and the climate dynamics in regional and local areas. The multi-temporal MODIS 250 m Vegetation Index (VI) datasets (period of 2000 to 2012) are integrated with precipitation data of the correspondent period (http://www.agritempo.gov.br/),one of the most important variable of the spatial phytophysiognomies distribution. The integration of meteorological data enable the development of an integrated approach to understand the relationship between climatic seasonality and the changes in the spatial patterns. A procedure to congregated diverse dynamics information is the Self Organizing Map (SOM, Kohonen, 2001), a technique that relies on unsupervised competitive learning (Kohonen and Somervuo 2002) to recognize patterns. In this approach, high-dimensional data are represented on two dimensions, making possible to obtain patterns that takes into account information from different natures. Observed advances will contribute to bring machine-learning techniques as a valid tool to provide improve in land use/land cover (LULC) analyzes at different hierarchical scales to support numerous science and policy applications.

Patterns of fish community composition along a river affected by agricultural and urban disturbance in south-central Chile

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orrego, Rodrigo; Barra, Ricardo; Chiang, Gustavo

2008-03-01

Patterns of fish community composition in a south-central Chile river were investigated along the altitudinal-spatial and environmental gradient and as a function of anthropogenic factors. The spatial pattern of fish communities in different biocoenotic zones of the Chillan River is influenced by both natural factors such a hydrologic features, habitat, and feeding types, and also by water quality variables which can reduce the diversity and abundance of sensitive species. A principal component analysis incorporating both water quality parameters and biomarker responses of representative fish species was used to evaluate the status of fish communities along the spatial gradient of themore » stream. The abundance and diversity of the fish community changed from a low in the upper reaches where the low pollution-tolerant species such as salmonid dominated, to a reduced diversity in the lower reaches of the river where tolerant browser species such as cypriniformes dominated. Even though the spatial pattern of fish community structure is similar to that found for the Chilean Rivers, the structure of these communities is highly influenced by human disturbance, particularly along the lower reaches of the river.« less

Structure and biodiversity of coralligenous assemblages dominated by the precious red coral Corallium rubrum over broad spatial scales

PubMed Central

Casas-Güell, Edgar; Cebrian, Emma; Garrabou, Joaquim; Ledoux, Jean-Baptiste; Linares, Cristina; Teixidó, Núria

2016-01-01

Data on species diversity and structure in coralligenous outcrops dominated by Corallium rubrum are lacking. A hierarchical sampling including 3 localities and 9 sites covering more than 400 km of rocky coasts in NW Mediterranean, was designed to characterize the spatial variability of structure, composition and diversity of perennial species inhabiting coralligenous outcrops. We estimated species/taxa composition and abundance. Eight morpho-functional groups were defined according to their life span and growth to characterize the structural complexity of the outcrops. The species composition and structural complexity differed consistently across all spatial scales considered. The lowest and the highest variability were found among localities (separated by >200 km) and within sites (separated by 1–5 km), respectively supporting differences in diversity indices. The morpho-functional groups displayed a consistent spatial arrangement in terms of the number, size and shape of patches across study sites. These results contribute to filling the gap on the understanding of assemblage composition and structure and to build baselines to assess the response of this of this highly threatened habitat to anthropogenic disturbances. PMID:27857209

Spatial grain and the causes of regional diversity gradients in ants.

PubMed

Kaspari, Michael; Yuan, May; Alonso, Leeanne

2003-03-01

Gradients of species richness (S; the number of species of a given taxon in a given area and time) are ubiquitous. A key goal in ecology is to understand whether and how the many processes that generate these gradients act at different spatial scales. Here we evaluate six hypotheses for diversity gradients with 49 New World ant communities, from tundra to rain forest. We contrast their performance at three spatial grains from S(plot), the average number of ant species nesting in a m2 plot, through Fisher's alpha, an index that treats our 30 1-m2 plots as subsamples of a locality's diversity. At the smallest grain, S(plot), was tightly correlated (r2 = 0.99) with colony abundance in a fashion indistinguishable from the packing of randomly selected individuals into a fixed space. As spatial grain increased, the coaction of two factors linked to high net rates of diversification--warm temperatures and large areas of uniform climate--accounted for 75% of the variation in Fisher's alpha. However, the mechanisms underlying these correlations (i.e., precisely how temperature and area shape the balance of speciation to extinction) remain elusive.

Monitoring biological diversity: strategies, tools, limitations, and challenges

USGS Publications Warehouse

Beever, E.A.

2006-01-01

Monitoring is an assessment of the spatial and temporal variability in one or more ecosystem properties, and is an essential component of adaptive management. Monitoring can help determine whether mandated environmental standards are being met and can provide an early-warning system of ecological change. Development of a strategy for monitoring biological diversity will likely be most successful when based upon clearly articulated goals and objectives and may be enhanced by including several key steps in the process. Ideally, monitoring of biological diversity will measure not only composition, but also structure and function at the spatial and temporal scales of interest. Although biodiversity monitoring has several key limitations as well as numerous theoretical and practical challenges, many tools and strategies are available to address or overcome such challenges; I summarize several of these. Due to the diversity of spatio-temporal scales and comprehensiveness encompassed by existing definitions of biological diversity, an effective monitoring design will reflect the desired sampling domain of interest and its key stressors, available funding, legal requirements, and organizational goals.

Environment and host as large-scale controls of ectomycorrhizal fungi.

PubMed

van der Linde, Sietse; Suz, Laura M; Orme, C David L; Cox, Filipa; Andreae, Henning; Asi, Endla; Atkinson, Bonnie; Benham, Sue; Carroll, Christopher; Cools, Nathalie; De Vos, Bruno; Dietrich, Hans-Peter; Eichhorn, Johannes; Gehrmann, Joachim; Grebenc, Tine; Gweon, Hyun S; Hansen, Karin; Jacob, Frank; Kristöfel, Ferdinand; Lech, Paweł; Manninger, Miklós; Martin, Jan; Meesenburg, Henning; Merilä, Päivi; Nicolas, Manuel; Pavlenda, Pavel; Rautio, Pasi; Schaub, Marcus; Schröck, Hans-Werner; Seidling, Walter; Šrámek, Vít; Thimonier, Anne; Thomsen, Iben Margrete; Titeux, Hugues; Vanguelova, Elena; Verstraeten, Arne; Vesterdal, Lars; Waldner, Peter; Wijk, Sture; Zhang, Yuxin; Žlindra, Daniel; Bidartondo, Martin I

2018-06-06

Explaining the large-scale diversity of soil organisms that drive biogeochemical processes-and their responses to environmental change-is critical. However, identifying consistent drivers of belowground diversity and abundance for some soil organisms at large spatial scales remains problematic. Here we investigate a major guild, the ectomycorrhizal fungi, across European forests at a spatial scale and resolution that is-to our knowledge-unprecedented, to explore key biotic and abiotic predictors of ectomycorrhizal diversity and to identify dominant responses and thresholds for change across complex environmental gradients. We show the effect of 38 host, environment, climate and geographical variables on ectomycorrhizal diversity, and define thresholds of community change for key variables. We quantify host specificity and reveal plasticity in functional traits involved in soil foraging across gradients. We conclude that environmental and host factors explain most of the variation in ectomycorrhizal diversity, that the environmental thresholds used as major ecosystem assessment tools need adjustment and that the importance of belowground specificity and plasticity has previously been underappreciated.

A test of multiple hypotheses for the species richness gradient of South American owls.

PubMed

Diniz-Filho, José Alexandre Felizola; Rangel, Thiago F L V B; Hawkins, Bradford A

2004-08-01

Many mechanisms have been proposed to explain broad scale spatial patterns in species richness. In this paper, we evaluate five explanations for geographic gradients in species richness, using South American owls as a model. We compared the explanatory power of contemporary climate, landcover diversity, spatial climatic heterogeneity, evolutionary history, and area. An important aspect of our analyses is that very different hypotheses, such as history and area, can be quantified at the same observation scale and, consequently can be incorporated into a single analytical framework. Both area effects and owl phylogenetic history were poorly associated with richness, whereas contemporary climate, climatic heterogeneity at the mesoscale and landcover diversity explained ca. 53% of the variation in species richness. We conclude that both climate and environmental heterogeneity should be retained as plausible explanations for the diversity gradient. Turnover rates and scaling effects, on the other hand, although perhaps useful for detecting faunal changes and beta diversity at local and regional scales, are not strong explanations for the owl diversity gradient.

A new technique for identification of minerals in hyperspectral images. Application to robust characterization of phyllosilicate deposits at Mawrth Vallis using CRISM images.

NASA Astrophysics Data System (ADS)

Parente, M.; Bishop, J. L.

2008-12-01

Mapping of Mars by MRO has revealed the presence of numerous small phyllosilicate outcrops. These are typically identified in CRISM images using "summary products" (Pelkey, 2007) that consist of band ratios, depths and spectral slopes around diagnostic wavelengths. The summary products are designed to capture spectral features related to both surface mineralogy and atmospheric gases and aerosols. Such products, as an analysis tool to characterize composition as well as a targeting tool to identify areas of mineralogical interest, have been successful in capturing the known diversity of the Martian surface, and in highlighting locations with strong spectral signatures. Here we present alternative mineral mapping technique that 1) aims to increase the robustness of mineral detections with respect to the specific CRISM artifacts, 2) takes advantage of the spatial context of each pixel and 3) develops new parameters for the discrimination of species in the phyllosilicates family. We include spatial context by evaluating spectral shapes, band depths and spectral slopes for the current pixel based on its spatial neighbors within the same geological unit. Furthermore, the parameters are based on estimates that are more robust to CRISM speckling noise that might alter the parameters and potentially the mineral interpretation. As an effort to distinguish between phyllosilicates species, we are augmenting the suite of existent parameters with a set of mineral parameters that involve the position, number and shapes of diagnostic phyllosilicate absorptions. We are comparing the effectiveness of this new approach to the summary product procedure. The study shows that homogeneous mineral maps and diagnostic spectral identifications are possible as a result of the application of such new parameters. We applied the technique to the discrimination of kaolinite in Mawrth Vallis. The experiments show several small kaolinite outcrops dispersed within the more extensive Al-rich phyllosilicates in regions around the MSL landing sites. Another test was the discrimination of montmorillonite and nontronite in Mawrth Vallis that can be successfully accomplished by band depths summary products near 2.2 and 2.3 μm. The new technique produces improved maps with lower noise levels and lower percentage of false detections.

Crosscutting Airborne Remote Sensing Technologies for Oil and Gas and Earth Science Applications

NASA Technical Reports Server (NTRS)

Aubrey, A. D.; Frankenberg, C.; Green, R. O.; Eastwood, M. L.; Thompson, D. R.; Thorpe, A. K.

2015-01-01

Airborne imaging spectroscopy has evolved dramatically since the 1980s as a robust remote sensing technique used to generate 2-dimensional maps of surface properties over large spatial areas. Traditional applications for passive airborne imaging spectroscopy include interrogation of surface composition, such as mapping of vegetation diversity and surface geological composition. Two recent applications are particularly relevant to the needs of both the oil and gas as well as government sectors: quantification of surficial hydrocarbon thickness in aquatic environments and mapping atmospheric greenhouse gas components. These techniques provide valuable capabilities for petroleum seepage in addition to detection and quantification of fugitive emissions. New empirical data that provides insight into the source strength of anthropogenic methane will be reviewed, with particular emphasis on the evolving constraints enabled by new methane remote sensing techniques. Contemporary studies attribute high-strength point sources as significantly contributing to the national methane inventory and underscore the need for high performance remote sensing technologies that provide quantitative leak detection. Imaging sensors that map spatial distributions of methane anomalies provide effective techniques to detect, localize, and quantify fugitive leaks. Airborne remote sensing instruments provide the unique combination of high spatial resolution (<1 m) and large coverage required to directly attribute methane emissions to individual emission sources. This capability cannot currently be achieved using spaceborne sensors. In this study, results from recent NASA remote sensing field experiments focused on point-source leak detection, will be highlighted. This includes existing quantitative capabilities for oil and methane using state-of-the-art airborne remote sensing instruments. While these capabilities are of interest to NASA for assessment of environmental impact and global climate change, industry similarly seeks to detect and localize leaks of both oil and methane across operating fields. In some cases, higher sensitivities desired for upstream and downstream applications can only be provided by new airborne remote sensing instruments tailored specifically for a given application. There exists a unique opportunity for alignment of efforts between commercial and government sectors to advance the next generation of instruments to provide more sensitive leak detection capabilities, including those for quantitative source strength determination.

Patterns of Racial Diversity and Segregation in the United States: 1990–2010*

PubMed Central

Wright, Richard; Ellis, Mark; Holloway, Steven R.; Wong, Sandy

2014-01-01

The growing ethnic and racial diversity of the United States is evident at all spatial scales. One of the striking features of this new mixture of peoples, however, is that this new diversity often occurs in tandem with racial concentration. This article surveys these new geographies from four points of view: the nation as a whole, states, large metropolitan areas, and neighborhoods. The analysis at each scale relies on a new taxonomy of racial composition that simultaneously appraises both diversity and the lack thereof (Holloway, Wright, and Ellis 2012). Urban analysis often posits neighborhood racial segregation and diversity as either endpoints on a continuum of racial dominance or mirror images of one another. We disturb that perspective and stress that segregation and diversity must be jointly understood—they are necessarily related, although not as inevitable binary opposites. Using census data from 1990, 2000, and 2010, the research points to how patterns of racial diversity and dominance interact across varying spatial scales. This investigation helps answer some basic questions about the changing geographies of racialized groups, setting the stage for the following articles that explore the relationship between geography and the participation of underrepresented groups in higher education. PMID:25083001

Environmental characteristics drive variation in Amazonian understorey bird assemblages

PubMed Central

Magnusson, William E.; Anderson, Marti J.; Schlegel, Martin; Pe’er, Guy; Henle, Klaus

2017-01-01

Tropical bird assemblages display patterns of high alpha and beta diversity and, as tropical birds exhibit strong habitat specificity, their spatial distributions are generally assumed to be driven primarily by environmental heterogeneity and interspecific interactions. However, spatial distributions of some Amazonian forest birds are also often restricted by large rivers and other large-scale topographic features, suggesting that dispersal limitation may also play a role in driving species’ turnover. In this study, we evaluated the effects of environmental characteristics, topographic and spatial variables on variation in local assemblage structure and diversity of birds in an old-growth forest in central Amazonia. Birds were mist-netted in 72 plots distributed systematically across a 10,000 ha reserve in each of three years. Alpha diversity remained stable through time, but species composition changed. Spatial variation in bird-assemblage structure was significantly related to environmental and topographic variables but not strongly related to spatial variables. At a broad scale, we found bird assemblages to be significantly distinct between two watersheds that are divided by a central ridgeline. We did not detect an effect of the ridgeline per se in driving these patterns, indicating that most birds are able to fly across it, and that differences in assemblage structure between watersheds may be due to unmeasured environmental variables or unique combinations of measured variables. Our study indicates that complex geography and landscape features can act together with environmental variables to drive changes in the diversity and composition of tropical bird assemblages at local scales, but highlights that we still know very little about what makes different parts of tropical forest suitable for different species. PMID:28225774

Evaluating population expansion of black bears using spatial capture-recapture

USGS Publications Warehouse

Sun, Catherine C.; Fuller, Angela K.; Hare, Matthew P.; Hurst, Jeremy E.

2017-01-01

The population of American black bears (Ursus americanus) in southern New York, USA has been growing and expanding in range since the 1990s. This has motivated a need to anticipate future patterns of range expansion. We conducted a non-invasive, genetic, spatial capture-recapture (SCR) study to estimate black bear density and identify spatial patterns of population density that are potentially associated with range expansion. We collected hair samples in a 2,519-km2 study area in southern New York with barbed-wire hair snares and identified individuals and measured genetic diversity using 7 microsatellite loci and 1 sex-linked marker. We estimated a mean density of black bears in the region of 13.7 bears/100 km2, and detected a slight latitudinal gradient in density consistent with the documented range expansion. However, elevation and the amounts of forest, crop, and developed landcover types did not influence density, suggesting that bears are using a diversity of resources in this heterogeneous landscape outside their previously described distribution. These results provide the first robust baseline estimates for population density and distribution associated with different landcover types in the expanded bear range. Further, genetic diversity was comparable to that of non-expanding black bear populations in the eastern United States, and in combination with the latitudinal density gradient, suggest that the study area is not at the colonizing front of the range expansion. In addition, the diversity of landcover types used by bears in the study area implies a possible lack of constraints for further northern expansion of the black bear range. Our non-invasive, genetic, spatial capture-recapture approach has utility for studying populations of other species that may be expanding in range because SCR allows for the testing of explicit, spatial ecological hypotheses. 

Present spatial diversity patterns of Theobroma cacao L. in the neotropics reflect genetic differentiation in pleistocene refugia followed by human-influenced dispersal.

PubMed

Thomas, Evert; van Zonneveld, Maarten; Loo, Judy; Hodgkin, Toby; Galluzzi, Gea; van Etten, Jacob

2012-01-01

Cacao (Theobroma cacao L.) is indigenous to the Amazon basin, but is generally believed to have been domesticated in Mesoamerica for the production of chocolate beverage. However, cacao's distribution of genetic diversity in South America is also likely to reflect pre-Columbian human influences that were superimposed on natural processes of genetic differentiation. Here we present the results of a spatial analysis of the intra-specific diversity of cacao in Latin America, drawing on a dataset of 939 cacao trees genotypically characterized by means of 96 SSR markers. To assess continental diversity patterns we performed grid-based calculations of allelic richness, Shannon diversity and Nei gene diversity, and distinguished different spatially coherent genetic groups by means of cluster analysis. The highest levels of genetic diversity were observed in the Upper Amazon areas from southern Peru to the Ecuadorian Amazon and the border areas between Colombia, Peru and Brazil. On the assumption that the last glaciation (22,000-13,000 BP) had the greatest pre-human impact on the current distribution and diversity of cacao, we modeled the species' Pleistocene niche suitability and overlaid this with present-day diversity maps. The results suggest that cacao was already widely distributed in the Western Amazon before the onset of glaciation. During glaciations, cacao populations were likely to have been restricted to several refugia where they probably underwent genetic differentiation, resulting in a number of genetic clusters which are representative for, or closest related to, the original wild cacao populations. The analyses also suggested that genetic differentiation and geographical distribution of a number of other clusters seem to have been significantly affected by processes of human management and accompanying genetic bottlenecks. We discuss the implications of these results for future germplasm collection and in situ, on farm and ex situ conservation of cacao.

Present Spatial Diversity Patterns of Theobroma cacao L. in the Neotropics Reflect Genetic Differentiation in Pleistocene Refugia Followed by Human-Influenced Dispersal

PubMed Central

Thomas, Evert; van Zonneveld, Maarten; Loo, Judy; Hodgkin, Toby; Galluzzi, Gea; van Etten, Jacob

2012-01-01

Cacao (Theobroma cacao L.) is indigenous to the Amazon basin, but is generally believed to have been domesticated in Mesoamerica for the production of chocolate beverage. However, cacao’s distribution of genetic diversity in South America is also likely to reflect pre-Columbian human influences that were superimposed on natural processes of genetic differentiation. Here we present the results of a spatial analysis of the intra-specific diversity of cacao in Latin America, drawing on a dataset of 939 cacao trees genotypically characterized by means of 96 SSR markers. To assess continental diversity patterns we performed grid-based calculations of allelic richness, Shannon diversity and Nei gene diversity, and distinguished different spatially coherent genetic groups by means of cluster analysis. The highest levels of genetic diversity were observed in the Upper Amazon areas from southern Peru to the Ecuadorian Amazon and the border areas between Colombia, Peru and Brazil. On the assumption that the last glaciation (22,000–13,000 BP) had the greatest pre-human impact on the current distribution and diversity of cacao, we modeled the species’ Pleistocene niche suitability and overlaid this with present-day diversity maps. The results suggest that cacao was already widely distributed in the Western Amazon before the onset of glaciation. During glaciations, cacao populations were likely to have been restricted to several refugia where they probably underwent genetic differentiation, resulting in a number of genetic clusters which are representative for, or closest related to, the original wild cacao populations. The analyses also suggested that genetic differentiation and geographical distribution of a number of other clusters seem to have been significantly affected by processes of human management and accompanying genetic bottlenecks. We discuss the implications of these results for future germplasm collection and in situ, on farm and ex situ conservation of cacao. PMID:23112832

Bayesian Integration of Spatial Information

ERIC Educational Resources Information Center

Cheng, Ken; Shettleworth, Sara J.; Huttenlocher, Janellen; Rieser, John J.

2007-01-01

Spatial judgments and actions are often based on multiple cues. The authors review a multitude of phenomena on the integration of spatial cues in diverse species to consider how nearly optimally animals combine the cues. Under the banner of Bayesian perception, cues are sometimes combined and weighted in a near optimal fashion. In other instances…

The effects of habitat connectivity and regional heterogeneity on artificial pond metacommunities.

PubMed

Pedruski, Michael T; Arnott, Shelley E

2011-05-01

Habitat connectivity and regional heterogeneity represent two factors likely to affect biodiversity across different spatial scales. We performed a 3 × 2 factorial design experiment to investigate the effects of connectivity, heterogeneity, and their interaction on artificial pond communities of freshwater invertebrates at the local (α), among-community (β), and regional (γ) scales. Despite expectations that the effects of connectivity would depend on levels of regional heterogeneity, no significant interactions were found for any diversity index investigated at any spatial scale. While observed responses of biodiversity to connectivity and heterogeneity depended to some extent on the diversity index and spatial partitioning formula used, the general pattern shows that these factors largely act at the β scale, as opposed to the α or γ scales. We conclude that the major role of connectivity in aquatic invertebrate communities is to act as a homogenizing force with relatively little effect on diversity at the α or γ levels. Conversely, heterogeneity acts as a force maintaining differences between communities.

Modeling Effects of Local Extinctions on Culture Change and Diversity in the Paleolithic

PubMed Central

Premo, L. S.; Kuhn, Steven L.

2010-01-01

The persistence of early stone tool technologies has puzzled archaeologists for decades. Cognitively based explanations, which presume either lack of ability to innovate or extreme conformism, do not account for the totality of the empirical patterns. Following recent research, this study explores the effects of demographic factors on rates of culture change and diversification. We investigate whether the appearance of stability in early Paleolithic technologies could result from frequent extinctions of local subpopulations within a persistent metapopulation. A spatially explicit agent-based model was constructed to test the influence of local extinction rate on three general cultural patterns that archaeologists might observe in the material record: total diversity, differentiation among spatially defined groups, and the rate of cumulative change. The model shows that diversity, differentiation, and the rate of cumulative cultural change would be strongly affected by local extinction rates, in some cases mimicking the results of conformist cultural transmission. The results have implications for understanding spatial and temporal patterning in ancient material culture. PMID:21179418

Fungal Diversity in Tomato Rhizosphere Soil under Conventional and Desert Farming Systems

PubMed Central

Kazerooni, Elham A.; Maharachchikumbura, Sajeewa S. N.; Rethinasamy, Velazhahan; Al-Mahrouqi, Hamed; Al-Sadi, Abdullah M.

2017-01-01

This study examined fungal diversity and composition in conventional (CM) and desert farming (DE) systems in Oman. Fungal diversity in the rhizosphere of tomato was assessed using 454-pyrosequencing and culture-based techniques. Both techniques produced variable results in terms of fungal diversity, with 25% of the fungal classes shared between the two techniques. In addition, pyrosequencing recovered more taxa compared to direct plating. These findings could be attributed to the ability of pyrosequencing to recover taxa that cannot grow or are slow growing on culture media. Both techniques showed that fungal diversity in the conventional farm was comparable to that in the desert farm. However, the composition of fungal classes and taxa in the two farming systems were different. Pyrosequencing revealed that Microsporidetes and Dothideomycetes are the two most common fungal classes in CM and DE, respectively. However, the culture-based technique revealed that Eurotiomycetes was the most abundant class in both farming systems and some classes, such as Microsporidetes, were not detected by the culture-based technique. Although some plant pathogens (e.g., Pythium or Fusarium) were detected in the rhizosphere of tomato, the majority of fungal species in the rhizosphere of tomato were saprophytes. Our study shows that the cultivation system may have an impact on fungal diversity. The factors which affected fungal diversity in both farms are discussed. PMID:28824590

Genotype diversity of Escherichia coli isolates in natural waters determined by PFGE and ERIC-PCR.

PubMed

Casarez, Elizabeth A; Pillai, Suresh D; Di Giovanni, George D

2007-08-01

Most library-dependent bacterial source tracking studies using Escherichia coli (E. coli) have focused on strain diversity of isolates obtained from known human and animal faecal sources for library development. In contrast, this study evaluated the genotype variation of E. coli isolated from natural surface water using pulsed field gel electrophoresis (PFGE) and enterobacterial repetitive intergenic consensus sequence polymerase chain reaction (ERIC-PCR) to better understand these naturally occurring populations. A total of 650 water samples were collected over a nine month period from eleven sampling stations from Lake Waco and Belton Lake in Central Texas. Of the 650 water samples collected, 412 were positive for E. coli, yielding a total of 631 E. coli isolates (1-12 isolates collected per sample). PFGE and ERIC-PCR patterns were successfully generated for 555 isolates and were compared using the curve-based Pearson's product-moment correlation coefficient. The 555 E. coli isolates represented 461 PFGE genotypes, with 84% (386/461) of the genotypes being represented by individual isolates. The remaining 75 genotypes were represented by 2-5 isolates each. Using ERIC-PCR, the 555 E. coli isolates represented 175 genotypes, with 63% (109/175) of the genotypes being represented by individual isolates. In contrast to the PFGE results, two ERIC-PCR genotypes represented 37% of the E. coli isolates, (83 and 124 isolates, respectively), and were found throughout the watersheds both spatially and temporally. Based on the PFGE genotype diversity of water isolates, there is little evidence that a small number of environmentally-adapted E. coli represent dominant populations in the studied waterbodies. However, with the lower discriminatory power technique ERIC-PCR, an opposing conclusion might have been drawn. These results emphasize the importance of considering the resolving power of the source tracking technique being used when assessing strain diversity and geographical stability.

Conservation Action Based on Threatened Species Capture Taxonomic and Phylogenetic Richness in Breeding and Wintering Populations of Central Asian Birds

PubMed Central

Schweizer, Manuel; Ayé, Raffael; Kashkarov, Roman; Roth, Tobias

2014-01-01

Although phylogenetic diversity has been suggested to be relevant from a conservation point of view, its role is still limited in applied nature conservation. Recently, the practice of investing conservation resources based on threatened species was identified as a reason for the slow integration of phylogenetic diversity in nature conservation planning. One of the main arguments is based on the observation that threatened species are not evenly distributed over the phylogenetic tree. However this argument seems to dismiss the fact that conservation action is a spatially explicit process, and even if threatened species are not evenly distributed over the phylogenetic tree, the occurrence of threatened species could still indicate areas with above average phylogenetic diversity and consequently could protect phylogenetic diversity. Here we aim to study the selection of important bird areas in Central Asia, which were nominated largely based on the presence of threatened bird species. We show that although threatened species occurring in Central Asia do not capture phylogenetically more distinct species than expected by chance, the current spatially explicit conservation approach of selecting important bird areas covers above average taxonomic and phylogenetic diversity of breeding and wintering birds. We conclude that the spatially explicit processes of conservation actions need to be considered in the current discussion of whether new prioritization methods are needed to complement conservation action based on threatened species. PMID:25337861

Spatial variability in community composition on a granite breakwater versus natural rocky shores: lack of microhabitats suppresses intertidal biodiversity.

PubMed

Aguilera, Moisés A; Broitman, Bernardo R; Thiel, Martin

2014-10-15

Strong differences have been observed between the assemblages on artificial reefs and on natural hard-bottom habitats worldwide, but little is known about the mechanisms that cause contrasting biodiversity patterns. We examined the influence of spatial attributes in relation to both biogenic and topographic microhabitats, in the distribution and composition of intertidal species on both artificial and natural reefs. We found higher small-scale spatial heterogeneity on the natural reef compared with the study breakwater. Species richness and diversity were associated with a higher availability of crevices, rock pools and mussels in natural habitats. Spatial distribution of certain grazers corresponded well with the spatial structure of microhabitats. In contrast, the lack of microhabitats on the breakwater resulted in the absence of several grazers reflected in lower species richness. Biogenic and topographic microhabitats can have interactive effects providing niche opportunities for multiple species, explaining differences in species diversity between artificial versus natural reefs. Copyright © 2014 Elsevier Ltd. All rights reserved.

Disaster Governance for Community Resilience in Coastal Towns: Chilean Case Studies.

PubMed

Villagra, Paula; Quintana, Carolina

2017-09-14

This study aimed to further our understanding of a characteristic of Community Resilience known as Disaster Governance. Three attributes of Disaster Governance-redundancy, diversity, and overlap-were studied in four coastal towns in southern Chile that are at risk of tsunamis. Overall, we explored how different spatial structures of human settlements influence Disaster Governance. Using the Projective Mapping Technique, the distribution of emergency institutions (N = 32) and uses given to specific sites (e.g., for refuge, sanitary purposes and medical attention) were mapped. Content and GIS analyses (Directional Distribution and Kernel Density Index) were used to explore the dispersion and concentration of institutions and uses in each town. Disaster Governance was found to be highly influenced by decisions taken during regional, urban, and emergency planning. Governance is better in towns of higher order in the communal hierarchical structure. Most of the emergency institutions were found to be located in central and urban areas, which, in turn, assures more redundancy, overlap, and diversity in governance in the event of a tsunami. Lack of flexibility of emergency plans also limits governance in rural and indigenous areas. While the spatial relationships found in this study indicate that urban sectors have better Disaster Governance than rural and indigenous sectors, the influence of resource availability after tsunamis, the role and responsibility of different levels of governments, and the politics of disaster also play an important role in Disaster Governance for determining Community Resilience. These findings shed light on emergency planning and aspects of the Disaster Management cycle.

Variable Gene Dispersal Conditions and Spatial Deforestation Patterns Can Interact to Affect Tropical Tree Conservation Outcomes

PubMed Central

Kashimshetty, Yamini; Pelikan, Stephan; Rogstad, Steven H.

2015-01-01

Tropical lowland rain forest (TLRF) biodiversity is under threat from anthropogenic factors including deforestation which creates forest fragments of different sizes that can further undergo various internal patterns of logging. Such interventions can modify previous equilibrium abundance and spatial distribution patterns of offspring recruitment and/or pollen dispersal. Little is known about how these aspects of deforestation and fragmentation might synergistically affect TLRF tree recovery demographics and population genetics in newly formed forest fragments. To investigate these TLRF anthropogenic disturbance processes we used the computer program NEWGARDEN (NG), which models spatially-explicit, individual-based plant populations, to simulate 10% deforestation in six different spatial logging patterns for the plant functional type of a long-lived TLRF canopy tree species. Further, each logging pattern was analyzed under nine varying patterns of offspring versus pollen dispersal distances that could have arisen post-fragmentation. Results indicated that gene dispersal condition (especially via offspring) had a greater effect on population growth and genetic diversity retention (explaining 98.5% and 88.8% of the variance respectively) than spatial logging pattern (0.2% and 4.7% respectively), with ‘Near’ distance dispersal maximizing population growth and genetic diversity relative to distant dispersal. Within logged regions of the fragment, deforestation patterns closer to fragment borders more often exhibited lower population recovery rates and founding genetic diversity retention relative to more centrally located logging. These results suggest newly isolated fragments have populations that are more sensitive to the way in which their offspring and pollen dispersers are affected than the spatial pattern in which subsequent logging occurs, and that large variation in the recovery rates of different TLRF tree species attributable to altered gene dispersal regimens will be a likely outcome of fragmentation. Conservation implications include possible manual interventions (manual manipulations of offspring dispersers and/or pollinators) in forest fragments to increase population recovery and genetic diversity retention. PMID:26000951

Variable gene dispersal conditions and spatial deforestation patterns can interact to affect tropical tree conservation outcomes.

PubMed

Kashimshetty, Yamini; Pelikan, Stephan; Rogstad, Steven H

2015-01-01

Tropical lowland rain forest (TLRF) biodiversity is under threat from anthropogenic factors including deforestation which creates forest fragments of different sizes that can further undergo various internal patterns of logging. Such interventions can modify previous equilibrium abundance and spatial distribution patterns of offspring recruitment and/or pollen dispersal. Little is known about how these aspects of deforestation and fragmentation might synergistically affect TLRF tree recovery demographics and population genetics in newly formed forest fragments. To investigate these TLRF anthropogenic disturbance processes we used the computer program NEWGARDEN (NG), which models spatially-explicit, individual-based plant populations, to simulate 10% deforestation in six different spatial logging patterns for the plant functional type of a long-lived TLRF canopy tree species. Further, each logging pattern was analyzed under nine varying patterns of offspring versus pollen dispersal distances that could have arisen post-fragmentation. Results indicated that gene dispersal condition (especially via offspring) had a greater effect on population growth and genetic diversity retention (explaining 98.5% and 88.8% of the variance respectively) than spatial logging pattern (0.2% and 4.7% respectively), with 'Near' distance dispersal maximizing population growth and genetic diversity relative to distant dispersal. Within logged regions of the fragment, deforestation patterns closer to fragment borders more often exhibited lower population recovery rates and founding genetic diversity retention relative to more centrally located logging. These results suggest newly isolated fragments have populations that are more sensitive to the way in which their offspring and pollen dispersers are affected than the spatial pattern in which subsequent logging occurs, and that large variation in the recovery rates of different TLRF tree species attributable to altered gene dispersal regimens will be a likely outcome of fragmentation. Conservation implications include possible manual interventions (manual manipulations of offspring dispersers and/or pollinators) in forest fragments to increase population recovery and genetic diversity retention.

Diversity in spatial scope of contrast adaptation among mouse retinal ganglion cells.

PubMed

Khani, Mohammad Hossein; Gollisch, Tim

2017-12-01

Retinal ganglion cells adapt to changes in visual contrast by adjusting their response kinetics and sensitivity. While much work has focused on the time scales of these adaptation processes, less is known about the spatial scale of contrast adaptation. For example, do small, localized contrast changes affect a cell's signal processing across its entire receptive field? Previous investigations have provided conflicting evidence, suggesting that contrast adaptation occurs either locally within subregions of a ganglion cell's receptive field or globally over the receptive field in its entirety. Here, we investigated the spatial extent of contrast adaptation in ganglion cells of the isolated mouse retina through multielectrode-array recordings. We applied visual stimuli so that ganglion cell receptive fields contained regions where the average contrast level changed periodically as well as regions with constant average contrast level. This allowed us to analyze temporal stimulus integration and sensitivity separately for stimulus regions with and without contrast changes. We found that the spatial scope of contrast adaptation depends strongly on cell identity, with some ganglion cells displaying clear local adaptation, whereas others, in particular large transient ganglion cells, adapted globally to contrast changes. Thus, the spatial scope of contrast adaptation in mouse retinal ganglion cells appears to be cell-type specific. This could reflect differences in mechanisms of contrast adaptation and may contribute to the functional diversity of different ganglion cell types. NEW & NOTEWORTHY Understanding whether adaptation of a neuron in a sensory system can occur locally inside the receptive field or whether it always globally affects the entire receptive field is important for understanding how the neuron processes complex sensory stimuli. For mouse retinal ganglion cells, we here show that both local and global contrast adaptation exist and that this diversity in spatial scope can contribute to the functional diversity of retinal ganglion cell types. Copyright © 2017 the American Physiological Society.

Diversity in spatial scope of contrast adaptation among mouse retinal ganglion cells

PubMed Central

Khani, Mohammad Hossein

2017-01-01

Retinal ganglion cells adapt to changes in visual contrast by adjusting their response kinetics and sensitivity. While much work has focused on the time scales of these adaptation processes, less is known about the spatial scale of contrast adaptation. For example, do small, localized contrast changes affect a cell’s signal processing across its entire receptive field? Previous investigations have provided conflicting evidence, suggesting that contrast adaptation occurs either locally within subregions of a ganglion cell’s receptive field or globally over the receptive field in its entirety. Here, we investigated the spatial extent of contrast adaptation in ganglion cells of the isolated mouse retina through multielectrode-array recordings. We applied visual stimuli so that ganglion cell receptive fields contained regions where the average contrast level changed periodically as well as regions with constant average contrast level. This allowed us to analyze temporal stimulus integration and sensitivity separately for stimulus regions with and without contrast changes. We found that the spatial scope of contrast adaptation depends strongly on cell identity, with some ganglion cells displaying clear local adaptation, whereas others, in particular large transient ganglion cells, adapted globally to contrast changes. Thus, the spatial scope of contrast adaptation in mouse retinal ganglion cells appears to be cell-type specific. This could reflect differences in mechanisms of contrast adaptation and may contribute to the functional diversity of different ganglion cell types. NEW & NOTEWORTHY Understanding whether adaptation of a neuron in a sensory system can occur locally inside the receptive field or whether it always globally affects the entire receptive field is important for understanding how the neuron processes complex sensory stimuli. For mouse retinal ganglion cells, we here show that both local and global contrast adaptation exist and that this diversity in spatial scope can contribute to the functional diversity of retinal ganglion cell types. PMID:28904106

Metabarcoding reveals environmental factors influencing spatio-temporal variation in pelagic micro-eukaryotes.

PubMed

Brannock, Pamela M; Ortmann, Alice C; Moss, Anthony G; Halanych, Kenneth M

2016-08-01

Marine environments harbour a vast diversity of micro-eukaryotic organisms (protists and other small eukaryotes) that play important roles in structuring marine ecosystems. However, micro-eukaryote diversity is not well understood. Likewise, knowledge is limited regarding micro-eukaryote spatial and seasonal distribution, especially over long temporal scales. Given the importance of this group for mobilizing energy from lower trophic levels near the base of the food chain to larger organisms, assessing community stability, diversity and resilience is important to understand ecosystem health. Herein, we use a metabarcoding approach to examine pelagic micro-eukaryote communities over a 2.5-year time series. Bimonthly surface sampling (July 2009 to December 2011) was conducted at four locations within Mobile Bay (Bay) and along the Alabama continental shelf (Shelf). Alpha-diversity only showed significant differences in Shelf sites, with the greatest differences observed between summer and winter. Beta-diversity showed significant differences in community composition in relation to season and the Bay was dominated by diatoms, while the Shelf was characterized by dinoflagellates and copepods. The northern Gulf of Mexico is heavily influenced by the Mobile River Basin, which brings low-salinity nutrient-rich water mostly during winter and spring. Community composition was correlated with salinity, temperature and dissolved silicate. However, species interactions (e.g. predation and parasitism) may also contribute to the observed variation, especially on the Shelf, which warrants further exploration. Metabarcoding revealed clear patterns in surface pelagic micro-eukaryote communities that were consistent over multiple years, demonstrating how these techniques could be greatly beneficial to ecological monitoring and management over temporal scales. © 2016 John Wiley & Sons Ltd.

Genome-Wide Diversity and Phylogeography of Mycobacterium avium subsp. paratuberculosis in Canadian Dairy Cattle

PubMed Central

Ahlstrom, Christina; Barkema, Herman W.; Stevenson, Karen; Zadoks, Ruth N.; Biek, Roman; Kao, Rowland; Trewby, Hannah; Haupstein, Deb; Kelton, David F.; Fecteau, Gilles; Labrecque, Olivia; Keefe, Greg P.; McKenna, Shawn L. B.; Tahlan, Kapil; De Buck, Jeroen

2016-01-01

Mycobacterium avium subsp. paratuberculosis (MAP) is the causative bacterium of Johne’s disease (JD) in ruminants. The control of JD in the dairy industry is challenging, but can be improved with a better understanding of the diversity and distribution of MAP subtypes. Previously established molecular typing techniques used to differentiate MAP have not been sufficiently discriminatory and/or reliable to accurately assess the population structure. In this study, the genetic diversity of 182 MAP isolates representing all Canadian provinces was compared to the known global diversity, using single nucleotide polymorphisms identified through whole genome sequencing. MAP isolates from Canada represented a subset of the known global diversity, as there were global isolates intermingled with Canadian isolates, as well as multiple global subtypes that were not found in Canada. One Type III and six “Bison type” isolates were found in Canada as well as one Type II subtype that represented 86% of all Canadian isolates. Rarefaction estimated larger subtype richness in Québec than in other Canadian provinces using a strict definition of MAP subtypes and lower subtype richness in the Atlantic region using a relaxed definition. Significant phylogeographic clustering was observed at the inter-provincial but not at the intra-provincial level, although most major clades were found in all provinces. The large number of shared subtypes among provinces suggests that cattle movement is a major driver of MAP transmission at the herd level, which is further supported by the lack of spatial clustering on an intra-provincial scale. PMID:26871723

Disentangling environmental correlates of vascular plant biodiversity in a Mediterranean hotspot.

PubMed

Molina-Venegas, Rafael; Aparicio, Abelardo; Pina, Francisco José; Valdés, Benito; Arroyo, Juan

2013-10-01

We determined the environmental correlates of vascular plant biodiversity in the Baetic-Rifan region, a plant biodiversity hotspot in the western Mediterranean. A catalog of the whole flora of Andalusia and northern Morocco, the region that includes most of the Baetic-Rifan complex, was compiled using recent comprehensive floristic catalogs. Hierarchical cluster analysis (HCA) and detrended correspondence analysis (DCA) of the different ecoregions of Andalusia and northern Morocco were conducted to determine their floristic affinities. Diversity patterns were studied further by focusing on regional endemic taxa. Endemic and nonendemic alpha diversities were regressed to several environmental variables. Finally, semi-partial regressions on distance matrices were conducted to extract the respective contributions of climatic, altitudinal, lithological, and geographical distance matrices to beta diversity in endemic and nonendemic taxa. We found that West Rifan plant assemblages had more similarities with Andalusian ecoregions than with other nearby northern Morocco ecoregions. The endemic alpha diversity was explained relatively well by the environmental variables related to summer drought and extreme temperature values. Of all the variables, geographical distance contributed by far the most to spatial turnover in species diversity in the Baetic-Rifan hotspot. In the Baetic range, elevation was the most significant driver of nonendemic species beta diversity, while lithology and elevation were the main drivers of endemic beta diversity. Despite the fact that Andalusia and northern Morocco are presently separated by the Atlantic Ocean and the Mediterranean Sea, the Baetic and Rifan mountain ranges have many floristic similarities - especially in their western ranges - due to past migration of species across the Strait of Gibraltar. Climatic variables could be shaping the spatial distribution of endemic species richness throughout the Baetic-Rifan hotspot. Determinants of spatial turnover in biodiversity in the Baetic-Rifan hotspot vary in importance between endemic and nonendemic species.

Reproductive phenology of coastal plain Atlantic forest vegetation: comparisons from seashore to foothills.

PubMed

Staggemeier, Vanessa Graziele; Morellato, Leonor Patrícia Cerdeira

2011-11-01

The diversity of tropical forest plant phenology has called the attention of researchers for a long time. We continue investigating the factors that drive phenological diversity on a wide scale, but we are unaware of the variation of plant reproductive phenology at a fine spatial scale despite the high spatial variation in species composition and abundance in tropical rainforests. We addressed fine scale variability by investigating the reproductive phenology of three contiguous vegetations across the Atlantic rainforest coastal plain in Southeastern Brazil. We asked whether the vegetations differed in composition and abundance of species, the microenvironmental conditions and the reproductive phenology, and how their phenology is related to regional and local microenvironmental factors. The study was conducted from September 2007 to August 2009 at three contiguous sites: (1) seashore dominated by scrub vegetation, (2) intermediary covered by restinga forest and (3) foothills covered by restinga pre-montane transitional forest. We conducted the microenvironmental, plant and phenological survey within 30 transects of 25 m × 4 m (10 per site). We detected significant differences in floristic, microenvironment and reproductive phenology among the three vegetations. The microenvironment determines the spatial diversity observed in the structure and composition of the flora, which in turn determines the distinctive flowering and fruiting peaks of each vegetation (phenological diversity). There was an exchange of species providing flowers and fruits across the vegetation complex. We conclude that plant reproductive patterns as described in most phenological studies (without concern about the microenvironmental variation) may conceal the fine scale temporal phenological diversity of highly diverse tropical vegetation. This phenological diversity should be taken into account when generating sensor-derived phenologies and when trying to understand tropical vegetation responses to environmental changes.

Scaling up the diversity-resilience relationship with trait databases and remote sensing data: the recovery of productivity after wildfire.

PubMed

Spasojevic, Marko J; Bahlai, Christie A; Bradley, Bethany A; Butterfield, Bradley J; Tuanmu, Mao-Ning; Sistla, Seeta; Wiederholt, Ruscena; Suding, Katharine N

2016-04-01

Understanding the mechanisms underlying ecosystem resilience - why some systems have an irreversible response to disturbances while others recover - is critical for conserving biodiversity and ecosystem function in the face of global change. Despite the widespread acceptance of a positive relationship between biodiversity and resilience, empirical evidence for this relationship remains fairly limited in scope and localized in scale. Assessing resilience at the large landscape and regional scales most relevant to land management and conservation practices has been limited by the ability to measure both diversity and resilience over large spatial scales. Here, we combined tools used in large-scale studies of biodiversity (remote sensing and trait databases) with theoretical advances developed from small-scale experiments to ask whether the functional diversity within a range of woodland and forest ecosystems influences the recovery of productivity after wildfires across the four-corner region of the United States. We additionally asked how environmental variation (topography, macroclimate) across this geographic region influences such resilience, either directly or indirectly via changes in functional diversity. Using path analysis, we found that functional diversity in regeneration traits (fire tolerance, fire resistance, resprout ability) was a stronger predictor of the recovery of productivity after wildfire than the functional diversity of seed mass or species richness. Moreover, slope, elevation, and aspect either directly or indirectly influenced the recovery of productivity, likely via their effect on microclimate, while macroclimate had no direct or indirect effects. Our study provides some of the first direct empirical evidence for functional diversity increasing resilience at large spatial scales. Our approach highlights the power of combining theory based on local-scale studies with tools used in studies at large spatial scales and trait databases to understand pressing environmental issues. © 2015 John Wiley & Sons Ltd.

Spatial and temporal variation at major histocompatibility complex class IIB genes in the endangered Blakiston's fish owl.

PubMed

Kohyama, Tetsuo I; Omote, Keita; Nishida, Chizuko; Takenaka, Takeshi; Saito, Keisuke; Fujimoto, Satoshi; Masuda, Ryuichi

2015-01-01

Quantifying intraspecific genetic variation in functionally important genes, such as those of the major histocompatibility complex (MHC), is important in the establishment of conservation plans for endangered species. The MHC genes play a crucial role in the vertebrate immune system and generally show high levels of diversity, which is likely due to pathogen-driven balancing selection. The endangered Blakiston's fish owl (Bubo blakistoni) has suffered marked population declines on Hokkaido Island, Japan, during the past several decades due to human-induced habitat loss and fragmentation. We investigated the spatial and temporal patterns of genetic diversity in MHC class IIβ genes in Blakiston's fish owl, using massively parallel pyrosequencing. We found that the Blakiston's fish owl genome contains at least eight MHC class IIβ loci, indicating recent gene duplications. An analysis of sequence polymorphism provided evidence that balancing selection acted in the past. The level of MHC variation, however, was low in the current fish owl populations in Hokkaido: only 19 alleles were identified from 174 individuals. We detected considerable spatial differences in MHC diversity among the geographically isolated populations. We also detected a decline of MHC diversity in some local populations during the past decades. Our study demonstrated that the current spatial patterns of MHC variation in Blakiston's fish owl populations have been shaped by loss of variation due to the decline and fragmentation of populations, and that the short-term effects of genetic drift have counteracted the long-term effects of balancing selection.

Exploring the relation between spatial configuration of buildings and remotely sensed temperatures

NASA Astrophysics Data System (ADS)

Myint, S. W.; Zheng, B.; Kaplan, S.; Huang, H.

2013-12-01

While the relationship between fractional cover of buildings and the UHI has been well studied, relationships of how spatial arrangements (e.g., clustered, dispersed) of buildings influence urban warming are not well understood. Since a diversity of spatial patterns can be observed under the same percentage of buildings cover, it is of great interest and importance to investigate the amount of variation in certain urban thermal feature such as surface temperature that is accounted for by the inclusion of spatial arrangement component. The various spatial arrangements of buildings cover can give rise to different urban thermal behaviors that may not be uncovered with the information of buildings fraction only, but can be captured to some extent using spatial analysis. The goal of this study is to examine how spatial arrangements of buildings influence and shape surface temperature in different urban settings. The study area selected is the Las-Vegas metropolitan area in Nevada, located in the Mojave Desert. An object-oriented approach was used to identify buildings using a Geoeye-1 image acquired on October 12, 2011. A spatial autocorrelation technique (i.e., Moran's I) that can measure spatial pattern (clustered, dispersed) was used to determine spatial configuration of buildings. A daytime temperature layer in degree Celsius, generated from Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) image, was integrated with Moran's I values of building cover and building fractions to achieve the goals set in the study. To avoid uncertainty and properly evaluate if spatial pattern of buildings has an impact on urban warming, the relation between Moran's I values and surface temperatures was observed at different levels according to their fractions (e.g., 0-0.1, 0.5-0.6, 0.9-1). There is a negative correlation exists between spatial pattern of buildings and surface temperatures implying that dispersed building arrangements elevate surface temperatures more severely than clustered buildings. This suggests that more clustered buildings have less impact on the urban heat island (UHI) effect. We conclude that having buildings as clustered as possible can be expected to protect the settlements from increased heat island effects, reduce pollution, and preserve the hydrological systems.

Diverse Region-Based CNN for Hyperspectral Image Classification.

PubMed

Zhang, Mengmeng; Li, Wei; Du, Qian

2018-06-01

Convolutional neural network (CNN) is of great interest in machine learning and has demonstrated excellent performance in hyperspectral image classification. In this paper, we propose a classification framework, called diverse region-based CNN, which can encode semantic context-aware representation to obtain promising features. With merging a diverse set of discriminative appearance factors, the resulting CNN-based representation exhibits spatial-spectral context sensitivity that is essential for accurate pixel classification. The proposed method exploiting diverse region-based inputs to learn contextual interactional features is expected to have more discriminative power. The joint representation containing rich spectral and spatial information is then fed to a fully connected network and the label of each pixel vector is predicted by a softmax layer. Experimental results with widely used hyperspectral image data sets demonstrate that the proposed method can surpass any other conventional deep learning-based classifiers and other state-of-the-art classifiers.

Monitoring of airborne biological particles in outdoor atmosphere. Part 2: Metagenomics applied to urban environments.

PubMed

Núñez, Andrés; Amo de Paz, Guillermo; Rastrojo, Alberto; García, Ana M; Alcamí, Antonio; Gutiérrez-Bustillo, A Montserrat; Moreno, Diego A

2016-06-01

The air we breathe contains microscopic biological particles such as viruses, bacteria, fungi and pollen, some of them with relevant clinic importance. These organisms and/or their propagules have been traditionally studied by different disciplines and diverse methodologies like culture and microscopy. These techniques require time, expertise and also have some important biases. As a consequence, our knowledge on the total diversity and the relationships between the different biological entities present in the air is far from being complete. Currently, metagenomics and next-generation sequencing (NGS) may resolve this shortage of information and have been recently applied to metropolitan areas. Although the procedures and methods are not totally standardized yet, the first studies from urban air samples confirm the previous results obtained by culture and microscopy regarding abundance and variation of these biological particles. However, DNA-sequence analyses call into question some preceding ideas and also provide new interesting insights into diversity and their spatial distribution inside the cities. Here, we review the procedures, results and perspectives of the recent works that apply NGS to study the main biological particles present in the air of urban environments. [Int Microbiol 19(2):69-80(2016)]. Copyright© by the Spanish Society for Microbiology and Institute for Catalan Studies.

Insights into the microbial diversity and bioburden in a South American spacecraft assembly clean room.

PubMed

Schwendner, Petra; Moissl-Eichinger, Christine; Barczyk, Simon; Bohmeier, Maria; Pukall, Rüdiger; Rettberg, Petra

2013-12-01

In this study, samples from the spacecraft assembly clean room BAF (final assembly building), located at Centre Spatial Guyanais in Kourou, French Guiana, were characterized by qualitative and quantitative methods to determine the bioburden and biodiversity. The cultivation assays mainly focused on extremotolerant microorganisms that have special metabolic skills, such as the ability to grow without oxygen, fix nitrogen, grow autotrophically, or reduce sulfate. A broad range of media and growth conditions were used to simulate possible extraterrestrial environments and clean room buildings. In addition to these alternative cultivation assays, the ESA standard protocol for bioburden estimation was also applied. The phylogenetic analysis of the isolates (mainly facultative anaerobes) showed an extraordinarily broad cultivable biodiversity. Overall, 49 species were isolated and identified as members of the bacterial phyla Actinobacteria, Firmicutes, α-, β-, γ-Proteobacteria, and Bacteroidetes/Chlorobi. In addition to cultivation-based analyses, molecular techniques were also applied, including construction of a 16S rRNA gene clone library. The results indicate a wide-ranging microbial diversity (12 bacterial phyla, 34 families) that not only confirms the results of the cultivation efforts but also deepens our understanding of the noncultivable variety. Our investigations hint at a very broad, mainly uncultivated microbial diversity.

Modelling vehicle colour and pattern for multiple deployment environments

NASA Astrophysics Data System (ADS)

Liggins, Eric; Moorhead, Ian R.; Pearce, Daniel A.; Baker, Christopher J.; Serle, William P.

2016-10-01

Military land platforms are often deployed around the world in very different climate zones. Procuring vehicles in a large range of camouflage patterns and colour schemes is expensive and may limit the environments in which they can be effectively used. As such this paper reports a modelling approach for use in the optimisation and selection of a colour palette, to support operations in diverse environments and terrains. Three different techniques were considered based upon the differences between vehicle and background in L*a*b* colour space, to predict the optimum (initially single) colour to reduce the vehicle signature in the visible band. Calibrated digital imagery was used as backgrounds and a number of scenes were sampled. The three approaches used, and reported here are a) background averaging behind the vehicle b) background averaging in the area surrounding the vehicle and c) use of the spatial extension to CIE L*a*b*; S-CIELAB (Zhang and Wandell, Society for Information Display Symposium Technical Digest, vol. 27, pp. 731-734, 1996). Results are compared with natural scene colour statistics. The models used showed good agreement in the colour predictions for individual and multiple terrains or climate zones. A further development of the technique examines the effect of different patterns and colour combinations on the S-CIELAB spatial colour difference metric, when scaled for appropriate viewing ranges.

Interactive effects of diversity and biomass on productivity: insights from succession

Treesearch

Q. Guo

2009-01-01

Do commonly observed spatial relationships also exist over time? As an example of attempting to answer this question, this article examines whether the frequently observed diversity-biomass-productivity-relationships over space can also be seen over time. Syntheses of long-term data and literature show that when the full successional cycles are examined, diversity and...

The Effects of Spatial Diversity and Imperfect Channel Estimation on Wideband MC-DS-CDMA and MC-CDMA

DTIC Science & Technology

2009-10-01

In our previous work, we compared the theoretical bit error rates of multi-carrier direct sequence code division multiple access (MC- DS - CDMA ) and...consider only those cases where MC- CDMA has higher frequency diversity than MC- DS - CDMA . Since increases in diversity yield diminishing gains, we conclude

Interactive Effects of Diversity and Biomass on Productivity: Insights from Succession

Treesearch

Qinfeng Guo

2008-01-01

Do commonly observed spatial relationships also exist over time? As an example of attempting to answer this question, this article examines whether the frequently observed diversity-biomass-productivity-relationships over space can also be seen over time. Syntheses of long-term data and literature show that when the full successional cycles are examined, diversity and...

Mapping the Wetland Vegetation Communities of the Australian Great Artesian Basin Springs Using SAM, Mtmf and Spectrally Segmented PCA Hyperspectral Analyses

NASA Astrophysics Data System (ADS)

White, D. C.; Lewis, M. M.

2012-07-01

The Australian Great Artesian Basin (GAB) supports a unique and diverse range of groundwater dependent wetland ecosystems termed GAB springs. In recent decades the ecological sustainability of the springs has become uncertain as demands on this iconic groundwater resource increase. The impacts of existing water extractions for mining and pastoral activities are unknown. This situation is compounded by the likelihood of future increasing demand for extractions. Hyperspectral remote sensing provides the necessary spectral and spatial detail to discriminate wetland vegetation communities. Therefore the objectives of this paper are to discriminate the spatial extent and distribution of key spring wetland vegetation communities associated with the GAB springs evaluating three hyperspectral techniques: Spectral Angle Mapper (SAM), Mixture Tuned Matched Filtering (MTMF) and Spectrally Segmented PCA. In addition, to determine if the hyperspectral techniques developed can be applied at a number of sites representative of the range of spring formations and geomorphic settings and at two temporal intervals. Two epochs of HyMap airborne hyperspectral imagery were captured for this research in March 2009 and April 2011 at a number of sites representative of the floristic and geomorphic diversity of GAB spring groups/complexes within South Australia. Colour digital aerial photography at 30 cm GSD was acquired concurrently with the HyMap imagery. The image acquisition coincided with a field campaign of spectroradiometry measurements and a botanical survey. To identify key wavebands which have the greatest capability to discriminate vegetation communities of the GAB springs and surrounding area three hyperspectral data reduction techniques were employed: (i) Spectrally Segmented PCA (SSPCA); (ii) the Minimum Noise Transform (MNF); and (iii) the Pixel Purity Index (PPI). SSPCA was applied to NDVI-masked vegetation portions of the HyMap imagery with wavelength regions spectrally segmented for the VIS-NIR (450-1,350 nm), SWIR 1 (1,400-1,800 nm) and SWIR 2 (1,950-2,480 nm). The resulting pure endmember image pixels of the vegetation communities identified were used as target spectra for input into the SAM and MTMF algorithms. Spring wetland vegetation communities successfully discriminated include low lying reeds and sedges along spring tails (Baumea spp. and Cyperus spp.), dense homogenous stands of Phragmites australis reeds, and sporadic patches of salt couch grass (Sparabolus spp.). Our results indicate that a combination of hyperspectral remote sensing techniques which reduce superfluous wavebands providing a targeted spectral matching approach are capable of discriminating and mapping key vegetation communities of the GAB springs. This approach provides reliable baseline mapping of the GAB spring wetland vegetation communities, with repeatability over space and time. In addition it has the capability to determine the sensitivity of spring wetland vegetation extent, distribution and diversity, to associated changes in spring flow rates due to water extractions. This approach will ultimately inform water allocation plan management policies.

Evaluation of phase-diversity techniques for solar-image restoration

NASA Technical Reports Server (NTRS)

Paxman, Richard G.; Seldin, John H.; Lofdahl, Mats G.; Scharmer, Goran B.; Keller, Christoph U.

1995-01-01

Phase-diversity techniques provide a novel observational method for overcomming the effects of turbulence and instrument-induced aberrations in ground-based astronomy. Two implementations of phase-diversity techniques that differ with regard to noise model, estimator, optimization algorithm, method of regularization, and treatment of edge effects are described. Reconstructions of solar granulation derived by applying these two implementations to common data sets are shown to yield nearly identical images. For both implementations, reconstructions from phase-diverse speckle data (involving multiple realizations of turbulence) are shown to be superior to those derived from conventional phase-diversity data (involving a single realization). Phase-diverse speckle reconstructions are shown to achieve near diffraction-limited resolution and are validated by internal and external consistency tests, including a comparison with a reconstruction using a well-accepted speckle-imaging method.

Clinal patterns of human Y chromosomal diversity in continental Italy and Greece are dominated by drift and founder effects.

PubMed

Di Giacomo, F; Luca, F; Anagnou, N; Ciavarella, G; Corbo, R M; Cresta, M; Cucci, F; Di Stasi, L; Agostiano, V; Giparaki, M; Loutradis, A; Mammi', C; Michalodimitrakis, E N; Papola, F; Pedicini, G; Plata, E; Terrenato, L; Tofanelli, S; Malaspina, P; Novelletto, A

2003-09-01

We explored the spatial distribution of human Y chromosomal diversity on a microgeographic scale, by typing 30 population samples from closely spaced locations in Italy and Greece for 9 haplogroups and their internal microsatellite variation. We confirm a significant difference in the composition of the Y chromosomal gene pools of the two countries. However, within each country, heterogeneity is not organized along the lines of clinal variation deduced from studies on larger spatial scales. Microsatellite data indicate that local increases of haplogroup frequencies can be often explained by a limited number of founders. We conclude that local founder or drift effects are the main determinants in shaping the microgeographic Y chromosomal diversity.

Drivers of coastal bacterioplankton community diversity and structure along a nutrient gradient in the East China Sea

NASA Astrophysics Data System (ADS)

He, Jiaying; Wang, Kai; Xiong, Jinbo; Guo, Annan; Zhang, Demin; Fei, Yuejun; Ye, Xiansen

2017-04-01

Anthropogenic nutrient discharge poses widespread threats to coastal ecosystems and has increased environmental gradients from coast to sea. Bacterioplankton play crucial roles in coastal biogeochemical cycling, and a variety of factors affect bacterial community diversity and structure. We used 16S rRNA gene pyrosequencing to investigate the spatial variation in bacterial community composition (BCC) across five sites on a coast-offshore gradient in the East China Sea. Overall, bacterial alpha-diversity did not differ across sites, except that richness and phylogenetic diversity were lower in the offshore sites, and the highest alpha-diversity was found in the most landward site, with Chl-a being the main factor. BCCs generally clustered into coastal and offshore groups. Chl-a explained 12.3% of the variation in BCCs, more than that explained by either the physicochemical (5.7%) or spatial (8.5%) variables. Nutrients (particularly nitrate and phosphate), along with phytoplankton abundance, were more important than other physicochemical factors, co-explaining 20.0% of the variation in BCCs. Additionally, a series of discriminant families (primarily affiliated with Gammaproteobacteria and Alphaproteobacteria), whose relative abundances correlated with Chl-a, DIN, and phosphate concentrations, were identified, implying their potential to indicate phytoplankton blooms and nutrient enrichment in this marine ecosystem. This study provides insight into bacterioplankton response patterns along a coast-offshore gradient, with phytoplankton abundance increasing in the offshore sites. Time-series sampling across multiple transects should be performed to determine the seasonal and spatial patterns in bacterial diversity and community structure along this gradient.

Drivers of coastal bacterioplankton community diversity and structure along a nutrient gradient in the East China Sea

NASA Astrophysics Data System (ADS)

He, Jiaying; Wang, Kai; Xiong, Jinbo; Guo, Annan; Zhang, Demin; Fei, Yuejun; Ye, Xiansen

2018-03-01

Anthropogenic nutrient discharge poses widespread threats to coastal ecosystems and has increased environmental gradients from coast to sea. Bacterioplankton play crucial roles in coastal biogeochemical cycling, and a variety of factors affect bacterial community diversity and structure. We used 16S rRNA gene pyrosequencing to investigate the spatial variation in bacterial community composition (BCC) across five sites on a coast-offshore gradient in the East China Sea. Overall, bacterial alpha-diversity did not differ across sites, except that richness and phylogenetic diversity were lower in the offshore sites, and the highest alpha-diversity was found in the most landward site, with Chl-a being the main factor. BCCs generally clustered into coastal and offshore groups. Chl-a explained 12.3% of the variation in BCCs, more than that explained by either the physicochemical (5.7%) or spatial (8.5%) variables. Nutrients (particularly nitrate and phosphate), along with phytoplankton abundance, were more important than other physicochemical factors, co-explaining 20.0% of the variation in BCCs. Additionally, a series of discriminant families (primarily affiliated with Gammaproteobacteria and Alphaproteobacteria), whose relative abundances correlated with Chl-a, DIN, and phosphate concentrations, were identified, implying their potential to indicate phytoplankton blooms and nutrient enrichment in this marine ecosystem. This study provides insight into bacterioplankton response patterns along a coast-offshore gradient, with phytoplankton abundance increasing in the offshore sites. Time-series sampling across multiple transects should be performed to determine the seasonal and spatial patterns in bacterial diversity and community structure along this gradient.

Few-mode fiber, splice and SDM component characterization by spatially-diverse optical vector network analysis.

PubMed

Rommel, Simon; Mendinueta, José Manuel Delgado; Klaus, Werner; Sakaguchi, Jun; Olmos, Juan José Vegas; Awaji, Yoshinari; Monroy, Idelfonso Tafur; Wada, Naoya

2017-09-18

This paper discusses spatially diverse optical vector network analysis for space division multiplexing (SDM) component and system characterization, which is becoming essential as SDM is widely considered to increase the capacity of optical communication systems. Characterization of a 108-channel photonic lantern spatial multiplexer, coupled to a 36-core 3-mode fiber, is experimentally demonstrated, extracting the full impulse response and complex transfer function matrices as well as insertion loss (IL) and mode-dependent loss (MDL) data. Moreover, the mode-mixing behavior of fiber splices in the few-mode multi-core fiber and their impact on system IL and MDL are analyzed, finding splices to cause significant mode-mixing and to be non-negligible in system capacity analysis.

Computed tomography imaging and angiography - principles.

PubMed

Kamalian, Shervin; Lev, Michael H; Gupta, Rajiv

2016-01-01

The evaluation of patients with diverse neurologic disorders was forever changed in the summer of 1973, when the first commercial computed tomography (CT) scanners were introduced. Until then, the detection and characterization of intracranial or spinal lesions could only be inferred by limited spatial resolution radioisotope scans, or by the patterns of tissue and vascular displacement on invasive pneumoencaphalography and direct carotid puncture catheter arteriography. Even the earliest-generation CT scanners - which required tens of minutes for the acquisition and reconstruction of low-resolution images (128×128 matrix) - could, based on density, noninvasively distinguish infarct, hemorrhage, and other mass lesions with unprecedented accuracy. Iodinated, intravenous contrast added further sensitivity and specificity in regions of blood-brain barrier breakdown. The advent of rapid multidetector row CT scanning in the early 1990s created renewed enthusiasm for CT, with CT angiography largely replacing direct catheter angiography. More recently, iterative reconstruction postprocessing techniques have made possible high spatial resolution, reduced noise, very low radiation dose CT scanning. The speed, spatial resolution, contrast resolution, and low radiation dose capability of present-day scanners have also facilitated dual-energy imaging which, like magnetic resonance imaging, for the first time, has allowed tissue-specific CT imaging characterization of intracranial pathology. © 2016 Elsevier B.V. All rights reserved.

An improved triangulation laser rangefinder using a custom CMOS HDR linear image sensor

NASA Astrophysics Data System (ADS)

Liscombe, Michael

3-D triangulation laser rangefinders are used in many modern applications, from terrain mapping to biometric identification. Although a wide variety of designs have been proposed, laser speckle noise still provides a fundamental limitation on range accuracy. These works propose a new triangulation laser rangefinder designed specifically to mitigate the effects of laser speckle noise. The proposed rangefinder uses a precision linear translator to laterally reposition the imaging system (e.g., image sensor and imaging lens). For a given spatial location of the laser spot, capturing N spatially uncorrelated laser spot profiles is shown to improve range accuracy by a factor of N . This technique has many advantages over past speckle-reduction technologies, such as a fixed system cost and form factor, and the ability to virtually eliminate laser speckle noise. These advantages are made possible through spatial diversity and come at the cost of increased acquisition time. The rangefinder makes use of the ICFYKWG1 linear image sensor, a custom CMOS sensor developed at the Vision Sensor Laboratory (York University). Tests are performed on the image sensor's innovative high dynamic range technology to determine its effects on range accuracy. As expected, experimental results have shown that the sensor provides a trade-off between dynamic range and range accuracy.

Spatial variability of soil properties and soil erodibility in the Alqueva reservoir watershed

NASA Astrophysics Data System (ADS)

Ferreira, V.; Panagopoulos, T.; Andrade, R.; Guerrero, C.; Loures, L.

2015-04-01

The aim of this work is to investigate how the spatial variability of soil properties and soil erodibility (K factor) were affected by the changes in land use allowed by irrigation with water from a reservoir in a semiarid area. To this end, three areas representative of different land uses (agroforestry grassland, lucerne crop and olive orchard) were studied within a 900 ha farm. The interrelationships between variables were analyzed by multivariate techniques and extrapolated using geostatistics. The results confirmed differences between land uses for all properties analyzed, which was explained mainly by the existence of diverse management practices (tillage, fertilization and irrigation), vegetation cover and local soil characteristics. Soil organic matter, clay and nitrogen content decreased significantly, while the K factor increased with intensive cultivation. The HJ-Biplot methodology was used to represent the variation of soil erodibility properties grouped in land uses. Native grassland was the least correlated with the other land uses. The K factor demonstrated high correlation mainly with very fine sand and silt. The maps produced with geostatistics were crucial to understand the current spatial variability in the Alqueva region. Facing the intensification of land-use conversion, a sustainable management is needed to introduce protective measures to control soil erosion.

Spatial variability of soil properties and soil erodibility in the Alqueva dam watershed, Portugal

NASA Astrophysics Data System (ADS)

Ferreira, V.; Panagopoulos, T.; Andrade, R.; Guerrero, C.; Loures, L.

2015-01-01

The aim of this work is to investigate how the spatial variability of soil properties and soil erodibility (K factor) were affected by the changes in land use allowed by irrigation with water from a reservoir in a semiarid area. To this, three areas representative of different land uses (agroforestry grassland, Lucerne crop and olive orchard) were studied within a 900 ha farm. The interrelationships between variables were analyzed by multivariate techniques and extrapolated using geostatistics. The results confirmed differences between land uses for all properties analyzed, which was explained mainly by the existence of diverse management practices (tillage, fertilization and irrigation), vegetation cover and local soil characteristics. Soil organic matter, clay and nitrogen content decreased significantly, while K factor increased with intensive cultivation. The HJ-biplot methodology was used to represent the variation of soil erodibility properties grouped in land uses. Native grassland was the least correlated with the other land uses. K factor demonstrated high correlation mainly with very fine sand and silt. The maps produced with geostatistics were crucial to understand the current spatial variability in the Alqueva region. Facing the intensification of land-use conversion, a sustainable management is needed to introduce protective measures to control soil erosion.

Contrasting spatial patterns in active-fire and fire-suppressed Mediterranean climate old-growth mixed conifer forests

Treesearch

Danny L. Fry; Scott L. Stephens; Brandon M. Collins; Malcolm North; Ernesto Franco-Vizcaino; Samantha J. Gill

2014-01-01

In Mediterranean environments in western North America, historic fire regimes in frequent-fire conifer forests are highly variable both temporally and spatially. This complexity influenced forest structure and spatial patterns, but some of this diversity has been lost due to anthropogenic disruption of ecosystem processes, including fire. Information from reference...

Multiple spatial scale analyses provide new clues on patterns and drivers of deep-sea nematode diversity

NASA Astrophysics Data System (ADS)

Danovaro, Roberto; Carugati, Laura; Corinaldesi, Cinzia; Gambi, Cristina; Guilini, Katja; Pusceddu, Antonio; Vanreusel, Ann

2013-08-01

The deep sea is the largest biome of the biosphere. The knowledge of the spatial variability of deep-sea biodiversity is one of the main challenges of marine ecology and evolutionary biology. The choice of the observational spatial scale is assumed to play a key role for understanding processes structuring the deep-sea benthic communities and one of the most typical features of marine biodiversity distribution is the existence of bathymetric gradients. However, the analysis of biodiversity bathymetric gradients and the associated changes in species composition (beta diversity) typically compared large depth ranges (with intervals of 500 to 1000 or even 2000 m depth among sites). To test whether significant changes in alpha and beta diversity occur also at fine-scale bathymetric gradients (i.e., within few hundred-meter depth intervals) the variability of deep-sea nematode biodiversity and assemblage composition along a bathymetric transect (200-1200 m depth) with intervals of 200 m among sampling depths, was investigated. A hierarchical sampling strategy for the analysis of nematode species richness, beta diversity, functional (trophic) diversity, and related environmental variables, was used. The results indicate the lack of significant differences in taxonomic and functional diversity across sampling depths, but the presence of high beta diversity at all spatial scales investigated: between cores collected from the same box corer (on average 56%), among deployments at the same depth (58%), and between all sampling depths (62%). Such high beta diversity is influenced by the presence of small-scale patchiness in the deep sea and is also related to the large number of rare or very rare species (typically accounting for >80% of total species richness). Moreover, the number of ubiquitous nematode species across all sampling depths is quite low (ca. 15%). Multiple regression analyses provide evidence that such patterns could be related to the different availability, composition and size spectra of food particles in the sediments. Additionally, though to a lesser extent, our results indicate, that selective predation can influence the nematode trophic composition. These findings suggest that a multiple scale analysis based on a nested sampling design could significantly improve our knowledge of bathymetric patterns of deep-sea biodiversity and its drivers.

Improved spatial resolution in PET scanners using sampling techniques

PubMed Central

Surti, Suleman; Scheuermann, Ryan; Werner, Matthew E.; Karp, Joel S.

2009-01-01

Increased focus towards improved detector spatial resolution in PET has led to the use of smaller crystals in some form of light sharing detector design. In this work we evaluate two sampling techniques that can be applied during calibrations for pixelated detector designs in order to improve the reconstructed spatial resolution. The inter-crystal positioning technique utilizes sub-sampling in the crystal flood map to better sample the Compton scatter events in the detector. The Compton scatter rejection technique, on the other hand, rejects those events that are located further from individual crystal centers in the flood map. We performed Monte Carlo simulations followed by measurements on two whole-body scanners for point source data. The simulations and measurements were performed for scanners using scintillators with Zeff ranging from 46.9 to 63 for LaBr3 and LYSO, respectively. Our results show that near the center of the scanner, inter-crystal positioning technique leads to a gain of about 0.5-mm in reconstructed spatial resolution (FWHM) for both scanner designs. In a small animal LYSO scanner the resolution improves from 1.9-mm to 1.6-mm with the inter-crystal technique. The Compton scatter rejection technique shows higher gains in spatial resolution but at the cost of reduction in scanner sensitivity. The inter-crystal positioning technique represents a modest acquisition software modification for an improvement in spatial resolution, but at a cost of potentially longer data correction and reconstruction times. The Compton scatter rejection technique, while also requiring a modest acquisition software change with no increased data correction and reconstruction times, will be useful in applications where the scanner sensitivity is very high and larger improvements in spatial resolution are desirable. PMID:19779586

Moving microphone arrays to reduce spatial aliasing in the beamforming technique: theoretical background and numerical investigation.

PubMed

Cigada, Alfredo; Lurati, Massimiliano; Ripamonti, Francesco; Vanali, Marcello

2008-12-01

This paper introduces a measurement technique aimed at reducing or possibly eliminating the spatial aliasing problem in the beamforming technique. Beamforming main disadvantages are a poor spatial resolution, at low frequency, and the spatial aliasing problem, at higher frequency, leading to the identification of false sources. The idea is to move the microphone array during the measurement operation. In this paper, the proposed approach is theoretically and numerically investigated by means of simple sound propagation models, proving its efficiency in reducing the spatial aliasing. A number of different array configurations are numerically investigated together with the most important parameters governing this measurement technique. A set of numerical results concerning the case of a planar rotating array is shown, together with a first experimental validation of the method.

Recruitment Techniques and Strategies in a Community-Based Colorectal Cancer Screening Study of Men and Women of African Ancestry.

PubMed

Davis, Stacy N; Govindaraju, Swapamthi; Jackson, Brittany; Williams, Kimberly R; Christy, Shannon M; Vadaparampil, Susan T; Quinn, Gwendolyn P; Shibata, David; Roetzheim, Richard; Meade, Cathy D; Gwede, Clement K

Recruiting ethnically diverse Black participants to an innovative, community-based research study to reduce colorectal cancer screening disparities requires multipronged recruitment techniques. This article describes active, passive, and snowball recruitment techniques, and challenges and lessons learned in recruiting a diverse sample of Black participants. For each of the three recruitment techniques, data were collected on strategies, enrollment efficiency (participants enrolled/participants evaluated), and reasons for ineligibility. Five hundred sixty individuals were evaluated, and 330 individuals were enrolled. Active recruitment yielded the highest number of enrolled participants, followed by passive and snowball. Snowball recruitment was the most efficient technique, with enrollment efficiency of 72.4%, followed by passive (58.1%) and active (55.7%) techniques. There were significant differences in gender, education, country of origin, health insurance, and having a regular physician by recruitment technique (p < .05). Multipronged recruitment techniques should be employed to increase reach, diversity, and study participation rates among Blacks. Although each recruitment technique had a variable enrollment efficiency, the use of multipronged recruitment techniques can lead to successful enrollment of diverse Blacks into cancer prevention and control interventions.

Relationship between spatial and genetic distance in Agrobacterium spp. in 1 cubic centimeter of soil.

PubMed

Vogel, J; Normand, P; Thioulouse, J; Nesme, X; Grundmann, G L

2003-03-01

The spatial and genetic unit of bacterial population structure is the clone. Surprisingly, very little is known about the spread of a clone (spatial distance between clonally related bacteria) and the relationship between spatial distance and genetic distance, especially at very short scale (microhabitat scale), where cell division takes place. Agrobacterium spp. Biovar 1 was chosen because it is a soil bacterial taxon easy to isolate. A total of 865 microsamples 500 microm in diameter were sampled with spatial coordinates in 1 cm(3) of undisturbed soil. The 55 isolates obtained yielded 42 ribotypes, covering three genomic species based on amplified ribosomal DNA restriction analysis (ARDRA) of the intergenic spacer 16S-23S, seven of which contained two to six isolates. These clonemates (identical ARDRA patterns) could be found in the same microsample or 1 cm apart. The genetic diversity did not change with distance, indicating the same habitat variability across the cube. The mixing of ribotypes, as assessed by the spatial position of clonemates, corresponded to an overlapping of clones. Although the population probably was in a recession stage in the cube (10(3) agrobacteria g(-1)), a high genetic diversity was maintained. In two independent microsamples (500 microm in diameter) at the invasion stage, the average genetic diversity was at the same level as in the cube. Quantification of the microdiversity landscape will help to estimate the probability of encounter between bacteria under realistic natural conditions and to set appropriate sampling strategies for population genetic analysis.

Capturing the genetic makeup of the active microbiome in situ.

PubMed

Singer, Esther; Wagner, Michael; Woyke, Tanja

2017-09-01

More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and that have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.

Capturing the genetic makeup of the active microbiome in situ

PubMed Central

Singer, Esther; Wagner, Michael; Woyke, Tanja

2017-01-01

More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and that have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions. PMID:28574490

Generalized Dissimilarity Modeling of Late-Quaternary Variations in Pollen-Based Compositional Dissimilarity

NASA Astrophysics Data System (ADS)

Williams, J. W.; Blois, J.; Ferrier, S.; Manion, G.; Fitzpatrick, M.; Veloz, S.; He, F.; Liu, Z.; Otto-Bliesner, B. L.

2011-12-01

In Quaternary paleoecology and paleoclimatology, compositionally dissimilar fossil assemblages usually indicate dissimilar environments; this relationship underpins assemblage-level techniques for paleoenvironmental reconstruction such as mutual climatic ranges or the modern analog technique. However, there has been relatively little investigation into the form of the relationship between compositional dissimilarity and climatic dissimilarity. Here we apply generalized dissimilarity modeling (GDM; Ferrier et al. 2007) as a tool for modeling the expected non-linear relationships between compositional and climatic dissimilarity. We use the CCSM3.0 transient paleoclimatic simulations from the SynTrace working group (Liu et al. 2009) and a new generation of fossil pollen maps from eastern North America (Blois et al. 2011) to 1) assess the spatial relationships between compositional dissimilarity and climatic dissimilarity and 2) whether these spatial relationships change over time. We used a taxonomic list of 106 genus-level pollen types, six climatic variables (winter precipitation and mean temperature, summer precipitation and temperature, seasonality of precipitation, and seasonality of temperature) that were chosen to minimize collinearity, and a cross-referenced pollen and climate dataset mapped for time slices spaced 1000 years apart. When GDM was trained for one time slice, the correlation between predicted and observed spatial patterns of community dissimilarity for other times ranged between 0.3 and 0.73. The selection of climatic predictor variables changed over time, as did the form of the relationship between compositional turnover and climatic predictors. Summer temperature was the only variable selected for all time periods. These results thus suggest that the relationship between compositional dissimilarity in pollen assemblages (and, by implication, beta diversity in plant communities) and climatic dissimilarity can change over time, for reasons to be further studied.

Predicting spatial distribution of privet (liguestrum spp.) in South Carolina from MODIS and forest inventory plot data

Treesearch

Dumitru Salajanu; Dennis M. Jacobs

2009-01-01

Privet's aggressive competitive behavior causes environmental harm to the ecosystem by degrading species diversity and wildlife habitat. Effective control of its spread requires high-quality spatial distribution information. Our...

Microbes on mountainsides: Contrasting elevational patterns of bacterial and plant diversity

PubMed Central

Bryant, Jessica A.; Lamanna, Christine; Morlon, Hélène; Kerkhoff, Andrew J.; Enquist, Brian J.; Green, Jessica L.

2008-01-01

The study of elevational diversity gradients dates back to the foundation of biogeography. Although elevational patterns of plant and animal diversity have been studied for centuries, such patterns have not been reported for microorganisms and remain poorly understood. Here, in an effort to assess the generality of elevational diversity patterns, we examined soil bacterial and plant diversity along an elevation gradient. To gain insight into the forces that structure these patterns, we adopted a multifaceted approach to incorporate information about the structure, diversity, and spatial turnover of montane communities in a phylogenetic context. We found that observed patterns of plant and bacterial diversity were fundamentally different. While bacterial taxon richness and phylogenetic diversity decreased monotonically from the lowest to highest elevations, plants followed a unimodal pattern, with a peak in richness and phylogenetic diversity at mid-elevations. At all elevations bacterial communities had a tendency to be phylogenetically clustered, containing closely related taxa. In contrast, plant communities did not exhibit a uniform phylogenetic structure across the gradient: they became more overdispersed with increasing elevation, containing distantly related taxa. Finally, a metric of phylogenetic beta-diversity showed that bacterial lineages were not randomly distributed, but rather exhibited significant spatial structure across the gradient, whereas plant lineages did not exhibit a significant phylogenetic signal. Quantifying the influence of sample scale in intertaxonomic comparisons remains a challenge. Nevertheless, our findings suggest that the forces structuring microorganism and macroorganism communities along elevational gradients differ. PMID:18695215

Characterizing fish community diversity across Virginia landscapes: Prerequisite for conservation

USGS Publications Warehouse

Angermeier, P.L.; Winston, M.R.

1999-01-01

The number of community types occurring within landscapes is an important, but often unprotected, component of biological diversity. Generally applicable protocols for characterizing community diversity need to be developed to facilitate conservation. We used several multivariate techniques to analyze geographic variation in the composition of fish communities in Virginia streams. We examined relationships between community composition and six landscape variables: drainage basin, physiography, stream order, elevation, channel slope, and map coordinates. We compared patterns at two scales (statewide and subdrainage-specific) to assess sensitivity of community classification to spatial scale. We also compared patterns based on characterizing communities by species composition vs. ecological composition. All landscape variables explained significant proportions of the variance in community composition. Statewide, they explained 32% of the variance in species composition and 48% of the variance in ecological composition. Typical communities in each drainage or physiography were statistically distinctive. Communities in different combinations of drainage, physiography, and stream size were even more distinctive, but composition was strongly spatially autocorrelated. Ecological similarity and species similarity of community pairs were strongly related, but replacement by ecologically similar species was common among drainage-physiography combinations. Landscape variables explained significant proportions of variance in community composition within selected subdrainages, but proportions were less than at the statewide scale, and the explanatory power of individual variables varied considerably among subdrainages. Community variation within subdrainages appeared to be much more closely related to environmental variation than to replacement among ecologically similar species. Our results suggest that taxonomic and ecological characterizations of community composition are complementary; both are useful in a conservation context. Landscape features such as drainage, physiography, and water body size generally may provide a basis for assessing aquatic community diversity, especially in regions where the biota is poorly known. Systematic conservation of community types would be a major advance relative to most current conservation programs, which typically focus narrowly on populations of imperiled species. More effective conservation of aquatic biodiversity will require new approaches that recognize the value of both species and assemblages, and that emphasize protection of key landscape-scale processes.

Mapping multi-scale vascular plant richness in a forest landscape with integrated LiDAR and hyperspectral remote-sensing.

PubMed

Hakkenberg, C R; Zhu, K; Peet, R K; Song, C

2018-02-01

The central role of floristic diversity in maintaining habitat integrity and ecosystem function has propelled efforts to map and monitor its distribution across forest landscapes. While biodiversity studies have traditionally relied largely on ground-based observations, the immensity of the task of generating accurate, repeatable, and spatially-continuous data on biodiversity patterns at large scales has stimulated the development of remote-sensing methods for scaling up from field plot measurements. One such approach is through integrated LiDAR and hyperspectral remote-sensing. However, despite their efficiencies in cost and effort, LiDAR-hyperspectral sensors are still highly constrained in structurally- and taxonomically-heterogeneous forests - especially when species' cover is smaller than the image resolution, intertwined with neighboring taxa, or otherwise obscured by overlapping canopy strata. In light of these challenges, this study goes beyond the remote characterization of upper canopy diversity to instead model total vascular plant species richness in a continuous-cover North Carolina Piedmont forest landscape. We focus on two related, but parallel, tasks. First, we demonstrate an application of predictive biodiversity mapping, using nonparametric models trained with spatially-nested field plots and aerial LiDAR-hyperspectral data, to predict spatially-explicit landscape patterns in floristic diversity across seven spatial scales between 0.01-900 m 2 . Second, we employ bivariate parametric models to test the significance of individual, remotely-sensed predictors of plant richness to determine how parameter estimates vary with scale. Cross-validated results indicate that predictive models were able to account for 15-70% of variance in plant richness, with LiDAR-derived estimates of topography and forest structural complexity, as well as spectral variance in hyperspectral imagery explaining the largest portion of variance in diversity levels. Importantly, bivariate tests provide evidence of scale-dependence among predictors, such that remotely-sensed variables significantly predict plant richness only at spatial scales that sufficiently subsume geolocational imprecision between remotely-sensed and field data, and best align with stand components including plant size and density, as well as canopy gaps and understory growth patterns. Beyond their insights into the scale-dependent patterns and drivers of plant diversity in Piedmont forests, these results highlight the potential of remotely-sensible essential biodiversity variables for mapping and monitoring landscape floristic diversity from air- and space-borne platforms. © 2017 by the Ecological Society of America.

Geostatistics: a new tool for describing spatially-varied surface conditions from timber harvested and burned hillslopes

Treesearch

Peter R. Robichaud

1997-01-01

Geostatistics provides a method to describe the spatial continuity of many natural phenomena. Spatial models are based upon the concept of scaling, kriging and conditional simulation. These techniques were used to describe the spatially-varied surface conditions on timber harvest and burned hillslopes. Geostatistical techniques provided estimates of the ground cover (...

Programming Cells for Dynamic Assembly of Inorganic Nano-Objects with Spatiotemporal Control.

PubMed

Wang, Xinyu; Pu, Jiahua; An, Bolin; Li, Yingfeng; Shang, Yuequn; Ning, Zhijun; Liu, Yi; Ba, Fang; Zhang, Jiaming; Zhong, Chao

2018-04-01

Programming living cells to organize inorganic nano-objects (NOs) in a spatiotemporally precise fashion would advance new techniques for creating ordered ensembles of NOs and new bio-abiotic hybrid materials with emerging functionalities. Bacterial cells often grow in cellular communities called biofilms. Here, a strategy is reported for programming dynamic biofilm formation for the synchronized assembly of discrete NOs or hetero-nanostructures on diverse interfaces in a dynamic, scalable, and hierarchical fashion. By engineering Escherichia coli to sense blue light and respond by producing biofilm curli fibers, biofilm formation is spatially controlled and the patterned NOs' assembly is simultaneously achieved. Diverse and complex fluorescent quantum dot patterns with a minimum patterning resolution of 100 µm are demonstrated. By temporally controlling the sequential addition of NOs into the culture, multilayered heterostructured thin films are fabricated through autonomous layer-by-layer assembly. It is demonstrated that biologically dynamic self-assembly can be used to advance a new repertoire of nanotechnologies and materials with increasing complexity that would be otherwise challenging to produce. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Design and demonstration of multimodal optical scanning microscopy for confocal and two-photon imaging

NASA Astrophysics Data System (ADS)

Chun, Wanhee; Do, Dukho; Gweon, Dae-Gab

2013-01-01

We developed a multimodal microscopy based on an optical scanning system in order to obtain diverse optical information of the same area of a sample. Multimodal imaging researches have mostly depended on a commercial microscope platform, easy to use but restrictive to extend imaging modalities. In this work, the beam scanning optics, especially including a relay lens, was customized to transfer broadband (400-1000 nm) lights to a sample without any optical error or loss. The customized scanning optics guarantees the best performances of imaging techniques utilizing the lights within the design wavelength. Confocal reflection, confocal fluorescence, and two-photon excitation fluorescence images were obtained, through respective implemented imaging channels, to demonstrate imaging feasibility for near-UV, visible, near-IR continuous light, and pulsed light in the scanning optics. The imaging performances for spatial resolution and image contrast were verified experimentally; the results were satisfactory in comparison with theoretical results. The advantages of customization, containing low cost, outstanding combining ability and diverse applications, will contribute to vitalize multimodal imaging researches.

A MULTI-LOCUS, MULTI-TAXA PHYLOGEOGRAPHICAL ANALYSIS OF GENETIC DIVERSITY

EPA Science Inventory

In addition to measuring spatial patterns of genetic diversity, population genetic measures of biological resources should include temporal data that indicate whether the observed patterns are the result of historical or contemporary processes. In general, genetic measures focus...

Bird diversity along a gradient of fragmented habitats of the Cerrado.

PubMed

Jesus, Shayana DE; Pedro, Wagner A; Bispo, Arthur A

2018-01-01

Understanding the factors that affect biodiversity is of central interest to ecology, and essential to species conservation and ecosystems management. We sampled bird communities in 17 forest fragments in the Cerrado biome, the Central-West region of Brazil. We aimed to know the communities structure pattern and the influence of geographical distance and environmental variables on them, along a gradient of fragmented habitats at both local and landscape scales. Eight structural variables of the fragments served as an environmental distance measurement at the local scale while five metrics served as an environmental distance measurement at the landscape scale. Species presence-absence data were used to calculate the dissimilarity index. Beta diversity was calculated using three indices (βsim, βnes and βsor), representing the spatial species turnover, nestedness and total beta diversity, respectively. Spatial species turnover was the predominant pattern in the structure of the communities. Variations in beta diversity were explained only by the environmental variables of the landscape with spatial configuration being more important than the composition. This fact indicates that, in Cerrado of Goiás avian communities structure, deterministic ecological processes associated to differences in species responses to landscape fragmentation are more important than stochastic processes driven by species dispersal.

Gradients, vegetation and climate: spatial and temporal dynamics in the Olympic Mountains, USA

USGS Publications Warehouse

Peterson, David L.; Schreiner, Edward G.; Buckingham, Nelsa M.

1997-01-01

The steep environmental gradients of mountains result in the juxtaposition of diverse vegetation associations with narrow ecotones because life zones are compressed. Variation in geologic substrate, landforms, and soils, in combination with steep environmental gradients, create habitat diversity across spatial scales from 106 ha to <10 m2. This leads to higher biodiversity in a smaller space than in landscapes with less topographic variation. Mountains are often considered to be refuges for biological diversity at the regional scale, although variation in landscape features creates refuges at a fine scale as well. Mountains should also be considered a source of biological diversity, because they provide the germplasm for migration into lowland areas following glacial recession. Many taxa are distributed over a broad range of elevations and habitats, which maximizes the potential to respond to environmental perturbations. Reorganization of species distribution and abundance as a result of climatic change may be impacted considerably by human-caused fragmentation of landscape features, especially at lower elevations. This paper uses palaeoecological and biogeographical data to investigate the spatial and temporal vegetation dynamics of a steep maritime range, the Olympic Mountains (USA). The role of resource management in protecting vegetation in a fragmented landscape is discussed, with emphasis on how to address uncertainties such as climatic change.

At limits of life: multidisciplinary insights reveal environmental constraints on biotic diversity in continental Antarctica.

PubMed

Magalhães, Catarina; Stevens, Mark I; Cary, S Craig; Ball, Becky A; Storey, Bryan C; Wall, Diana H; Türk, Roman; Ruprecht, Ulrike

2012-01-01

Multitrophic communities that maintain the functionality of the extreme Antarctic terrestrial ecosystems, while the simplest of any natural community, are still challenging our knowledge about the limits to life on earth. In this study, we describe and interpret the linkage between the diversity of different trophic level communities to the geological morphology and soil geochemistry in the remote Transantarctic Mountains (Darwin Mountains, 80°S). We examined the distribution and diversity of biota (bacteria, cyanobacteria, lichens, algae, invertebrates) with respect to elevation, age of glacial drift sheets, and soil physicochemistry. Results showed an abiotic spatial gradient with respect to the diversity of the organisms across different trophic levels. More complex communities, in terms of trophic level diversity, were related to the weakly developed younger drifts (Hatherton and Britannia) with higher soil C/N ratio and lower total soluble salts content (thus lower conductivity). Our results indicate that an increase of ion concentration from younger to older drift regions drives a succession of complex to more simple communities, in terms of number of trophic levels and diversity within each group of organisms analysed. This study revealed that integrating diversity across multi-trophic levels of biotic communities with abiotic spatial heterogeneity and geological history is fundamental to understand environmental constraints influencing biological distribution in Antarctic soil ecosystems.

A computationally efficient Bayesian sequential simulation approach for the assimilation of vast and diverse hydrogeophysical datasets

NASA Astrophysics Data System (ADS)

Nussbaumer, Raphaël; Gloaguen, Erwan; Mariéthoz, Grégoire; Holliger, Klaus

2016-04-01

Bayesian sequential simulation (BSS) is a powerful geostatistical technique, which notably has shown significant potential for the assimilation of datasets that are diverse with regard to the spatial resolution and their relationship. However, these types of applications of BSS require a large number of realizations to adequately explore the solution space and to assess the corresponding uncertainties. Moreover, such simulations generally need to be performed on very fine grids in order to adequately exploit the technique's potential for characterizing heterogeneous environments. Correspondingly, the computational cost of BSS algorithms in their classical form is very high, which so far has limited an effective application of this method to large models and/or vast datasets. In this context, it is also important to note that the inherent assumption regarding the independence of the considered datasets is generally regarded as being too strong in the context of sequential simulation. To alleviate these problems, we have revisited the classical implementation of BSS and incorporated two key features to increase the computational efficiency. The first feature is a combined quadrant spiral - superblock search, which targets run-time savings on large grids and adds flexibility with regard to the selection of neighboring points using equal directional sampling and treating hard data and previously simulated points separately. The second feature is a constant path of simulation, which enhances the efficiency for multiple realizations. We have also modified the aggregation operator to be more flexible with regard to the assumption of independence of the considered datasets. This is achieved through log-linear pooling, which essentially allows for attributing weights to the various data components. Finally, a multi-grid simulating path was created to enforce large-scale variance and to allow for adapting parameters, such as, for example, the log-linear weights or the type of simulation path at various scales. The newly implemented search method for kriging reduces the computational cost from an exponential dependence with regard to the grid size in the original algorithm to a linear relationship, as each neighboring search becomes independent from the grid size. For the considered examples, our results show a sevenfold reduction in run time for each additional realization when a constant simulation path is used. The traditional criticism that constant path techniques introduce a bias to the simulations was explored and our findings do indeed reveal a minor reduction in the diversity of the simulations. This bias can, however, be largely eliminated by changing the path type at different scales through the use of the multi-grid approach. Finally, we show that adapting the aggregation weight at each scale considered in our multi-grid approach allows for reproducing both the variogram and histogram, and the spatial trend of the underlying data.

Compartmentalized Platforms for Neuro-pharmacological Research

PubMed Central

Jadhav, Amol D.; Wei, Li; Shi, Peng

2016-01-01

Dissociated primary neuronal cell culture remains an indispensable approach for neurobiology research in order to investigate basic mechanisms underlying diverse neuronal functions, drug screening and pharmacological investigation. Compartmentalization, a widely adopted technique since its emergence in 1970s enables spatial segregation of neuronal segments and detailed investigation that is otherwise limited with traditional culture methods. Although these compartmental chambers (e.g. Campenot chamber) have been proven valuable for the investigation of Peripheral Nervous System (PNS) neurons and to some extent within Central Nervous System (CNS) neurons, their utility has remained limited given the arduous manufacturing process, incompatibility with high-resolution optical imaging and limited throughput. The development in the area of microfabrication and microfluidics has enabled creation of next generation compartmentalized devices that are cheap, easy to manufacture, require reduced sample volumes, enable precise control over the cellular microenvironment both spatially as well as temporally, and permit highthroughput testing. In this review we briefly evaluate the various compartmentalization tools used for neurobiological research, and highlight application of the emerging microfluidic platforms towards in vitro single cell neurobiology. PMID:26813122

X-ray diffraction tomography of polycrystalline materials: present and future (Conference Presentation)

NASA Astrophysics Data System (ADS)

Stock, Stuart R.; Almer, Jonathan D.; Birkedal, Henrik

2016-10-01

Scattered x-radiation can be used for computed tomographic reconstruction of the distribution of crystallographic phases within the interior of specimens, and diffraction patterns can be measured for each volume element (voxel) within a reconstructed slice. This modality has been applied to systems as diverse as mineralized tissues and inorganic composites. Use of high energy x-rays (E < 40 keV) offers advantages including the ability to study volumes deep with specimens and to sample large ranges of reciprocal space, i.e., many reflections. The bases of diffraction tomography are reviewed, and the power of the technique is illustrated by the results obtained for specimens containing: a) different materials (SiC/Al composite), b) different polytypes (calcite/aragonite in a bivalve attachment system); c) mixtures of nanocrystalline and amorphous phases; d) a single phase, but volumes with different lattice parameters (hydroxyapatite, hAp, the mineral in bone and tooth); e) a single phase containing a spatial distribution of crystallographic texture (bone); a single phase with a spatial distribution of strains produced by in situ loading (bone). Finally, challenges and future directions are discussed.

Studying plant–pollinator interactions in a changing climate: A review of approaches1

PubMed Central

Byers, Diane L.

2017-01-01

Plant–pollinator interactions are potentially at risk due to climate change. Because of the spatial and temporal variation associated with the effects of climate change and the responses of both actors, research to assess this interaction requires creative approaches. This review focuses on assessments of plants’ and pollinators’ altered phenology in response to environmental changes, as phenology is one of the key responses. I reviewed research methods with the goal of presenting the wide diversity of available techniques for addressing changes in these interactions. Approaches ranged from use of historical specimens to multisite experimental community studies; while differing in depth of historical information and community interactions, all contribute to assessment of phenology changes. Particularly insightful were those studies that directly assessed the environmental changes across spatial and temporal scales and the responses of plants and pollinators at these scales. Longer-term studies across environmental gradients, potentially with reciprocal transplants, enable an assessment of climate impacts at both scales. While changes in phenology are well studied, the impacts of phenology changes are not. Future research should include approaches to address this gap. PMID:28690933

Electrochemical camera chip for simultaneous imaging of multiple metabolites in biofilms

PubMed Central

Bellin, Daniel L.; Sakhtah, Hassan; Zhang, Yihan; Price-Whelan, Alexa; Dietrich, Lars E. P.; Shepard, Kenneth L.

2016-01-01

Monitoring spatial distribution of metabolites in multicellular structures can enhance understanding of the biochemical processes and regulation involved in cellular community development. Here we report on an electrochemical camera chip capable of simultaneous spatial imaging of multiple redox-active phenazine metabolites produced by Pseudomonas aeruginosa PA14 colony biofilms. The chip features an 8 mm × 8 mm array of 1,824 electrodes multiplexed to 38 parallel output channels. Using this chip, we demonstrate potential-sweep-based electrochemical imaging of whole-biofilms at measurement rates in excess of 0.2 s per electrode. Analysis of mutants with various capacities for phenazine production reveals distribution of phenazine-1-carboxylic acid (PCA) throughout the colony, with 5-methylphenazine-1-carboxylic acid (5-MCA) and pyocyanin (PYO) localized to the colony edge. Anaerobic growth on nitrate confirms the O2-dependence of PYO production and indicates an effect of O2 availability on 5-MCA synthesis. This integrated-circuit-based technique promises wide applicability in detecting redox-active species from diverse biological samples. PMID:26813638

Glyph guessing for ‘oo’ and ‘ee’: spatial frequency information in sound symbolic matching for ancient and unfamiliar scripts

PubMed Central

2017-01-01

In three experiments, we asked whether diverse scripts contain interpretable information about the speech sounds they represent. When presented with a pair of unfamiliar letters, adult readers correctly guess which is /i/ (the ‘ee’ sound in ‘feet’), and which is /u/ (the ‘oo’ sound in ‘shoe’) at rates higher than expected by chance, as shown in a large sample of Singaporean university students (Experiment 1) and replicated in a larger sample of international Internet users (Experiment 2). To uncover what properties of the letters contribute to different scripts' ‘guessability,’ we analysed the visual spatial frequencies in each letter (Experiment 3). We predicted that the lower spectral frequencies in the formants of the vowel /u/ would pattern with lower spatial frequencies in the corresponding letters. Instead, we found that across all spatial frequencies, the letter with more black/white cycles (i.e. more ink) was more likely to be guessed as /u/, and the larger the difference between the glyphs in a pair, the higher the script's guessability. We propose that diverse groups of humans across historical time and geographical space tend to employ similar iconic strategies for representing speech in visual form, and provide norms for letter pairs from 56 diverse scripts. PMID:28989784

Scale dependence of the diversity–stability relationship in a temperate grassland

PubMed Central

Zhang, Yunhai; He, Nianpeng; Loreau, Michel; Pan, Qingmin; Han, Xingguo

2018-01-01

A positive relationship between biodiversity and ecosystem stability has been reported in many ecosystems; however, it has yet to be determined whether and how spatial scale affects this relationship. Here, for the first time, we assessed the effects of alpha, beta and gamma diversity on ecosystem stability and the scale dependence of the slope of the diversity–stability relationship.By employing a long-term (33 years) dataset from a temperate grassland, northern China, we calculated the all possible spatial scales with the complete combination from the basic 1-m2 plots.Species richness was positively associated with ecosystem stability through species asynchrony and overyielding at all spatial scales (1, 2, 3, 4 and 5 m2). Both alpha and beta diversity were positively associated with gamma stability.Moreover, the slope of the diversity–area relationship was significantly higher than that of the stability–area relationship, resulting in a decline of the slope of the diversity–stability relationship with increasing area.Synthesis. With the positive species diversity effect on ecosystem stability from small to large spatial scales, our findings demonstrate the need to maintain a high biodiversity and biotic heterogeneity as insurance against the risks incurred by ecosystems in the face of global environmental changes. PMID:29725139

Spatial genetic structuring of baobab (Adansonia digitata, Malvaceae) in the traditional agroforestry systems of West Africa.

PubMed

Kyndt, Tina; Assogbadjo, Achille E; Hardy, Olivier J; Glele Kakaï, Romain; Sinsin, Brice; Van Damme, Patrick; Gheysen, Godelieve

2009-05-01

This study evaluates the spatial genetic structure of baobab (Adansonia digitata) populations from West African agroforestry systems at different geographical scales using AFLP fingerprints. Eleven populations from four countries (Benin, Ghana, Burkina Faso, and Senegal) had comparable levels of genetic diversity, although the two populations in the extreme west (Senegal) had less diversity. Pairwise F(ST) ranged from 0.02 to 0.28 and increased with geographic distance, even at a regional scale. Gene pools detected by Bayesian clustering seem to be a byproduct of the isolation-by-distance pattern rather than representing actual discrete entities. The organization of genetic diversity appears to result essentially from spatially restricted gene flow, with some influences of human seed exchange. Despite the potential for relatively long-distance pollen and seed dispersal by bats within populations, statistically significant spatial genetic structuring within populations (SGS) was detected and gave a mean indirect estimate of neighborhood size of ca. 45. This study demonstrated that relatively high levels of genetic structuring are present in baobab at both large and within-population level, which was unexpected in regard to its dispersal by bats and the influence of human exchange of seeds. Implications of these results for the conservation of baobab populations are discussed.

Molecular Phylogenetic Diversity and Spatial Distribution of Bacterial Communities in Cooling Stage during Swine Manure Composting

PubMed Central

Guo, Yan; Zhang, Jinliang; Yan, Yongfeng; Wu, Jian; Zhu, Nengwu; Deng, Changyan

2015-01-01

Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and subsequent sub-cloning and sequencing were used in this study to analyze the molecular phylogenetic diversity and spatial distribution of bacterial communities in different spatial locations during the cooling stage of composted swine manure. Total microbial DNA was extracted, and bacterial near full-length 16S rRNA genes were subsequently amplified, cloned, RFLP-screened, and sequenced. A total of 420 positive clones were classified by RFLP and near-full-length 16S rDNA sequences. Approximately 48 operational taxonomic units (OTUs) were found among 139 positive clones from the superstratum sample; 26 among 149 were from the middle-level sample and 35 among 132 were from the substrate sample. Thermobifida fusca was common in the superstratum layer of the pile. Some Bacillus spp. were remarkable in the middle-level layer, and Clostridium sp. was dominant in the substrate layer. Among 109 OTUs, 99 displayed homology with those in the GenBank database. Ten OTUs were not closely related to any known species. The superstratum sample had the highest microbial diversity, and different and distinct bacterial communities were detected in the three different layers. This study demonstrated the spatial characteristics of the microbial community distribution in the cooling stage of swine manure compost. PMID:25925066

A metric for quantifying El Niño pattern diversity with implications for ENSO-mean state interaction

NASA Astrophysics Data System (ADS)

Lemmon, Danielle E.; Karnauskas, Kristopher B.

2018-04-01

Recent research on the El Niño-Southern Oscillation (ENSO) phenomenon increasingly reveals the highly complex and diverse nature of ENSO variability. A method of quantifying ENSO spatial pattern uniqueness and diversity is presented, which enables (1) formally distinguishing between unique and "canonical" El Niño events, (2) testing whether historical model simulations aptly capture ENSO diversity by comparing with instrumental observations, (3) projecting future ENSO diversity using future model simulations, (4) understanding the dynamics that give rise to ENSO diversity, and (5) analyzing the associated diversity of ENSO-related atmospheric teleconnection patterns. Here we develop a framework for measuring El Niño spatial SST pattern uniqueness and diversity for a given set of El Niño events using two indices, the El Niño Pattern Uniqueness (EPU) index and El Niño Pattern Diversity (EPD) index, respectively. By applying this framework to instrumental records, we independently confirm a recent regime shift in El Niño pattern diversity with an increase in unique El Niño event sea surface temperature patterns. However, the same regime shift is not observed in historical CMIP5 model simulations; moreover, a comparison between historical and future CMIP5 model scenarios shows no robust change in future ENSO diversity. Finally, we support recent work that asserts a link between the background cooling of the eastern tropical Pacific and changes in ENSO diversity. This robust link between an eastern Pacific cooling mode and ENSO diversity is observed not only in instrumental reconstructions and reanalysis, but also in historical and future CMIP5 model simulations.

The effects of forest conversion to oil palm on ground-foraging ant communities depend on beta diversity and sampling grain.

PubMed

Wang, Wendy Y; Foster, William A

2015-08-01

Beta diversity - the variation in species composition among spatially discrete communities - and sampling grain - the size of samples being compared - may alter our perspectives of diversity within and between landscapes before and after agricultural conversion. Such assumptions are usually based on point comparisons, which do not accurately capture actual differences in total diversity. Beta diversity is often not rigorously examined. We investigated the beta diversity of ground-foraging ant communities in fragmented oil palm and forest landscapes in Sabah, Malaysia, using diversity metrics transformed from Hill number equivalents to remove dependences on alpha diversity. We compared the beta diversities of oil palm and forest, across three hierarchically nested sampling grains. We found that oil palm and forest communities had a greater percentage of total shared species when larger samples were compared. Across all grains and disregarding relative abundances, there was higher beta diversity of all species among forest communities. However, there were higher beta diversities of common and very abundant (dominant) species in oil palm as compared to forests. Differences in beta diversities between oil palm and forest were greatest at the largest sampling grain. Larger sampling grains in oil palm may generate bigger species pools, increasing the probability of shared species with forest samples. Greater beta diversity of all species in forest may be attributed to rare species. Oil palm communities may be more heterogeneous in common and dominant species because of variable community assembly events. Rare and also common species are better captured at larger grains, boosting differences in beta diversity between larger samples of forest and oil palm communities. Although agricultural landscapes support a lower total diversity than natural forests, diversity especially of abundant species is still important for maintaining ecosystem stability. Diversity in agricultural landscapes may be greater than expected when beta diversity is accounted for at large spatial scales.

Evolutionary history and functional traits determine the spatial pattern of multifaceted plant diversity in a typical temperate desert disturbed by an expressway.

PubMed

Li, Shuai; Dong, Shikui; Zhang, Xiangfeng; Liu, Shiliang; Shi, Jianbin; Gao, Xiaoxia; Swift, David; Xu, Yudan; Shen, Hao; Yang, Mingyue; Margarida, Canhoto Coxixo Ana

2018-04-20

Temperate desert is one of the globally important biomes with unique and valuable biodiversity, which might be threatened by environmental stresses and human disturbance associated with rapid development. However, few studies have documented the spatial distribution of the multifaceted plant diversity of the temperate desert and their relationships with external impacting factors. We sampled multifaceted plant species diversity including taxonomic diversity, functional diversity and phylogenetic diversity in the Alashan Desert along Beijing-Xinjiang Expressway (G6) in Northern China to identify the key factors and process which regulate the multifaceted plant diversity of the temperate desert. We found that the dynamics of species richness, functional richness, and phylogenetic richness along the elevational gradient corresponded to the unimodal model. Species phylogenetic development shifted from aggregation to divergence, while species functional traits were the opposite along the elevational gradient. The sites at an elevation around 1200-1400 m were the key habitats for the occurrence of high plant diversity including species richness, functional richness and phylogenetic richness. There were no significant differences (p > 0.05) in plant diversity at different distances from the road (500 m, 1000 m and 1500 m) and human disturbances (the distance from the nearest human settlements). Temperature, temperature variability, precipitation, precipitation variability, soil physical and chemistry properties showed no significant effects on plant diversity. It was concluded that evolutionary history and functional traits, not environmental or anthropogenic factors were the key determinants of the pattern of multifaceted plant diversity. Copyright © 2018 Elsevier B.V. All rights reserved.

Twenty-million-year relationship between mammalian diversity and primary productivity

NASA Astrophysics Data System (ADS)

Fritz, Susanne A.; Eronen, Jussi T.; Schnitzler, Jan; Hof, Christian; Janis, Christine M.; Mulch, Andreas; Böhning-Gaese, Katrin; Graham, Catherine H.

2016-09-01

At global and regional scales, primary productivity strongly correlates with richness patterns of extant animals across space, suggesting that resource availability and climatic conditions drive patterns of diversity. However, the existence and consistency of such diversity-productivity relationships through geological history is unclear. Here we provide a comprehensive quantitative test of the diversity-productivity relationship for terrestrial large mammals through time across broad temporal and spatial scales. We combine >14,000 occurrences for 690 fossil genera through the Neogene (23-1.8 Mya) with regional estimates of primary productivity from fossil plant communities in North America and Europe. We show a significant positive diversity-productivity relationship through the 20-million-year record, providing evidence on unprecedented spatial and temporal scales that this relationship is a general pattern in the ecology and paleo-ecology of our planet. Further, we discover that genus richness today does not match the fossil relationship, suggesting that a combination of human impacts and Pleistocene climate variability has modified the 20-million-year ecological relationship by strongly reducing primary productivity and driving many mammalian species into decline or to extinction.

Geography of Genetic Structure in Barley Wild Relative Hordeum vulgare subsp. spontaneum in Jordan.

PubMed

Thormann, Imke; Reeves, Patrick; Reilley, Ann; Engels, Johannes M M; Lohwasser, Ulrike; Börner, Andreas; Pillen, Klaus; Richards, Christopher M

2016-01-01

Informed collecting, conservation, monitoring and utilization of genetic diversity requires knowledge of the distribution and structure of the variation occurring in a species. Hordeum vulgare subsp. spontaneum (K. Koch) Thell., a primary wild relative of barley, is an important source of genetic diversity for barley improvement and co-occurs with the domesticate within the center of origin. We studied the current distribution of genetic diversity and population structure in H. vulgare subsp. spontaneum in Jordan and investigated whether it is correlated with either spatial or climatic variation inferred from publically available climate layers commonly used in conservation and ecogeographical studies. The genetic structure of 32 populations collected in 2012 was analyzed with 37 SSRs. Three distinct genetic clusters were identified. Populations were characterized by admixture and high allelic richness, and genetic diversity was concentrated in the northern part of the study area. Genetic structure, spatial location and climate were not correlated. This may point out a limitation in using large scale climatic data layers to predict genetic diversity, especially as it is applied to regional genetic resources collections in H. vulgare subsp. spontaneum.

Geography of Genetic Structure in Barley Wild Relative Hordeum vulgare subsp. spontaneum in Jordan

PubMed Central

Reeves, Patrick; Reilley, Ann; Engels, Johannes M. M.; Lohwasser, Ulrike; Börner, Andreas; Pillen, Klaus; Richards, Christopher M.

2016-01-01

Informed collecting, conservation, monitoring and utilization of genetic diversity requires knowledge of the distribution and structure of the variation occurring in a species. Hordeum vulgare subsp. spontaneum (K. Koch) Thell., a primary wild relative of barley, is an important source of genetic diversity for barley improvement and co-occurs with the domesticate within the center of origin. We studied the current distribution of genetic diversity and population structure in H. vulgare subsp. spontaneum in Jordan and investigated whether it is correlated with either spatial or climatic variation inferred from publically available climate layers commonly used in conservation and ecogeographical studies. The genetic structure of 32 populations collected in 2012 was analyzed with 37 SSRs. Three distinct genetic clusters were identified. Populations were characterized by admixture and high allelic richness, and genetic diversity was concentrated in the northern part of the study area. Genetic structure, spatial location and climate were not correlated. This may point out a limitation in using large scale climatic data layers to predict genetic diversity, especially as it is applied to regional genetic resources collections in H. vulgare subsp. spontaneum. PMID:27513459

Extinction and the spatial dynamics of biodiversity

PubMed Central

Jablonski, David

2008-01-01

The fossil record amply shows that the spatial fabric of extinction has profoundly shaped the biosphere; this spatial dimension provides a powerful context for integration of paleontological and neontological approaches. Mass extinctions evidently alter extinction selectivity, with many factors losing effectiveness except for a positive relation between survivorship and geographic range at the clade level (confirmed in reanalyses of end-Cretaceous extinction data). This relation probably also holds during “normal” times, but changes both slope and intercept with increasing extinction. The strong geographical component to clade dynamics can obscure causation in the extinction of a feature or a clade, owing to hitchhiking effects on geographic range, so that multifactorial analyses are needed. Some extinctions are spatially complex, and regional extinctions might either reset a diversity ceiling or create a diversification debt open to further diversification or invasion. Evolutionary recoveries also exhibit spatial dynamics, including regional differences in invasibilty, and expansion of clades from the tropics fuels at least some recoveries, as well as biodiversity dynamics during normal times. Incumbency effects apparently correlate more closely with extinction intensities than with standing diversities, so that regions with higher local and global extinctions are more subject to invasion; the latest Cenozoic temperate zones evidently received more invaders than the tropics or poles, but this dynamic could shift dramatically if tropical diversity is strongly depleted. The fossil record can provide valuable insights, and their application to present-day issues will be enhanced by partitioning past and present-day extinctions by driving mechanism rather than emphasizing intensity. PMID:18695229

Spatial Genetic Structure and Clonal Diversity in an Alpine Population of Salix herbacea (Salicaceae)

PubMed Central

Reisch, Christoph; Schurm, Sophia; Poschlod, Peter

2007-01-01

Background and Aims Many alpine plant species combine clonal and sexual reproduction to minimize the risks of flowering and seed production in high mountain regions. The spatial genetic structure and diversity of these alpine species is strongly affected by different clonal strategies (phalanx or guerrilla) and the proportion of generative and vegetative reproduction. Methods The clonal structure of the alpine plant species Salix herbacea was investigated in a 3 × 3 m plot of an alpine meadow using microsatellite (simple sequence repeat; SSR) analysis. The data obtained were compared with the results of a random amplified polymorphic DNA (RAPD) analysis. Key Results SSR analysis, based on three loci and 16 alleles, revealed 24 different genotypes and a proportion of distinguishable genotypes of 0·18. Six SSR clones were found consisting of at least five samples, 17 clones consisting of more than two samples and seven single genotypes. Mean clone size comprising at least five samples was 0·96 m2, and spatial autocorrelation analysis showed strong similarity of samples up to 130 cm. RAPD analysis revealed a higher level of clonal diversity but a comparable number of larger clones and a similar spatial structure. Conclusions The spatial genetic structure as well as the occurrence of single genotypes revealed in this study suggests both clonal and sexual propagation and repeated seedling recruitment in established populations of S. herbacea and is thus suggestive of a relaxed phalanx strategy. PMID:17242040

Spatial and temporal variability in forest growth in the Olympic Mountains, Washington: sensitivity to climatic variability.

Treesearch

Melisa L. Holman; David L. Peterson

2006-01-01

We compared annual basal area increment (BAI) at different spatial scales among all size classes and species at diverse locations in the wet western and dry northeastern Olympic Mountains. Weak growth correlations at small spatial scales (average R = 0.084-0.406) suggest that trees are responding to local growth conditions. However, significant...

Adapting populations in space: clonal interference and genetic diversity

NASA Astrophysics Data System (ADS)

Weissman, Daniel; Barton, Nick

Most species inhabit ranges much larger than the scales over which individuals interact. How does this spatial structure interact with adaptive evolution? We consider a simple model of a spatially-extended, adapting population and show that, while clonal interference severely limits the adaptation of purely asexual populations, even rare recombination is enough to allow adaptation at rates approaching those of well-mixed populations. We also find that the genetic hitchhiking produced by the adaptive alleles sweeping through the population has strange effects on the patterns of genetic diversity. In large spatial ranges, even low rates of adaptation cause all individuals in the population to rapidly trace their ancestry back to individuals living in a small region in the center of the range. The probability of fixation of an allele is thus strongly dependent on the allele's spatial location, with alleles from the center favored. Surprisingly, these effects are seen genome-wide (instead of being localized to the regions of the genome undergoing the sweeps). The spatial concentration of ancestry produces a power-law dependence of relatedness on distance, so that even individuals sampled far apart are likely to be fairly closely related, masking the underlying spatial structure.

Spatial congruence in language and species richness but not threat in the world's top linguistic hotspot.

PubMed

Turvey, Samuel T; Pettorelli, Nathalie

2014-12-07

Languages share key evolutionary properties with biological species, and global-level spatial congruence in richness and threat is documented between languages and several taxonomic groups. However, there is little understanding of the functional connection between diversification or extinction in languages and species, or the relationship between linguistic and species richness across different spatial scales. New Guinea is the world's most linguistically rich region and contains extremely high biological diversity. We demonstrate significant positive relationships between language and mammal richness in New Guinea across multiple spatial scales, revealing a likely functional relationship over scales at which infra-island diversification may occur. However, correlations are driven by spatial congruence between low levels of language and species richness. Regional biocultural richness may have showed closer congruence before New Guinea's linguistic landscape was altered by Holocene demographic events. In contrast to global studies, we demonstrate a significant negative correlation across New Guinea between areas with high levels of threatened languages and threatened mammals, indicating that landscape-scale threats differ between these groups. Spatial resource prioritization to conserve biodiversity may not benefit threatened languages, and conservation policy must adopt a multi-faceted approach to protect biocultural diversity as a whole.

Disturbance History,Spatial Variability, and Patterns of Biodiversity

NASA Astrophysics Data System (ADS)

Bendix, J.; Wiley, J. J.; Commons, M.

2012-12-01

The intermediate disturbance hypothesis predicts that species diversity will be maximized in environments experiencing intermediate intensity disturbance, after an intermediate timespan. Because many landscapes comprise mosaics with complex disturbance histories, the theory implies that each patch in those mosaics should have a distinct level of diversity reflecting combined impact of the magnitude of disturbance and the time since it occurred. We modeled the changing patterns of species richness across a landscape experiencing varied scenarios of simulated disturbance. Model outputs show that individual landscape patches have highly variable species richness through time, with the details reflecting the timing, intensity and sequence of their disturbance history. When the results are mapped across the landscape, the resulting temporal and spatial complexity illustrates both the contingent nature of diversity and the danger of generalizing about the impacts of disturbance.

[Maintaining mechanism of species diversity of land plant communities].

PubMed

Shang, Wenyan; Wu, Gang; Fu, Xiao; Liu, Yang

2005-03-01

The maintaining mechanism of species diversity of land plant communities is a key and advancing edge in biodiversity study. Botanists and ecologists have presented many hypotheses and theories with controversies, and no general theory system was available. In this paper, the problem was reviewed mainly on two scales. The first was big spatial scale, aiming at the physical and natural factors that affect the species diversity, including histories and ages of plant communities, gradient changes such as latitude gradient, water gradient, altitude gradient and soil nutrients gradient, area effect, and isolation; and the second was concentrated on a special plant community, and mainly discussed the relationships of biodiversity with biotic factors (primary productivity, relationship between species, and gap dynamics) and abiotic factors (succession, disturbance and spatial heterogeneity, and human activity).

Invasive plants have scale-dependent effects on diversity by altering species-area relationships.

PubMed

Powell, Kristin I; Chase, Jonathan M; Knight, Tiffany M

2013-01-18

Although invasive plant species often reduce diversity, they rarely cause plant extinctions. We surveyed paired invaded and uninvaded plant communities from three biomes. We reconcile the discrepancy in diversity loss from invaders by showing that invaded communities have lower local richness but steeper species accumulation with area than that of uninvaded communities, leading to proportionately fewer species loss at broader spatial scales. We show that invaders drive scale-dependent biodiversity loss through strong neutral sampling effects on the number of individuals in a community. We also show that nonneutral species extirpations are due to a proportionately larger effect of invaders on common species, suggesting that rare species are buffered against extinction. Our study provides a synthetic perspective on the threat of invasions to biodiversity loss across spatial scales.

SPATIAL DYNAMICS OF LAND COVER AND INFECTIOUS DISEASE RISK

EPA Science Inventory

Climate changes may allow for vector-transmitted tropical diseases to spread into temperate areas. Areas of low ecological diversity are at higher risk of infectious disease transmission due to decreased zooprophylaxis, the diversion of disease carrying insects from humans to
...

Genetic structuring of northern myotis (Myotis septentrionalis) at multiple spatial scales

USGS Publications Warehouse

Johnson, Joshua B.; Roberts, James H.; King, Timothy L.; Edwards, John W.; Ford, W. Mark; Ray, David A.

2014-01-01

Although groups of bats may be genetically distinguishable at large spatial scales, the effects of forest disturbances, particularly permanent land use conversions on fine-scale population structure and gene flow of summer aggregations of philopatric bat species are less clear. We genotyped and analyzed variation at 10 nuclear DNA microsatellite markers in 182 individuals of the forest-dwelling northern myotis (Myotis septentrionalis) at multiple spatial scales, from within first-order watersheds scaling up to larger regional areas in West Virginia and New York. Our results indicate that groups of northern myotis were genetically indistinguishable at any spatial scale we considered, and the collective population maintained high genetic diversity. It is likely that the ability to migrate, exploit small forest patches, and use networks of mating sites located throughout the Appalachian Mountains, Interior Highlands, and elsewhere in the hibernation range have allowed northern myotis to maintain high genetic diversity and gene flow regardless of forest disturbances at local and regional spatial scales. A consequence of maintaining high gene flow might be the potential to minimize genetic founder effects following population declines caused currently by the enzootic White-nose Syndrome.

Compatible Spatial Discretizations for Partial Differential Equations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arnold, Douglas, N, ed.

From May 11--15, 2004, the Institute for Mathematics and its Applications held a hot topics workshop on Compatible Spatial Discretizations for Partial Differential Equations. The numerical solution of partial differential equations (PDE) is a fundamental task in science and engineering. The goal of the workshop was to bring together a spectrum of scientists at the forefront of the research in the numerical solution of PDEs to discuss compatible spatial discretizations. We define compatible spatial discretizations as those that inherit or mimic fundamental properties of the PDE such as topology, conservation, symmetries, and positivity structures and maximum principles. A wide varietymore » of discretization methods applied across a wide range of scientific and engineering applications have been designed to or found to inherit or mimic intrinsic spatial structure and reproduce fundamental properties of the solution of the continuous PDE model at the finite dimensional level. A profusion of such methods and concepts relevant to understanding them have been developed and explored: mixed finite element methods, mimetic finite differences, support operator methods, control volume methods, discrete differential forms, Whitney forms, conservative differencing, discrete Hodge operators, discrete Helmholtz decomposition, finite integration techniques, staggered grid and dual grid methods, etc. This workshop seeks to foster communication among the diverse groups of researchers designing, applying, and studying such methods as well as researchers involved in practical solution of large scale problems that may benefit from advancements in such discretizations; to help elucidate the relations between the different methods and concepts; and to generally advance our understanding in the area of compatible spatial discretization methods for PDE. Particular points of emphasis included: + Identification of intrinsic properties of PDE models that are critical for the fidelity of numerical simulations. + Identification and design of compatible spatial discretizations of PDEs, their classification, analysis, and relations. + Relationships between different compatible spatial discretization methods and concepts which have been developed; + Impact of compatible spatial discretizations upon physical fidelity, verification and validation of simulations, especially in large-scale, multiphysics settings. + How solvers address the demands placed upon them by compatible spatial discretizations. This report provides information about the program and abstracts of all the presentations.« less

Assessing biomass of diverse coastal marsh ecosystems using statistical and machine learning models

NASA Astrophysics Data System (ADS)

Mo, Yu; Kearney, Michael S.; Riter, J. C. Alexis; Zhao, Feng; Tilley, David R.

2018-06-01

The importance and vulnerability of coastal marshes necessitate effective ways to closely monitor them. Optical remote sensing is a powerful tool for this task, yet its application to diverse coastal marsh ecosystems consisting of different marsh types is limited. This study samples spectral and biophysical data from freshwater, intermediate, brackish, and saline marshes in Louisiana, and develops statistical and machine learning models to assess the marshes' biomass with combined ground, airborne, and spaceborne remote sensing data. It is found that linear models derived from NDVI and EVI are most favorable for assessing Leaf Area Index (LAI) using multispectral data (R2 = 0.7 and 0.67, respectively), and the random forest models are most useful in retrieving LAI and Aboveground Green Biomass (AGB) using hyperspectral data (R2 = 0.91 and 0.84, respectively). It is also found that marsh type and plant species significantly impact the linear model development (P < .05 in both cases). Sensors with coarser spatial resolution yield lower LAI values because the fine water networks are not detected and mixed into the vegetation pixels. The Landsat OLI-derived map shows the LAI of coastal mashes in Louisiana mostly ranges from 0 to 5.0, and is highest for freshwater marshes and for marshes in the Atchafalaya Bay delta. The CASI-derived maps show that LAI of saline marshes at Bay Batiste typically ranges from 0.9 to 1.5, and the AGB is mostly less than 900 g/m2. This study provides solutions for assessing the biomass of Louisiana's coastal marshes using various optical remote sensing techniques, and highlights the impacts of the marshes' species composition on the model development and the sensors' spatial resolution on biomass mapping, thereby providing useful tools for monitoring the biomass of coastal marshes in Louisiana and diverse coastal marsh ecosystems elsewhere.

The relative importance of regional, local, and evolutionary factors structuring cryptobenthic coral-reef assemblages

NASA Astrophysics Data System (ADS)

Ahmadia, Gabby N.; Tornabene, Luke; Smith, David J.; Pezold, Frank L.

2018-03-01

Factors shaping coral-reef fish species assemblages can operate over a wide range of spatial scales (local versus regional) and across both proximate and evolutionary time. Niche theory and neutral theory provide frameworks for testing assumptions and generating insights about the importance of local versus regional processes. Niche theory postulates that species assemblages are an outcome of evolutionary processes at regional scales followed by local-scale interactions, whereas neutral theory presumes that species assemblages are formed by largely random processes drawing from regional species pools. Indo-Pacific cryptobenthic coral-reef fishes are highly evolved, ecologically diverse, temporally responsive, and situated on a natural longitudinal diversity gradient, making them an ideal group for testing predictions from niche and neutral theories and effects of regional and local processes on species assemblages. Using a combination of ecological metrics (fish density, diversity, assemblage composition) and evolutionary analyses (testing for phylogenetic niche conservatism), we demonstrate that the structure of cryptobenthic fish assemblages can be explained by a mixture of regional factors, such as the size of regional species pools and broad-scale barriers to gene flow/drivers of speciation, coupled with local-scale factors, such as the relative abundance of specific microhabitat types. Furthermore, species of cryptobenthic fishes have distinct microhabitat associations that drive significant differences in assemblage community structure between microhabitat types, and these distinct microhabitat associations are phylogenetically conserved over evolutionary timescales. The implied differential fitness of cryptobenthic fishes across varied microhabitats and the conserved nature of their ecology are consistent with predictions from niche theory. Neutral theory predictions may still hold true for early life-history stages, where stochastic factors may be more important in explaining recruitment. Overall, through integration of ecological and evolutionary techniques, and using multiple spatial scales, our study offers a unique perspective on factors determining coral-reef fish assemblages.

Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism.

PubMed

Hoek, Milan J A van; Merks, Roeland M H

2017-05-16

The human gut contains approximately 10 14 bacteria, belonging to hundreds of different species. Together, these microbial species form a complex food web that can break down nutrient sources that our own digestive enzymes cannot handle, including complex polysaccharides, producing short chain fatty acids and additional metabolites, e.g., vitamin K. Microbial diversity is important for colonic health: Changes in the composition of the microbiota have been associated with inflammatory bowel disease, diabetes, obesity and Crohn's disease, and make the microbiota more vulnerable to infestation by harmful species, e.g., Clostridium difficile. To get a grip on the controlling factors of microbial diversity in the gut, we here propose a multi-scale, spatiotemporal dynamic flux-balance analysis model to study the emergence of metabolic diversity in a spatial gut-like, tubular environment. The model features genome-scale metabolic models (GEM) of microbial populations, resource sharing via extracellular metabolites, and spatial population dynamics and evolution. In this model, cross-feeding interactions emerge readily, despite the species' ability to metabolize sugars autonomously. Interestingly, the community requires cross-feeding for producing a realistic set of short-chain fatty acids from an input of glucose, If we let the composition of the microbial subpopulations change during invasion of adjacent space, a complex and stratified microbiota evolves, with subspecies specializing on cross-feeding interactions via a mechanism of compensated trait loss. The microbial diversity and stratification collapse if the flux through the gut is enhanced to mimic diarrhea. In conclusion, this in silico model is a helpful tool in systems biology to predict and explain the controlling factors of microbial diversity in the gut. It can be extended to include, e.g., complex nutrient sources, and host-microbiota interactions via the intestinal wall.

Spatial and temporal genetic diversity of lake whitefish (Coregonus clupeaformis (Mitchill)) from Lake Huron and Lake Erie

USGS Publications Warehouse

Stott, Wendylee; Ebener, Mark P.; Mohr, Lloyd; Hartman, Travis; Johnson, Jim; Roseman, Edward F.

2013-01-01

Lake whitefish (Coregonus clupeaformis (Mitchill)) are important commercially, culturally, and ecologically in the Laurentian Great Lakes. Stocks of lake whitefish in the Great Lakes have recovered from low levels of abundance in the 1960s. Reductions in abundance, loss of habitat and environmental degradation can be accompanied by losses of genetic diversity and overall fitness that may persist even as populations recover demographically. Therefore, it is important to be able to identify stocks that have reduced levels of genetic diversity. In this study, we investigated patterns of genetic diversity at microsatellite DNA loci in lake whitefish collected between 1927 and 1929 (historical period) and between 1997 and 2005 (contemporary period) from Lake Huron and Lake Erie. Genetic analysis of lake whitefish from Lakes Huron and Erie shows that the amount of population structuring varies from lake to lake. Greater genetic divergences among collections from Lake Huron may be the result of sampling scale, migration patterns and demographic processes. Fluctuations in abundance of lake whitefish populations may have resulted in periods of increased genetic drift that have resulted in changes in allele frequencies over time, but periodic genetic drift was not severe enough to result in a significant loss of genetic diversity. Migration among stocks may have decreased levels of genetic differentiation while not completely obscuring stock boundaries. Recent changes in spatial boundaries to stocks, the number of stocks and life history characteristics of stocks further demonstrate the potential of coregonids for a swift and varied response to environmental change and emphasise the importance of incorporating both spatial and temporal considerations into management plans to ensure that diversity is preserved.

Quantifying spatial scaling patterns and their local and regional correlates in headwater streams: Implications for resilience

USGS Publications Warehouse

Gothe, Emma; Sandin, Leonard; Allen, Craig R.; Angeler, David G.

2014-01-01

The distribution of functional traits within and across spatiotemporal scales has been used to quantify and infer the relative resilience across ecosystems. We use explicit spatial modeling to evaluate within- and cross-scale redundancy in headwater streams, an ecosystem type with a hierarchical and dendritic network structure. We assessed the cross-scale distribution of functional feeding groups of benthic invertebrates in Swedish headwater streams during two seasons. We evaluated functional metrics, i.e., Shannon diversity, richness, and evenness, and the degree of redundancy within and across modeled spatial scales for individual feeding groups. We also estimated the correlates of environmental versus spatial factors of both functional composition and the taxonomic composition of functional groups for each spatial scale identified. Measures of functional diversity and within-scale redundancy of functions were similar during both seasons, but both within- and cross-scale redundancy were low. This apparent low redundancy was partly attributable to a few dominant taxa explaining the spatial models. However, rare taxa with stochastic spatial distributions might provide additional information and should therefore be considered explicitly for complementing future resilience assessments. Otherwise, resilience may be underestimated. Finally, both environmental and spatial factors correlated with the scale-specific functional and taxonomic composition. This finding suggests that resilience in stream networks emerges as a function of not only local conditions but also regional factors such as habitat connectivity and invertebrate dispersal.

Local loss and spatial homogenization of plant diversity reduce ecosystem multifunctionality

USDA-ARS?s Scientific Manuscript database

Experimental studies show that local plant species loss decreases ecosystem functioning and services, but it remains unclear how other changes in biodiversity, such as spatial homogenization, alter multiple processes (multifunctionality) in natural ecosystems. We present a global analysis of eight ...

Nature and Age of Neighbours Matter: Interspecific Associations among Tree Species Exist and Vary across Life Stages in Tropical Forests

PubMed Central

Ledo, Alicia

2015-01-01

Detailed information about interspecific spatial associations among tropical tree species is scarce, and hence the ecological importance of those associations may have been underestimated. However, they can play a role in community assembly and species diversity maintenance. This study investigated the spatial dependence between pairs of species. First, the spatial associations (spatial attraction and spatial repulsion) that arose between species were examined. Second, different sizes of trees were considered in order to evaluate whether the spatial relationships between species are constant or vary during the lifetime of individuals. Third, the consistency of those spatial associations with the species-habitat associations found in previous studies was assessed. Two different tropical ecosystems were investigated: a montane cloud forest and a lowland moist forest. The results showed that spatial associations among species exist, and these vary among life stages and species. The rarity of negative spatial interactions suggested that exclusive competition was not common in the studied forests. On the other hand, positive interactions were common, and the results of this study strongly suggested that habitat associations were not the only cause of spatial attraction among species. If this is true, habitat associations and density dependence are not the only mechanisms that explain species distribution and diversity; other ecological interactions, such as facilitation among species, may also play a role. These spatial associations could be important in the assembly of tropical tree communities and forest succession, and should be taken into account in future studies. PMID:26581110

The Evolving Contribution of Mass Spectrometry to Integrative Structural Biology

NASA Astrophysics Data System (ADS)

Faini, Marco; Stengel, Florian; Aebersold, Ruedi

2016-06-01

Protein complexes are key catalysts and regulators for the majority of cellular processes. Unveiling their assembly and structure is essential to understanding their function and mechanism of action. Although conventional structural techniques such as X-ray crystallography and NMR have solved the structure of important protein complexes, they cannot consistently deal with dynamic and heterogeneous assemblies, limiting their applications to small scale experiments. A novel methodological paradigm, integrative structural biology, aims at overcoming such limitations by combining complementary data sources into a comprehensive structural model. Recent applications have shown that a range of mass spectrometry (MS) techniques are able to generate interaction and spatial restraints (cross-linking MS) information on native complexes or to study the stoichiometry and connectivity of entire assemblies (native MS) rapidly, reliably, and from small amounts of substrate. Although these techniques by themselves do not solve structures, they do provide invaluable structural information and are thus ideally suited to contribute to integrative modeling efforts. The group of Brian Chait has made seminal contributions in the use of mass spectrometric techniques to study protein complexes. In this perspective, we honor the contributions of the Chait group and discuss concepts and milestones of integrative structural biology. We also review recent examples of integration of structural MS techniques with an emphasis on cross-linking MS. We then speculate on future MS applications that would unravel the dynamic nature of protein complexes upon diverse cellular states.

Specificity of plant-microbe interactions in the tree mycorrhizosphere biome and consequences for soil C cycling

PubMed Central

Churchland, Carolyn; Grayston, Sue J.

2014-01-01

Mycorrhizal associations are ubiquitous and form a substantial component of the microbial biomass in forest ecosystems and fluxes of C to these belowground organisms account for a substantial portion of carbon assimilated by forest vegetation. Climate change has been predicted to alter belowground plant-allocated C which may cause compositional shifts in soil microbial communities, and it has been hypothesized that this community change will influence C mitigation in forest ecosystems. Some 10,000 species of ectomycorrhizal fungi are currently recognized, some of which are host specific and will only associate with a single tree species, for example, Suillus grevillei with larch. Mycorrhizae are a strong sink for plant C, differences in mycorrhizal anatomy, particularly the presence and extent of emanating hyphae, can affect the amount of plant C allocated to these assemblages. Mycorrhizal morphology affects not only spatial distribution of C in forests, but also differences in the longevity of these diverse structures may have important consequences for C sequestration in soil. Mycorrhizal growth form has been used to group fungi into distinctive functional groups that vary qualitatively and spatially in their foraging and nutrient acquiring potential. Through new genomic techniques we are beginning to understand the mechanisms involved in the specificity and selection of ectomycorrhizal associations though much less is known about arbuscular mycorrhizal associations. In this review we examine evidence for tree species- mycorrhizal specificity, and the mechanisms involved (e.g., signal compounds). We also explore what is known about the effects of these associations and interactions with other soil organisms on the quality and quantity of C flow into the mycorrhizosphere (the area under the influence of mycorrhizal root tips), including spatial and seasonal variations. The enormity of the mycorrhizosphere biome in forests and its potential to sequester substantial C belowground highlights the vital importance of increasing our knowledge of the dynamics of the different mycorrhizal functional groups in diverse forests. PMID:24917855

Assessment of spatial variability of heavy metals in Metropolitan Zone of Toluca Valley, Mexico, using the biomonitoring technique in mosses and TXRF analysis.

PubMed

Zarazúa-Ortega, Graciela; Poblano-Bata, Josefina; Tejeda-Vega, Samuel; Ávila-Pérez, Pedro; Zepeda-Gómez, Carmen; Ortiz-Oliveros, Huemantzin; Macedo-Miranda, Guadalupe

2013-01-01

This study is aimed at assessing atmospheric deposition of heavy metals using the epiphytic moss genera Fabronia ciliaris collected from six urban sites in the Metropolitan Zone of the Toluca Valley in Mexico. The concentrations of K, Ca, Ti, V, Cr, Mn, Fe, Ni, Cu, Zn, Rb, Sr, and Pb were determined by total reflection X-ray fluorescence technique. Results show that the average metal concentration decrease in the following order: Fe (8207 mg/Kg) > Ca (7315 mg/Kg) > K (3842 mg/Kg) > Ti (387 mg/Kg) > Mn, Zn (191 mg/Kg) > Sr (71 mg/Kg) > Pb (59 mg/Kg) > Cu, V (32 mg/Kg) > Cr (24 mg/Kg) > Rb (13 mg/Kg) > Ni (10 mg/Kg). Enrichment factors show a high enrichment for Cr, Cu, Zn, and Pb which provides an evidence of anthropogenic impact in the industrial and urban areas, mainly due to the intense vehicular traffic and the fossil fuel combustion. Monitoring techniques in mosses have proved to be a powerful tool for determining the deposition of heavy metals coming from diverse point sources of pollution.

Mitigating the Effects of Fog Attenuation in FSO Communication Link Using Multiple Transceivers and EDFA

NASA Astrophysics Data System (ADS)

Singh, Mehtab

2017-05-01

Free Space Optics (FSO) technique is an advanced form of the wireless communication system capable of transmitting data at higher transmission rates with higher channel bandwidth and over longer link distances. One of the major challenges faced by FSO technology is the distortion of received signal due to atmospheric effects which degrade the performance of the communication link by increasing the bit error rate (BER). By implementing Erbium Doped Fiber Amplifier (EDFA) in the FSO link, the degradation of the information signal due to atmospheric effects can be minimized. Also, by deploying spatial diversity technique in the FSO link, where multiple copies of the information signal are transmitted to increase the redundancy of the system, the system performance can be enhanced. In this paper, the performance of an FSO communication link has been analyzed under fog weather condition using a different number of Tx/Rx pairs and EDFA amplifier using OPTISYSTEM simulation software. Performance has been analyzed on the basis of Q Factor, SNR, BER, and total power of the received signal. Results show a significant improvement in the system performance by deploying multiple transceiver techniques.

Functional diversity response to hardwood forest management varies across taxa and spatial scales.

PubMed

Murray, Bryan D; Holland, Jeffrey D; Summerville, Keith S; Dunning, John B; Saunders, Michael R; Jenkins, Michael A

2017-06-01

Contemporary forest management offers a trade-off between the potential positive effects of habitat heterogeneity on biodiversity, and the potential harm to mature forest communities caused by habitat loss and perforation of the forest canopy. While the response of taxonomic diversity to forest management has received a great deal of scrutiny, the response of functional diversity is largely unexplored. However, functional diversity may represent a more direct link between biodiversity and ecosystem function. To examine how forest management affects diversity at multiple spatial scales, we analyzed a long-term data set that captured changes in taxonomic and functional diversity of moths (Lepidoptera), longhorned beetles (Coleoptera: Cerambycidae), and breeding birds in response to contemporary silvicultural systems in oak-hickory hardwood forests. We used these data sets to address the following questions: how do even- and uneven-aged silvicultural systems affect taxonomic and functional diversity at the scale of managed landscapes compared to the individual harvested and unharvested forest patches that comprise the landscapes, and how do these silvicultural systems affect the functional similarity of assemblages at the scale of managed landscapes and patches? Due to increased heterogeneity within landscapes, we expected even-aged silviculture to increase and uneven-aged silviculture to decrease functional diversity at the landscape level regardless of impacts at the patch level. Functional diversity responses were taxon-specific with respect to the direction of change and time since harvest. Responses were also consistent across patch and landscape levels within each taxon. Moth assemblage species richness, functional richness, and functional divergence were negatively affected by harvesting, with stronger effects resulting from uneven-aged than even-aged management. Longhorned beetle assemblages exhibited a peak in species richness two years after harvesting, while functional diversity metrics did not differ between harvested and unharvested patches and managed landscapes. The species and functional richness of breeding bird assemblages increased in response to harvesting with more persistent effects in uneven- than in even-aged managed landscapes. For moth and bird assemblages, species turnover was driven by species with more extreme trait combinations. Our study highlights the variability of multi-taxon functional diversity in response to forest management across multiple spatial scales. © 2017 by the Ecological Society of America.

Disturbance, A Mechanism for Increased Microbial Diversity in a Yellowstone National Park Hot Spring Mixing Zone

NASA Astrophysics Data System (ADS)

Howells, A. E.; Oiler, J.; Fecteau, K.; Boyd, E. S.; Shock, E.

2014-12-01

The parameters influencing species diversity in natural ecosystems are difficult to assess due to the long and experimentally prohibitive timescales needed to develop causative relationships among measurements. Ecological diversity-disturbance models suggest that disturbance is a mechanism for increased species diversity, allowing for coexistence of species at an intermediate level of disturbance. Observing this mechanism often requires long timescales, such as the succession of a forest after a fire. In this study we evaluated the effect of mixing of two end member hydrothermal fluids on the diversity and structure of a microbial community where disturbance occurs on small temporal and spatial scales. Outflow channels from two hot springs of differing geochemical composition in Yellowstone National Park, one pH 3.3 and 36 °C and the other pH 7.6 and 61 °C flow together to create a mixing zone on the order of a few meters. Geochemical measurements were made at both in-coming streams and at a site of complete mixing downstream of the mixing zone, at pH 6.5 and 46 °C. Compositions were estimated across the mixing zone at 1 cm intervals using microsensor temperature and conductivity measurements and a mixing model. Qualitatively, there are four distinct ecotones existing over ranges in temperature and pH across the mixing zone. Community analysis of the 16S rRNA genes of these ecotones show a peak in diversity at maximal mixing. Principle component analysis of community 16S rRNA genes reflects coexistence of species with communities at maximal mixing plotting intermediate to communities at distal ends of the mixing zone. These spatial biological and geochemical observations suggest that the mixing zone is a dynamic ecosystem where geochemistry and biological diversity are governed by changes in the flow rate and geochemical composition of the two hot spring sources. In ecology, understanding how environmental disruption increases species diversity is a foundation for ecosystem conservation. By studying a hot spring environment where detailed measurements of geochemical variation and community diversity can be made at small spatial scales, the mechanisms by which maximal diversity is achieved can be tested and may assist in applications of diversity-disturbance models for larger ecosystems.

Dimensions of biodiversity loss: Spatial mismatch in land-use impacts on species, functional and phylogenetic diversity of European bees.

PubMed

De Palma, Adriana; Kuhlmann, Michael; Bugter, Rob; Ferrier, Simon; Hoskins, Andrew J; Potts, Simon G; Roberts, Stuart P M; Schweiger, Oliver; Purvis, Andy

2017-12-01

Agricultural intensification and urbanization are important drivers of biodiversity change in Europe. Different aspects of bee community diversity vary in their sensitivity to these pressures, as well as independently influencing ecosystem service provision (pollination). To obtain a more comprehensive understanding of human impacts on bee diversity across Europe, we assess multiple, complementary indices of diversity. One Thousand four hundred and forty six sites across Europe. We collated data on bee occurrence and abundance from the published literature and supplemented them with the PREDICTS database. Using Rao's Quadratic Entropy, we assessed how species, functional and phylogenetic diversity of 1,446 bee communities respond to land-use characteristics including land-use class, cropland intensity, human population density and distance to roads. We combined these models with statistically downscaled estimates of land use in 2005 to estimate and map-at a scale of approximately 1 km 2 -the losses in diversity relative to semi-natural/natural baseline (the predicted diversity of an uninhabited grid square, consisting only of semi-natural/natural vegetation). We show that-relative to the predicted local diversity in uninhabited semi-natural/natural habitat-half of all EU27 countries have lost over 10% of their average local species diversity and two-thirds of countries have lost over 5% of their average local functional and phylogenetic diversity. All diversity measures were generally lower in pasture and higher-intensity cropland than in semi-natural/natural vegetation, but facets of diversity showed less consistent responses to human population density. These differences have led to marked spatial mismatches in losses: losses in phylogenetic diversity were in some areas almost 20 percentage points (pp.) more severe than losses in species diversity, but in other areas losses were almost 40 pp. less severe. These results highlight the importance of exploring multiple measures of diversity when prioritizing and evaluating conservation actions, as species-diverse assemblages may be phylogenetically and functionally impoverished, potentially threatening pollination service provision.

MICROBIAL DIVERSITY IN SURFACE SEDIMENTS: A COMPARISON OF TWO ESTUARINE CONTINUUMS

EPA Science Inventory

The microbial diversity in estuarine sediments of the Altamaha and Savannah Rivers in Georgia were compared temporally and spatially using phospholipid fatty acid (PLFA) analysis. Surface sediment samples collected along a salinity gradient were also analyzed for ATP, TOC, and C ...

S-Band propagation measurements

NASA Technical Reports Server (NTRS)

Briskman, Robert D.

1994-01-01

A geosynchronous satellite system capable of providing many channels of digital audio radio service (DARS) to mobile platforms within the contiguous United States using S-band radio frequencies is being implemented. The system is designed uniquely to mitigate both multipath fading and outages from physical blockage in the transmission path by use of satellite spatial diversity in combination with radio frequency and time diversity. The system also employs a satellite orbital geometry wherein all mobile platforms in the contiguous United States have elevation angles greater than 20 deg to both of the diversity satellites. Since implementation of the satellite system will require three years, an emulation has been performed using terrestrial facilities in order to allow evaluation of DARS capabilities in advance of satellite system operations. The major objective of the emulation was to prove the feasibility of broadcasting from satellites 30 channels of CD quality programming using S-band frequencies to an automobile equipped with a small disk antenna and to obtain quantitative performance data on S-band propagation in a satellite spatial diversity system.

Relevant genetic differentiation among Brazilian populations of Anastrepha fraterculus (Diptera, Tephritidae)

PubMed Central

Manni, Mosè; Lima, Kátia Manuela; Guglielmino, Carmela Rosalba; Lanzavecchia, Silvia Beatriz; Juri, Marianela; Vera, Teresa; Cladera, Jorge; Scolari, Francesca; Gomulski, Ludvik; Bonizzoni, Mariangela; Gasperi, Giuliano; Silva, Janisete Gomes; Malacrida, Anna Rodolfa

2015-01-01

Abstract We used a population genetic approach to detect the presence of genetic diversity among six populations of Anastrepha fraterculus across Brazil. To this aim, we used Simple Sequence Repeat (SSR) markers, which may capture the presence of differentiative processes across the genome in distinct populations. Spatial analyses of molecular variance were used to identify groups of populations that are both genetically and geographically homogeneous while also being maximally differentiated from each other. The spatial analysis of genetic diversity indicates that the levels of diversity among the six populations vary significantly on an eco-geographical basis. Particularly, altitude seems to represent a differentiating adaptation, as the main genetic differentiation is detected between the two populations present at higher altitudes and the other four populations at sea level. The data, together with the outcomes from different cluster analyses, identify a genetic diversity pattern that overlaps with the distribution of the known morphotypes in the Brazilian area. PMID:26798258

Spatial and vertical distribution of bacterial community in the northern South China Sea.

PubMed

Sun, Fu-Lin; Wang, You-Shao; Wu, Mei-Lin; Sun, Cui-Ci; Cheng, Hao

2015-10-01

Microbial communities are highly diverse in coastal oceans and response rapidly with changing environments. Learning about this will help us understand the ecology of microbial populations in marine ecosystems. This study aimed to assess the spatial and vertical distributions of the bacterial community in the northern South China Sea. Multi-dimensional scaling analyses revealed structural differences of the bacterial community among sampling sites and vertical depth. Result also indicated that bacterial community in most sites had higher diversity in 0-75 m depths than those in 100-200 m depths. Bacterial community of samples was positively correlation with salinity and depth, whereas was negatively correlation with temperature. Proteobacteria and Cyanobacteria were the dominant groups, which accounted for the majority of sequences. The α-Proteobacteria was highly diverse, and sequences belonged to Rhodobacterales bacteria were dominant in all characterized sequences. The current data indicate that the Rhodobacterales bacteria, especially Roseobacter clade are the diverse group in the tropical waters.

Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity.

PubMed

Almendro, Vanessa; Cheng, Yu-Kang; Randles, Amanda; Itzkovitz, Shalev; Marusyk, Andriy; Ametller, Elisabet; Gonzalez-Farre, Xavier; Muñoz, Montse; Russnes, Hege G; Helland, Aslaug; Rye, Inga H; Borresen-Dale, Anne-Lise; Maruyama, Reo; van Oudenaarden, Alexander; Dowsett, Mitchell; Jones, Robin L; Reis-Filho, Jorge; Gascon, Pere; Gönen, Mithat; Michor, Franziska; Polyak, Kornelia

2014-02-13

Cancer therapy exerts a strong selection pressure that shapes tumor evolution, yet our knowledge of how tumors change during treatment is limited. Here, we report the analysis of cellular heterogeneity for genetic and phenotypic features and their spatial distribution in breast tumors pre- and post-neoadjuvant chemotherapy. We found that intratumor genetic diversity was tumor-subtype specific, and it did not change during treatment in tumors with partial or no response. However, lower pretreatment genetic diversity was significantly associated with pathologic complete response. In contrast, phenotypic diversity was different between pre- and posttreatment samples. We also observed significant changes in the spatial distribution of cells with distinct genetic and phenotypic features. We used these experimental data to develop a stochastic computational model to infer tumor growth patterns and evolutionary dynamics. Our results highlight the importance of integrated analysis of genotypes and phenotypes of single cells in intact tissues to predict tumor evolution. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of cellular diversity for genetic and phenotypic features

PubMed Central

Almendro, Vanessa; Cheng, Yu-Kang; Randles, Amanda; Itzkovitz, Shalev; Marusyk, Andriy; Ametller, Elisabet; Gonzalez-Farre, Xavier; Muñoz, Montse; Russnes, Hege G.; Helland, Åslaug; Rye, Inga H.; Borresen-Dale, Anne-Lise; Maruyama, Reo; van Oudenaarden, Alexander; Dowsett, Mitchell; Jones, Robin L.; Reis-Filho, Jorge; Gascon, Pere; Gönen, Mithat; Michor, Franziska; Polyak, Kornelia

2014-01-01

SUMMARY Cancer therapy exerts a strong selection pressure that shapes tumor evolution, yet our knowledge of how tumors change during treatment is limited. Here we report the analysis of cellular heterogeneity for genetic and phenotypic features and their spatial distribution in breast tumors pre- and post-neoadjuvant chemotherapy. We found that intratumor genetic diversity was tumor subtype-specific and it did not change during treatment in tumors with partial or no response. However, lower pre-treatment genetic diversity was significantly associated with complete pathologic response. In contrast, phenotypic diversity was different between pre- and post-treatment samples. We also observed significant changes in the spatial distribution of cells with distinct genetic and phenotypic features. We used these experimental data to develop a stochastic computational model to infer tumor growth patterns and evolutionary dynamics. Our results highlight the importance of integrated analysis of genotypes and phenotypes of single cells in intact tissues to predict tumor evolution. PMID:24462293

Bibliography of spatial interferometry in optical astronomy

NASA Technical Reports Server (NTRS)

Gezari, Daniel Y.; Roddier, Francois; Roddier, Claude

1990-01-01

The Bibliography of Spatial Interferometry in Optical Astronomy is a guide to the published literature in applications of spatial interferometry techniques to astronomical observations, theory and instrumentation at visible and infrared wavelengths. The key words spatial and optical define the scope of this discipline, distinguishing it from spatial interferometry at radio wavelengths, interferometry in the frequency domain applied to spectroscopy, or more general electro-optics theoretical and laboratory research. The main bibliography is a listing of all technical articles published in the international scientific literature and presented at the major international meetings and workshops attended by the spatial interferometry community. Section B summarizes publications dealing with the basic theoretical concepts and algorithms proposed and applied to optical spatial interferometry and imaging through a turbulent atmosphere. The section on experimental techniques is divided into twelve categories, representing the most clearly identified major areas of experimental research work. Section D, Observations, identifies publications dealing specifically with observations of astronomical sources, in which optical spatial interferometry techniques have been applied.

Beta-diversity of ectoparasites at two spatial scales: nested hierarchy, geography and habitat type.

PubMed

Warburton, Elizabeth M; van der Mescht, Luther; Stanko, Michal; Vinarski, Maxim V; Korallo-Vinarskaya, Natalia P; Khokhlova, Irina S; Krasnov, Boris R

2017-06-01

Beta-diversity of biological communities can be decomposed into (a) dissimilarity of communities among units of finer scale within units of broader scale and (b) dissimilarity of communities among units of broader scale. We investigated compositional, phylogenetic/taxonomic and functional beta-diversity of compound communities of fleas and gamasid mites parasitic on small Palearctic mammals in a nested hierarchy at two spatial scales: (a) continental scale (across the Palearctic) and (b) regional scale (across sites within Slovakia). At each scale, we analyzed beta-diversity among smaller units within larger units and among larger units with partitioning based on either geography or ecology. We asked (a) whether compositional, phylogenetic/taxonomic and functional dissimilarities of flea and mite assemblages are scale dependent; (b) how geographical (partitioning of sites according to geographic position) or ecological (partitioning of sites according to habitat type) characteristics affect phylogenetic/taxonomic and functional components of dissimilarity of ectoparasite assemblages and (c) whether assemblages of fleas and gamasid mites differ in their degree of dissimilarity, all else being equal. We found that compositional, phylogenetic/taxonomic, or functional beta-diversity was greater on a continental rather than a regional scale. Compositional and phylogenetic/taxonomic components of beta-diversity were greater among larger units than among smaller units within larger units, whereas functional beta-diversity did not exhibit any consistent trend regarding site partitioning. Geographic partitioning resulted in higher values of beta-diversity of ectoparasites than ecological partitioning. Compositional and phylogenetic components of beta-diversity were higher in fleas than mites but the opposite was true for functional beta-diversity in some, but not all, traits.

Estimation of the high-spatial-resolution variability in extreme wind speeds for forestry applications

NASA Astrophysics Data System (ADS)

Venäläinen, Ari; Laapas, Mikko; Pirinen, Pentti; Horttanainen, Matti; Hyvönen, Reijo; Lehtonen, Ilari; Junila, Päivi; Hou, Meiting; Peltola, Heli M.

2017-07-01

The bioeconomy has an increasing role to play in climate change mitigation and the sustainable development of national economies. In Finland, a forested country, over 50 % of the current bioeconomy relies on the sustainable management and utilization of forest resources. Wind storms are a major risk that forests are exposed to and high-spatial-resolution analysis of the most vulnerable locations can produce risk assessment of forest management planning. In this paper, we examine the feasibility of the wind multiplier approach for downscaling of maximum wind speed, using 20 m spatial resolution CORINE land-use dataset and high-resolution digital elevation data. A coarse spatial resolution estimate of the 10-year return level of maximum wind speed was obtained from the ERA-Interim reanalyzed data. Using a geospatial re-mapping technique the data were downscaled to 26 meteorological station locations to represent very diverse environments. Applying a comparison, we find that the downscaled 10-year return levels represent 66 % of the observed variation among the stations examined. In addition, the spatial variation in wind-multiplier-downscaled 10-year return level wind was compared with the WAsP model-simulated wind. The heterogeneous test area was situated in northern Finland, and it was found that the major features of the spatial variation were similar, but in some locations, there were relatively large differences. The results indicate that the wind multiplier method offers a pragmatic and computationally feasible tool for identifying at a high spatial resolution those locations with the highest forest wind damage risks. It can also be used to provide the necessary wind climate information for wind damage risk model calculations, thus making it possible to estimate the probability of predicted threshold wind speeds for wind damage and consequently the probability (and amount) of wind damage for certain forest stand configurations.

Mind your crossings: Mining GIS imagery for crosswalk localization.

PubMed

Ahmetovic, Dragan; Manduchi, Roberto; Coughlan, James M; Mascetti, Sergio

2017-04-01

For blind travelers, finding crosswalks and remaining within their borders while traversing them is a crucial part of any trip involving street crossings. While standard Orientation & Mobility (O&M) techniques allow blind travelers to safely negotiate street crossings, additional information about crosswalks and other important features at intersections would be helpful in many situations, resulting in greater safety and/or comfort during independent travel. For instance, in planning a trip a blind pedestrian may wish to be informed of the presence of all marked crossings near a desired route. We have conducted a survey of several O&M experts from the United States and Italy to determine the role that crosswalks play in travel by blind pedestrians. The results show stark differences between survey respondents from the U.S. compared with Italy: the former group emphasized the importance of following standard O&M techniques at all legal crossings (marked or unmarked), while the latter group strongly recommended crossing at marked crossings whenever possible. These contrasting opinions reflect differences in the traffic regulations of the two countries and highlight the diversity of needs that travelers in different regions may have. To address the challenges faced by blind pedestrians in negotiating street crossings, we devised a computer vision-based technique that mines existing spatial image databases for discovery of zebra crosswalks in urban settings. Our algorithm first searches for zebra crosswalks in satellite images; all candidates thus found are validated against spatially registered Google Street View images. This cascaded approach enables fast and reliable discovery and localization of zebra crosswalks in large image datasets. While fully automatic, our algorithm can be improved by a final crowdsourcing validation. To this end, we developed a Pedestrian Crossing Human Validation (PCHV) web service, which supports crowdsourcing to rule out false positives and identify false negatives.

Mind your crossings: Mining GIS imagery for crosswalk localization

PubMed Central

Ahmetovic, Dragan; Manduchi, Roberto; Coughlan, James M.; Mascetti, Sergio

2017-01-01

For blind travelers, finding crosswalks and remaining within their borders while traversing them is a crucial part of any trip involving street crossings. While standard Orientation & Mobility (O&M) techniques allow blind travelers to safely negotiate street crossings, additional information about crosswalks and other important features at intersections would be helpful in many situations, resulting in greater safety and/or comfort during independent travel. For instance, in planning a trip a blind pedestrian may wish to be informed of the presence of all marked crossings near a desired route. We have conducted a survey of several O&M experts from the United States and Italy to determine the role that crosswalks play in travel by blind pedestrians. The results show stark differences between survey respondents from the U.S. compared with Italy: the former group emphasized the importance of following standard O&M techniques at all legal crossings (marked or unmarked), while the latter group strongly recommended crossing at marked crossings whenever possible. These contrasting opinions reflect differences in the traffic regulations of the two countries and highlight the diversity of needs that travelers in different regions may have. To address the challenges faced by blind pedestrians in negotiating street crossings, we devised a computer vision-based technique that mines existing spatial image databases for discovery of zebra crosswalks in urban settings. Our algorithm first searches for zebra crosswalks in satellite images; all candidates thus found are validated against spatially registered Google Street View images. This cascaded approach enables fast and reliable discovery and localization of zebra crosswalks in large image datasets. While fully automatic, our algorithm can be improved by a final crowdsourcing validation. To this end, we developed a Pedestrian Crossing Human Validation (PCHV) web service, which supports crowdsourcing to rule out false positives and identify false negatives. PMID:28757907

Verification of Agricultural Methane Emission Inventories

NASA Astrophysics Data System (ADS)

Desjardins, R. L.; Pattey, E.; Worth, D. E.; VanderZaag, A.; Mauder, M.; Srinivasan, R.; Worthy, D.; Sweeney, C.; Metzger, S.

2017-12-01

It is estimated that agriculture contributes more than 40% of anthropogenic methane (CH4) emissions in North America. However, these estimates, which are either based on the Intergovernmental Panel on Climate Change (IPCC) methodology or inverse modeling techniques, are poorly validated due to the challenges of separating interspersed CH4 sources within agroecosystems. A flux aircraft, instrumented with a fast-response Picarro CH4 analyzer for the eddy covariance (EC) technique and a sampling system for the relaxed eddy accumulation technique (REA), was flown at an altitude of about 150 m along several 20-km transects over an agricultural region in Eastern Canada. For all flight days, the top-down CH4 flux density measurements were compared to the footprint adjusted bottom-up estimates based on an IPCC Tier II methodology. Information on the animal population, land use type and atmospheric and surface variables were available for each transect. Top-down and bottom-up estimates of CH4 emissions were found to be poorly correlated, and wetlands were the most frequent confounding source of CH4; however, there were other sources such as waste treatment plants and biodigesters. Spatially resolved wavelet covariance estimates of CH4 emissions helped identify the contribution of wetlands to the overall CH4 flux, and the dependence of these emissions on temperature. When wetland contribution in the flux footprint was minimized, top-down and bottom-up estimates agreed to within measurement error. This research demonstrates that although existing aircraft-based technology can be used to verify regional ( 100 km2) agricultural CH4 emissions, it remains challenging due to diverse sources of CH4 present in many regions. The use of wavelet covariance to generate spatially-resolved flux estimates was found to be the best way to separate interspersed sources of CH4.

Fine-scale spatial patterns in the demersal fish and invertebrate community in a northwest Atlantic ecosystem

NASA Astrophysics Data System (ADS)

Malek, Anna J.; Collie, Jeremy S.; Gartland, James

2014-06-01

The abundance, biomass, diversity, and species composition of the demersal fish and invertebrate community in Rhode Island Sound and Block Island Sound, an area identified for offshore renewable energy development, were evaluated for spatial and seasonal structure. We conducted 58 otter trawls and 51 beam trawls in the spring, summer and fall of 2009-2012, and incorporated additional data from 88 otter trawls conducted by the Northeast Area Monitoring and Assessment Program. We used regionally-grouped abundance, biomass, diversity, and size spectra to assess spatial patterns in the aggregate fish community, and hierarchical cluster analysis to evaluate trends in species assemblages. Our analyses revealed coherent gradients in fish community biomass, diversity and species composition extending from inshore to offshore waters, as well as patterns related to the differing bathymetry of Rhode Island and Block Island Sounds. The fish communities around Block Island and Cox's Ledge are particularly diverse, suggesting that the proximity of hard bottom habitat may be important in structuring fish communities in this area. Species assemblages in Rhode Island and Block Island Sounds are characterized by a combination of piscivores (silver hake, summer flounder, spiny dogfish), benthivores (American lobster, black sea bass, Leucoraja spp. skates, scup) and planktivores (sea scallop), and exhibit geographic patterns that are persistent from year to year, yet variable by season. Such distributions reflect the cross-shelf migration of fish and invertebrate species in the spring and fall, highlighting the importance of considering seasonal fish behavior when planning construction schedules for offshore development projects. The fine spatial scale (10 s of kms) of this research makes it especially valuable for local marine spatial planning efforts by identifying local-scale patterns in fish community structure that will enable future assessment of the ecological impacts of offshore development. As such, this knowledge of the spatial and temporal structure of the demersal fish community in Rhode Island and Block Island Sounds will help to guide the placement of offshore structures so as to preserve the ecological and economic value of the area.

Landscape pattern of seed banks and anthropogenic impacts in forested wetlands of the northern Mississippi River Alluvial Valley

USGS Publications Warehouse

Middleton, B.; Wu, X.B.

2008-01-01

Agricultural development on floodplains contributes to hydrologic alteration and forest fragmentation, which may alter landscape-level processes. These changes may be related to shifts in the seed bank composition of floodplain wetlands. We examined the patterns of seed bank composition across a floodplain watershed by looking at the number of seeds germinating per m2 by species in 60 farmed and intact forested wetlands along the Cache River watershed in Illinois. The seed bank composition was compared above and below a water diversion (position), which artificially subdivides the watershed. Position of these wetlands represented the most variability of Axis I in a Nonmetric Multidimensional Scaling (NMS) analysis of site environmental variables and their relationship to seed bank composition (coefficient of determination for Axis 1: r2 = 0.376; Pearson correlation of position to Axis 1: r = 0.223). The 3 primary axes were also represented by other site environmental variables, including farming status (farmed or unfarmed), distance from the mouth of the river, latitude, and longitude. Spatial analysis based on Mantel correlograms showed that both water-dispersed and wind/water-dispersed seed assemblages had strong spatial structure in the upper Cache (above the water diversion), bur the spatial structure of water-dispersed seed assemblage was diminished in the lower Cache (below the water diversion), which lost floodpulsing. Bearing analysis also Suggested that water-dispersal process had a stronger influence on the overall spatial pattern of seed assemblage in the upper Cache, while wind/water-dispersal process had a stronger influence in the lower Cache. An analysis of the landscapes along the river showed that the mid-lower Cache (below the water diversion) had undergone greater land cover changes associated with agriculture than did the upper Cache watershed. Thus, the combination of forest fragmentation and hydrologic changes in the surrounding landscape may have had an influence on the seed bank composition and spatial distribution of the seed banks of the Cache River watershed. Our study suggests that the spatial pattern of seed bank composition may be influenced by landscape-level factors and processes.

Investigations of structure and metabolism within Shewanella oneidensis MR-1 biofilms.

PubMed

McLean, Jeffrey S; Majors, Paul D; Reardon, Catherine L; Bilskis, Christina L; Reed, Samantha B; Romine, Margaret F; Fredrickson, James K

2008-07-01

Biofilms possess spatially and temporally varying metabolite concentration profiles at the macroscopic and microscopic scales. This results in varying growth environments that may ultimately drive species diversity, determine biofilm structure and the spatial distribution of the community members. Using non-invasive nuclear magnetic resonance (NMR) microscopic imaging/spectroscopy and confocal imaging, we investigated the kinetics and stratification of anaerobic metabolism within live biofilms of the dissimilatory metal-reducing bacterium Shewanella oneidensis strain MR-1. Biofilms were pre-grown using a defined minimal medium in a constant-depth film bioreactor and subsequently transferred to an in-magnet sample chamber under laminar flow for NMR measurements. Biofilms generated in this manner were subjected to changing substrate/electron acceptor combinations (fumarate, dimethyl sulfoxide, and nitrate) and the metabolic responses measured. Localized NMR spectroscopy was used to non-invasively measure hydrogen-containing metabolites at high temporal resolution (4.5 min) under O(2)-limited conditions. Reduction of electron acceptor under anaerobic conditions was immediately observed upon switching feed solutions indicating that no gene induction (transcriptional response) was needed for MR-1 to switch metabolism from O(2) to fumarate, dimethyl sulfoxide or nitrate. In parallel experiments, confocal microscopy was used with constitutively expressed fluorescent reporters to independently investigate changes in population response to the availability of electron acceptor and to probe metabolic competition under O(2)-limited conditions. A clearer understanding of the metabolic diversity and plasticity of the biofilm mode of growth as well as how these factors relate to environmental fitness is made possible through the use of non-invasive and non-destructive techniques such as described herein.

Disaster Governance for Community Resilience in Coastal Towns: Chilean Case Studies

PubMed Central

Quintana, Carolina

2017-01-01

This study aimed to further our understanding of a characteristic of Community Resilience known as Disaster Governance. Three attributes of Disaster Governance—redundancy, diversity, and overlap—were studied in four coastal towns in southern Chile that are at risk of tsunamis. Overall, we explored how different spatial structures of human settlements influence Disaster Governance. Using the Projective Mapping Technique, the distribution of emergency institutions (N = 32) and uses given to specific sites (e.g., for refuge, sanitary purposes and medical attention) were mapped. Content and GIS analyses (Directional Distribution and Kernel Density Index) were used to explore the dispersion and concentration of institutions and uses in each town. Disaster Governance was found to be highly influenced by decisions taken during regional, urban, and emergency planning. Governance is better in towns of higher order in the communal hierarchical structure. Most of the emergency institutions were found to be located in central and urban areas, which, in turn, assures more redundancy, overlap, and diversity in governance in the event of a tsunami. Lack of flexibility of emergency plans also limits governance in rural and indigenous areas. While the spatial relationships found in this study indicate that urban sectors have better Disaster Governance than rural and indigenous sectors, the influence of resource availability after tsunamis, the role and responsibility of different levels of governments, and the politics of disaster also play an important role in Disaster Governance for determining Community Resilience. These findings shed light on emergency planning and aspects of the Disaster Management cycle. PMID:28906480

Mammalian phylogenetic diversity-area relationships at a continental scale

PubMed Central

Mazel, Florent; Renaud, Julien; Guilhaumon, François; Mouillot, David; Gravel, Dominique; Thuiller, Wilfried

2015-01-01

In analogy to the species-area relationship (SAR), one of the few laws in Ecology, the phylogenetic diversity-area relationship (PDAR) describes the tendency of phylogenetic diversity (PD) to increase with area. Although investigating PDAR has the potential to unravel the underlying processes shaping assemblages across spatial scales and to predict PD loss through habitat reduction, it has been little investigated so far. Focusing on PD has noticeable advantages compared to species richness (SR) since PD also gives insights on processes such as speciation/extinction, assembly rules and ecosystem functioning. Here we investigate the universality and pervasiveness of the PDAR at continental scale using terrestrial mammals as study case. We define the relative robustness of PD (compared to SR) to habitat loss as the area between the standardized PDAR and standardized SAR (i.e. standardized by the diversity of the largest spatial window) divided by the area under the standardized SAR only. This metric quantifies the relative increase of PD robustness compared to SR robustness. We show that PD robustness is higher than SR robustness but that it varies among continents. We further use a null model approach to disentangle the relative effect of phylogenetic tree shape and non random spatial distribution of evolutionary history on the PDAR. We find that for most spatial scales and for all continents except Eurasia, PDARs are not different from expected by a model using only the observed SAR and the shape of the phylogenetic tree at continental scale. Interestingly, we detect a strong phylogenetic structure of the Eurasian PDAR that can be predicted by a model that specifically account for a finer biogeographical delineation of this continent. In conclusion, the relative robustness of PD to habitat loss compared to species richness is determined by the phylogenetic tree shape but also depends on the spatial structure of PD. PMID:26649401

IN-STREAM AND WATERSHED PREDICTORS OF GENETIC DIVERSITY, EFFECTIVE POPULATION SIZE AND IMMIGRATION ACROSS RIVER-STREAM NETWORKS

EPA Science Inventory

The influence of spatial processes on population dynamics within river-stream networks is poorly understood. Utilizing spatially explicit analyses of temporal genetic variance, we examined whether persistence of Central Stonerollers (Campostoma anomalum) reflects differences in h...

A SPATIALLY EXPLICIT HIERARCHICAL APPROACH TO MODELING COMPLEX ECOLOGICAL SYSTEMS: THEORY AND APPLICATIONS. (R827676)

EPA Science Inventory

Ecological systems are generally considered among the most complex because they are characterized by a large number of diverse components, nonlinear interactions, scale multiplicity, and spatial heterogeneity. Hierarchy theory, as well as empirical evidence, suggests that comp...

Additive diversity partitioning of fish in a Caribbean coral reef undergoing shift transition.

PubMed

Acosta-González, Gilberto; Rodríguez-Zaragoza, Fabián A; Hernández-Landa, Roberto C; Arias-González, Jesús E

2013-01-01

Shift transitions in dominance on coral reefs from hard coral cover to fleshy macroalgae are having negative effects on Caribbean coral reef communities. Data on spatiotemporal changes in biodiversity during these modifications are important for decision support for coral reef biodiversity protection. The main objective of this study is to detect the spatiotemporal patterns of coral reef fish diversity during this transition using additive diversity-partitioning analysis. We examined α, β and γ fish diversity from 2000 to 2010, during which time a shift transition occurred at Mahahual Reef, located in Quintana Roo, Mexico. Data on coral reef fish and benthic communities were obtained from 12 transects per geomorphological unit (GU) in two GUs (reef slope and terrace) over six years (2000, 2005, 2006, 2007, 2008, 2010). Spatial analysis within and between the GUs indicated that the γ-diversity was primarily related to higher β-diversity. Throughout the six study years, there were losses of α, β and γ-diversity associated spatially with the shallow (reef slope) and deeper (reef terrace) GUs and temporally with the transition in cover from mound corals to fleshy macroalgae and boulder corals. Despite a drastic reduction in the number of species over time, β-diversity continues to be the highest component of γ-diversity. The shift transition had a negative effect on α, β and γ-diversity, primarily by impacting rare species, leading a group of small and less vulnerable fish species to become common and an important group of rare species to become locally extinct. The maintenance of fish heterogeneity (β-diversity) over time may imply the abetment of vulnerability in the face of local and global changes.

Land-use intensification causes multitrophic homogenization of grassland communities

NASA Astrophysics Data System (ADS)

Gossner, Martin M.; Lewinsohn, Thomas M.; Kahl, Tiemo; Grassein, Fabrice; Boch, Steffen; Prati, Daniel; Birkhofer, Klaus; Renner, Swen C.; Sikorski, Johannes; Wubet, Tesfaye; Arndt, Hartmut; Baumgartner, Vanessa; Blaser, Stefan; Blüthgen, Nico; Börschig, Carmen; Buscot, Francois; Diekötter, Tim; Jorge, Leonardo Ré; Jung, Kirsten; Keyel, Alexander C.; Klein, Alexandra-Maria; Klemmer, Sandra; Krauss, Jochen; Lange, Markus; Müller, Jörg; Overmann, Jörg; Pašalić, Esther; Penone, Caterina; Perović, David J.; Purschke, Oliver; Schall, Peter; Socher, Stephanie A.; Sonnemann, Ilja; Tschapka, Marco; Tscharntke, Teja; Türke, Manfred; Venter, Paul Christiaan; Weiner, Christiane N.; Werner, Michael; Wolters, Volkmar; Wurst, Susanne; Westphal, Catrin; Fischer, Markus; Weisser, Wolfgang W.; Allan, Eric

2016-12-01

Land-use intensification is a major driver of biodiversity loss. Alongside reductions in local species diversity, biotic homogenization at larger spatial scales is of great concern for conservation. Biotic homogenization means a decrease in β-diversity (the compositional dissimilarity between sites). Most studies have investigated losses in local (α)-diversity and neglected biodiversity loss at larger spatial scales. Studies addressing β-diversity have focused on single or a few organism groups (for example, ref. 4), and it is thus unknown whether land-use intensification homogenizes communities at different trophic levels, above- and belowground. Here we show that even moderate increases in local land-use intensity (LUI) cause biotic homogenization across microbial, plant and animal groups, both above- and belowground, and that this is largely independent of changes in α-diversity. We analysed a unique grassland biodiversity dataset, with abundances of more than 4,000 species belonging to 12 trophic groups. LUI, and, in particular, high mowing intensity, had consistent effects on β-diversity across groups, causing a homogenization of soil microbial, fungal pathogen, plant and arthropod communities. These effects were nonlinear and the strongest declines in β-diversity occurred in the transition from extensively managed to intermediate intensity grassland. LUI tended to reduce local α-diversity in aboveground groups, whereas the α-diversity increased in belowground groups. Correlations between the β-diversity of different groups, particularly between plants and their consumers, became weaker at high LUI. This suggests a loss of specialist species and is further evidence for biotic homogenization. The consistently negative effects of LUI on landscape-scale biodiversity underscore the high value of extensively managed grasslands for conserving multitrophic biodiversity and ecosystem service provision. Indeed, biotic homogenization rather than local diversity loss could prove to be the most substantial consequence of land-use intensification.

Land-use intensification causes multitrophic homogenization of grassland communities.

PubMed

Gossner, Martin M; Lewinsohn, Thomas M; Kahl, Tiemo; Grassein, Fabrice; Boch, Steffen; Prati, Daniel; Birkhofer, Klaus; Renner, Swen C; Sikorski, Johannes; Wubet, Tesfaye; Arndt, Hartmut; Baumgartner, Vanessa; Blaser, Stefan; Blüthgen, Nico; Börschig, Carmen; Buscot, Francois; Diekötter, Tim; Jorge, Leonardo Ré; Jung, Kirsten; Keyel, Alexander C; Klein, Alexandra-Maria; Klemmer, Sandra; Krauss, Jochen; Lange, Markus; Müller, Jörg; Overmann, Jörg; Pašalić, Esther; Penone, Caterina; Perović, David J; Purschke, Oliver; Schall, Peter; Socher, Stephanie A; Sonnemann, Ilja; Tschapka, Marco; Tscharntke, Teja; Türke, Manfred; Venter, Paul Christiaan; Weiner, Christiane N; Werner, Michael; Wolters, Volkmar; Wurst, Susanne; Westphal, Catrin; Fischer, Markus; Weisser, Wolfgang W; Allan, Eric

2016-12-08

Land-use intensification is a major driver of biodiversity loss. Alongside reductions in local species diversity, biotic homogenization at larger spatial scales is of great concern for conservation. Biotic homogenization means a decrease in β-diversity (the compositional dissimilarity between sites). Most studies have investigated losses in local (α)-diversity and neglected biodiversity loss at larger spatial scales. Studies addressing β-diversity have focused on single or a few organism groups (for example, ref. 4), and it is thus unknown whether land-use intensification homogenizes communities at different trophic levels, above- and belowground. Here we show that even moderate increases in local land-use intensity (LUI) cause biotic homogenization across microbial, plant and animal groups, both above- and belowground, and that this is largely independent of changes in α-diversity. We analysed a unique grassland biodiversity dataset, with abundances of more than 4,000 species belonging to 12 trophic groups. LUI, and, in particular, high mowing intensity, had consistent effects on β-diversity across groups, causing a homogenization of soil microbial, fungal pathogen, plant and arthropod communities. These effects were nonlinear and the strongest declines in β-diversity occurred in the transition from extensively managed to intermediate intensity grassland. LUI tended to reduce local α-diversity in aboveground groups, whereas the α-diversity increased in belowground groups. Correlations between the β-diversity of different groups, particularly between plants and their consumers, became weaker at high LUI. This suggests a loss of specialist species and is further evidence for biotic homogenization. The consistently negative effects of LUI on landscape-scale biodiversity underscore the high value of extensively managed grasslands for conserving multitrophic biodiversity and ecosystem service provision. Indeed, biotic homogenization rather than local diversity loss could prove to be the most substantial consequence of land-use intensification.

A STATISTICAL THERMODYNAMIC MODEL OF THE ORGANIZATIONAL ORDER OF VEGETATION. (R827676)

EPA Science Inventory

The complex pattern of vegetation is the macroscopic manifestation of biological diversity and the ecological order in space and time. How is this overwhelmingly diverse, yet wonderfully ordered spatial pattern formed, and how does it evolve? To answer these questions, most tr...

Design and Implementation of Secure and Reliable Communication using Optical Wireless Communication

NASA Astrophysics Data System (ADS)

Saadi, Muhammad; Bajpai, Ambar; Zhao, Yan; Sangwongngam, Paramin; Wuttisittikulkij, Lunchakorn

2014-11-01

Wireless networking intensify the tractability in the home and office environment to connect the internet without wires but at the cost of risks associated with stealing the data or threat of loading malicious code with the intention of harming the network. In this paper, we proposed a novel method of establishing a secure and reliable communication link using optical wireless communication (OWC). For security, spatial diversity based transmission using two optical transmitters is used and the reliability in the link is achieved by a newly proposed method for the construction of structured parity check matrix for binary Low Density Parity Check (LDPC) codes. Experimental results show that a successful secure and reliable link between the transmitter and the receiver can be achieved by using the proposed novel technique.

Bioprinting a cardiac valve.

PubMed

Jana, Soumen; Lerman, Amir

2015-12-01

Heart valve tissue engineering could be a possible solution for the limitations of mechanical and biological prostheses, which are commonly used for heart valve replacement. In tissue engineering, cells are seeded into a 3-dimensional platform, termed the scaffold, to make the engineered tissue construct. However, mimicking the mechanical and spatial heterogeneity of a heart valve structure in a fabricated scaffold with uniform cell distribution is daunting when approached conventionally. Bioprinting is an emerging technique that can produce biological products containing matrix and cells, together or separately with morphological, structural and mechanical diversity. This advance increases the possibility of fabricating the structure of a heart valve in vitro and using it as a functional tissue construct for implantation. This review describes the use of bioprinting technology in heart valve tissue engineering. Copyright © 2015 Elsevier Inc. All rights reserved.

Simultaneous narrowband ultrasonic strain-flow imaging

NASA Astrophysics Data System (ADS)

Tsou, Jean K.; Mai, Jerome J.; Lupotti, Fermin A.; Insana, Michael F.

2004-04-01

We are summarizing new research aimed at forming spatially and temporally registered combinations of strain and color-flow images using echo data recorded from a commercial ultrasound system. Applications include diagnosis of vascular diseases and tumor malignancies. The challenge is to meet the diverse needs of each measurement. The approach is to first apply eigenfilters that separate echo components from moving tissues and blood flow, and then estimate blood velocity and tissue displacement from the filtered-IQ-signal phase modulations. At the cost of a lower acquisition frame rate, we find the autocorrelation strain estimator yields higher resolution strain estimate than the cross-correlator since estimates are made from ensembles at a single point in space. The technique is applied to in vivo carotid imaging, to demonstrate the sensitivity for strain-flow vascular imaging.

Application of Hyperspectral Remote Sensing Techniques to Evaluate Water Quality in Turbid Coastal Waters of South Carolina.

NASA Astrophysics Data System (ADS)

Ali, K. A.; Ryan, K.

2014-12-01

Coastal and inland waters represent a diverse set of resources that support natural habitat and provide valuable ecosystem services to the human population. Conventional techniques to monitor water quality using in situ sensors and laboratory analysis of water samples can be very time- and cost-intensive. Alternatively, remote sensing techniques offer better spatial coverage and temporal resolution to accurately characterize the dynamic and unique water quality parameters. Existing remote sensing ocean color products, such as the water quality proxy chlorophyll-a, are based on ocean derived bio-optical models that are primarily calibrated in Case 1 type waters. These traditional models fail to work when applied in turbid (Case 2 type), coastal waters due to spectral interference from other associated color producing agents such as colored dissolved organic matter and suspended sediments. In this work, we introduce a novel technique for the predictive modeling of chlorophyll-a using a multivariate-based approach applied to in situ hyperspectral radiometric data collected from the coastal waters of Long Bay, South Carolina. This method uses a partial least-squares regression model to identify prominent wavelengths that are more sensitive to chlorophyll-a relative to other associated color-producing agents. The new model was able to explain 80% of the observed chlorophyll-a variability in Long Bay with RMSE = 2.03 μg/L. This approach capitalizes on the spectral advantage gained from current and future hyperspectral sensors, thus providing a more robust predicting model. This enhanced mode of water quality monitoring in marine environments will provide insight to point-sources and problem areas that may contribute to a decline in water quality. The utility of this tool is in its versatility to a diverse set of coastal waters and its use by coastal and fisheries managers with regard to recreation, regulation, economic and public health purposes.

Greater diversity of soil fungal communities and distinguishable seasonal variation in temperate deciduous forests compared with subtropical evergreen forests of eastern China.

PubMed

He, Jinhong; Tedersoo, Leho; Hu, Ang; Han, Conghai; He, Dan; Wei, Hui; Jiao, Min; Anslan, Sten; Nie, Yanxia; Jia, Yongxia; Zhang, Gengxin; Yu, Guirui; Liu, Shirong; Shen, Weijun

2017-07-01

Whether and how seasonality of environmental variables impacts the spatial variability of soil fungal communities remain poorly understood. We assessed soil fungal diversity and community composition of five Chinese zonal forests along a latitudinal gradient spanning 23°N to 42°N in three seasons to address these questions. We found that soil fungal diversity increased linearly or parabolically with latitude. The seasonal variations in fungal diversity were more distinguishable in three temperate deciduous forests than in two subtropical evergreen forests. Soil fungal diversity was mainly correlated with edaphic factors such as pH and nutrient contents. Both latitude and its interactions with season also imposed significant impacts on soil fungal community composition (FCC), but the effects of latitude were stronger than those of season. Vegetational properties such as plant diversity and forest age were the dominant factors affecting FCC in the subtropical evergreen forests while edaphic properties were the dominant ones in the temperate deciduous forests. Our results indicate that latitudinal variation patterns of soil fungal diversity and FCC may differ among seasons. The stronger effect of latitude relative to that of season suggests a more important influence by the spatial than temporal heterogeneity in shaping soil fungal communities across zonal forests. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

At Limits of Life: Multidisciplinary Insights Reveal Environmental Constraints on Biotic Diversity in Continental Antarctica

PubMed Central

Magalhães, Catarina; Stevens, Mark I.; Cary, S. Craig; Ball, Becky A.; Storey, Bryan C.; Wall, Diana H.; Türk, Roman; Ruprecht, Ulrike

2012-01-01

Multitrophic communities that maintain the functionality of the extreme Antarctic terrestrial ecosystems, while the simplest of any natural community, are still challenging our knowledge about the limits to life on earth. In this study, we describe and interpret the linkage between the diversity of different trophic level communities to the geological morphology and soil geochemistry in the remote Transantarctic Mountains (Darwin Mountains, 80°S). We examined the distribution and diversity of biota (bacteria, cyanobacteria, lichens, algae, invertebrates) with respect to elevation, age of glacial drift sheets, and soil physicochemistry. Results showed an abiotic spatial gradient with respect to the diversity of the organisms across different trophic levels. More complex communities, in terms of trophic level diversity, were related to the weakly developed younger drifts (Hatherton and Britannia) with higher soil C/N ratio and lower total soluble salts content (thus lower conductivity). Our results indicate that an increase of ion concentration from younger to older drift regions drives a succession of complex to more simple communities, in terms of number of trophic levels and diversity within each group of organisms analysed. This study revealed that integrating diversity across multi-trophic levels of biotic communities with abiotic spatial heterogeneity and geological history is fundamental to understand environmental constraints influencing biological distribution in Antarctic soil ecosystems. PMID:23028563

Psychometric Evaluation of Lexical Diversity Indices: Assessing Length Effects

ERIC Educational Resources Information Center

Fergadiotis, Gerasimos; Wright, Heather Harris; Green, Samuel B.

2015-01-01

Purpose: Several novel techniques have been developed recently to assess the breadth of a speaker's vocabulary exhibited in a language sample. The specific aim of this study was to increase our understanding of the validity of the scores generated by different lexical diversity (LD) estimation techniques. Four techniques were explored: D, Maas,…

Generation of Earth's First-Order Biodiversity Pattern

NASA Astrophysics Data System (ADS)

Krug, Andrew Z.; Jablonski, David; Valentine, James W.; Roy, Kaustuv

2009-02-01

The first-order biodiversity pattern on Earth today and at least as far back as the Paleozoic is the latitudinal diversity gradient (LDG), a decrease in richness of species and higher taxa from the equator to the poles. LDGs are produced by geographic trends in origination, extinction, and dispersal over evolutionary timescales, so that analyses of static patterns will be insufficient to reveal underlying processes. The fossil record of marine bivalve genera, a model system for the analysis of biodiversity dynamics over large temporal and spatial scales, shows that an origination and range-expansion gradient plays a major role in generating the LDG. Peak origination rates and peak diversities fall within the tropics, with range expansion out of the tropics the predominant spatial dynamic thereafter. The origination-diversity link occurs even in a "contrarian" group whose diversity peaks at midlatitudes, an exception proving the rule that spatial variations in origination are key to latitudinal diversity patterns. Extinction rates are lower in polar latitudes (≥60°) than in temperate zones and thus cannot create the observed gradient alone. They may, however, help to explain why origination and immigration are evidently damped in higher latitudes. We suggest that species require more resources in higher latitudes, for the seasonality of primary productivity increases by more than an order of magnitude from equatorial to polar regions. Higher-latitude species are generalists that, unlike potential immigrants, are adapted to garner the large share of resources required for incumbency in those regions. When resources are opened up by extinctions, lineages spread chiefly poleward and chiefly through speciation.

Generation of Earth's first-order biodiversity pattern.

PubMed

Krug, Andrew Z; Jablonski, David; Valentine, James W; Roy, Kaustuv

2009-01-01

The first-order biodiversity pattern on Earth today and at least as far back as the Paleozoic is the latitudinal diversity gradient (LDG), a decrease in richness of species and higher taxa from the equator to the poles. LDGs are produced by geographic trends in origination, extinction, and dispersal over evolutionary timescales, so that analyses of static patterns will be insufficient to reveal underlying processes. The fossil record of marine bivalve genera, a model system for the analysis of biodiversity dynamics over large temporal and spatial scales, shows that an origination and range-expansion gradient plays a major role in generating the LDG. Peak origination rates and peak diversities fall within the tropics, with range expansion out of the tropics the predominant spatial dynamic thereafter. The origination-diversity link occurs even in a "contrarian" group whose diversity peaks at midlatitudes, an exception proving the rule that spatial variations in origination are key to latitudinal diversity patterns. Extinction rates are lower in polar latitudes (> or =60 degrees ) than in temperate zones and thus cannot create the observed gradient alone. They may, however, help to explain why origination and immigration are evidently damped in higher latitudes. We suggest that species require more resources in higher latitudes, for the seasonality of primary productivity increases by more than an order of magnitude from equatorial to polar regions. Higher-latitude species are generalists that, unlike potential immigrants, are adapted to garner the large share of resources required for incumbency in those regions. When resources are opened up by extinctions, lineages spread chiefly poleward and chiefly through speciation.

Taxa-area relationship of aquatic fungi on deciduous leaves.

PubMed

Duarte, Sofia; Cássio, Fernanda; Pascoal, Cláudia; Bärlocher, Felix

2017-01-01

One of the fundamental patterns in macroecology is the increase in the number of observed taxa with size of sampled area. For microbes, the shape of this relationship remains less clear. The current study assessed the diversity of aquatic fungi, by the traditional approach based on conidial morphology (captures reproducing aquatic hyphomycetes) and next generation sequencing (NGS; captures other fungi as well), on graded sizes of alder leaves (0.6 to 13.6 cm2). Leaves were submerged in two streams in geographically distant locations: the Oliveira Stream in Portugal and the Boss Brook in Canada. Decay rates of alder leaves and fungal sporulation rates did not differ between streams. Fungal biomass was higher in Boss Brook than in Oliveira Stream, and in both streams almost 100% of the reads belonged to active fungal taxa. In general, larger leaf areas tended to harbour more fungi, but these findings were not consistent between techniques. Morphospecies-based diversity increased with leaf area in Boss Brook, but not in Oliveira Stream; metabarcoding data showed an opposite trend. The higher resolution of metabarcoding resulted in steeper taxa-accumulation curves than morphospecies-based assessments (fungal conidia morphology). Fungal communities assessed by metabarcoding were spatially structured by leaf area in both streams. Metabarcoding promises greater resolution to assess biodiversity patterns in aquatic fungi and may be more accurate for assessing taxa-area relationships and local to global diversity ratios.

A single European aspen (Populus tremula) tree individual may potentially harbour dozens of Cenococcum geophilum ITS genotypes and hundreds of species of ectomycorrhizal fungi.

PubMed

Bahram, Mohammad; Põlme, Sergei; Kõljalg, Urmas; Tedersoo, Leho

2011-02-01

Ectomycorrhizal fungi (EcMF) form diverse communities and link different host plants into mycorrhizal networks, yet little is known about the magnitude of mycobiont diversity of a single tree individual. This study addresses species richness and spatial structure of EcMF in the root system of a single European aspen (Populus tremula) individual in an old-growth boreal mixed forest ecosystem in Estonia. Combining morphological and molecular identification methods for both plant and fungi, 122 species of EcMF were recovered from 103 root samples of the single tree. Richness estimators predicted the total EcMF richness to range from 182 to 207 species, reflecting the observation of 62.3% singletons and doubletons within the community. Fine-scale genetic diversity in Cenococcum geophilum indicates the presence of 23 internal transcribed spacer genotypes. EcMF community was significantly spatially autocorrelated only at the lineage level up to 3 m distance, but not at the species level. Proximity of other hosts had a significant effect on the spatial distribution of EcMF lineages. This study demonstrates that a single tree may host as many EcMF species and individuals as recovered on multiple hosts in diverse communities over larger areas. © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Psychometric Evaluation of Lexical Diversity Indices: Assessing Length Effects.

PubMed

Fergadiotis, Gerasimos; Wright, Heather Harris; Green, Samuel B

2015-06-01

Several novel techniques have been developed recently to assess the breadth of a speaker's vocabulary exhibited in a language sample. The specific aim of this study was to increase our understanding of the validity of the scores generated by different lexical diversity (LD) estimation techniques. Four techniques were explored: D, Maas, measure of textual lexical diversity, and moving-average type-token ratio. Four LD indices were estimated for language samples on 4 discourse tasks (procedures, eventcasts, story retell, and recounts) from 442 adults who are neurologically intact. The resulting data were analyzed using structural equation modeling. The scores for measure of textual lexical diversity and moving-average type-token ratio were stronger indicators of the LD of the language samples. The results for the other 2 techniques were consistent with the presence of method factors representing construct-irrelevant sources. These findings offer a deeper understanding of the relative validity of the 4 estimation techniques and should assist clinicians and researchers in the selection of LD measures of language samples that minimize construct-irrelevant sources.

Spatially explicit watershed modeling: tracking water, mercury and nitrogen in multiple systems under diverse conditions

EPA Science Inventory

Environmental decision-making and the influences of various stressors, such as landscape and climate changes on water quantity and quality, requires the application of environmental modeling. Spatially explicit environmental and watershed-scale models using GIS as a base framewor...

Insights and challenges to Intergrating data from diverse ecological networks

USDA-ARS?s Scientific Manuscript database

Many of the most dramatic and surprising effects of global change occur across large spatial extents, from regions to continents, that impact multiple ecosystem types across a range of interacting spatial and temporal scales. The ability of ecologists and interdisciplinary scientists to understand a...

Induced spatial heterogeneity in forest canopies: responses of small mammals.

Treesearch

A.B. Carey

2001-01-01

We hypothesized that creating a mosaic of interspersed patches of different densities of canopy trees in a second-growth Douglas-fir (Pseudotsuga menziesiz) forest would accelerate development of biocomplexity (diversity in ecosystem structure, composition, and processes) by promoting spatial heterogeneity in understory, midstory, and canopy,...

Spatial Homogeneity of Bacterial Communities Associated with the Surface Mucus Layer of the Reef-Building Coral Acropora palmata.

PubMed

Kemp, Dustin W; Rivers, Adam R; Kemp, Keri M; Lipp, Erin K; Porter, James W; Wares, John P

2015-01-01

Coral surface mucus layer (SML) microbiota are critical components of the coral holobiont and play important roles in nutrient cycling and defense against pathogens. We sequenced 16S rRNA amplicons to examine the structure of the SML microbiome within and between colonies of the threatened Caribbean reef-building coral Acropora palmata in the Florida Keys. Samples were taken from three spatially distinct colony regions--uppermost (high irradiance), underside (low irradiance), and the colony base--representing microhabitats that vary in irradiance and water flow. Phylogenetic diversity (PD) values of coral SML bacteria communities were greater than surrounding seawater and lower than adjacent sediment. Bacterial diversity and community composition was consistent among the three microhabitats. Cyanobacteria, Bacteroidetes, Alphaproteobacteria, and Proteobacteria, respectively were the most abundant phyla represented in the samples. This is the first time spatial variability of the surface mucus layer of A. palmata has been studied. Homogeneity in the microbiome of A. palmata contrasts with SML heterogeneity found in other Caribbean corals. These findings suggest that, during non-stressful conditions, host regulation of SML microbiota may override diverse physiochemical influences induced by the topographical complexity of A. palmata. Documenting the spatial distribution of SML microbes is essential to understanding the functional roles these microorganisms play in coral health and adaptability to environmental perturbations.

Spatial Distribution Patterns in the Very Rare and Species-Rich Picea chihuahuana Tree Community (Mexico).

PubMed

Wehenkel, Christian; Brazão-Protázio, João Marcelo; Carrillo-Parra, Artemio; Martínez-Guerrero, José Hugo; Crecente-Campo, Felipe

2015-01-01

The very rare Mexican Picea chihuahuana tree community covers an area of no more than 300 ha in the Sierra Madre Occidental. This special tree community has been the subject of several studies aimed at learning more about the genetic structure and ecology of the species and the potential effects of climate change. The spatial distribution of trees is a result of many ecological processes and can affect the degree of competition between neighbouring trees, tree density, variability in size and distribution, regeneration, survival, growth, mortality, crown formation and the biological diversity within forest communities. Numerous scale-dependent measures have been established in order to describe spatial forest structure. The overall aim of most of these studies has been to obtain data to help design preservation and conservation strategies. In this study, we examined the spatial distribution pattern of trees in the P. chihuahuana tree community in 12 localities, in relation to i) tree stand density, ii) diameter distribution (vertical structure), iii) tree species diversity, iv) geographical latitude and v) tree dominance at a fine scale (in 0.25 ha plots), with the aim of obtaining a better understanding of the complex ecosystem processes and biological diversity. Because of the strongly mixed nature of this tree community, which often produces low population densities of each tree species and random tree fall gaps caused by tree death, we expect aggregated patterns in individual Picea chihuahuana trees and in the P. chihuahuana tree community, repulsive Picea patterns to other tree species and repulsive patterns of young to adult trees. Each location was represented by one plot of 50 x 50 m (0.25 ha) established in the centre of the tree community. The findings demonstrate that the hypothesis of aggregated tree pattern is not applicable to the mean pattern measured by Clark-Evans index, Uniform Angle index and Mean Directional index of the uneven-aged P. chihuahuana trees and P. chihuahuana tree community and but to specific spatial scales measured by the univariate L-function. The spatial distribution pattern of P. chihuahuana trees was found to be independent of patches of other tree species measured by the bivariate L-function. The spatial distribution was not significantly related to tree density, diameter distribution or tree species diversity. The index of Clark and Evans decreased significantly from the southern to northern plots containing all tree species. Self-thinning due to intra and inter-specific competition-induced mortality is probably the main cause of the decrease in aggregation intensity during the course of population development in this tree community. We recommend the use of larger sampling plots (> 0.25 ha) in uneven-aged and species-rich forest ecosystems to detect less obvious, but important, relationships between spatial tree pattern and functioning and diversity in these forests.

Spatial Distribution Patterns in the Very Rare and Species-Rich Picea chihuahuana Tree Community (Mexico)

PubMed Central

Wehenkel, Christian; Brazão-Protázio, João Marcelo; Carrillo-Parra, Artemio; Martínez-Guerrero, José Hugo; Crecente-Campo, Felipe

2015-01-01

The very rare Mexican Picea chihuahuana tree community covers an area of no more than 300 ha in the Sierra Madre Occidental. This special tree community has been the subject of several studies aimed at learning more about the genetic structure and ecology of the species and the potential effects of climate change. The spatial distribution of trees is a result of many ecological processes and can affect the degree of competition between neighbouring trees, tree density, variability in size and distribution, regeneration, survival, growth, mortality, crown formation and the biological diversity within forest communities. Numerous scale-dependent measures have been established in order to describe spatial forest structure. The overall aim of most of these studies has been to obtain data to help design preservation and conservation strategies. In this study, we examined the spatial distribution pattern of trees in the P. chihuahuana tree community in 12 localities, in relation to i) tree stand density, ii) diameter distribution (vertical structure), iii) tree species diversity, iv) geographical latitude and v) tree dominance at a fine scale (in 0.25 ha plots), with the aim of obtaining a better understanding of the complex ecosystem processes and biological diversity. Because of the strongly mixed nature of this tree community, which often produces low population densities of each tree species and random tree fall gaps caused by tree death, we expect aggregated patterns in individual Picea chihuahuana trees and in the P. chihuahuana tree community, repulsive Picea patterns to other tree species and repulsive patterns of young to adult trees. Each location was represented by one plot of 50 x 50 m (0.25 ha) established in the centre of the tree community. The findings demonstrate that the hypothesis of aggregated tree pattern is not applicable to the mean pattern measured by Clark-Evans index, Uniform Angle index and Mean Directional index of the uneven-aged P. chihuahuana trees and P. chihuahuana tree community and but to specific spatial scales measured by the univariate L-function. The spatial distribution pattern of P. chihuahuana trees was found to be independent of patches of other tree species measured by the bivariate L-function. The spatial distribution was not significantly related to tree density, diameter distribution or tree species diversity. The index of Clark and Evans decreased significantly from the southern to northern plots containing all tree species. Self-thinning due to intra and inter-specific competition-induced mortality is probably the main cause of the decrease in aggregation intensity during the course of population development in this tree community. We recommend the use of larger sampling plots (> 0.25 ha) in uneven-aged and species-rich forest ecosystems to detect less obvious, but important, relationships between spatial tree pattern and functioning and diversity in these forests. PMID:26496189

Initial results of the Global Thermospheric Mapping Study (GTMS)

NASA Technical Reports Server (NTRS)

Oliver, W. L.; Salah, J. E.; Musgrove, R. G.; Holt, J. M.; Wickwar, V. B.; Hernandez, G. J.; Roble, R. G.

1986-01-01

The Global Thermospheric Mapping Study (GTMS) is a multi-technique experimental study of the thermosphere designed to map simultaneously its spatial and temporal morphology with a thoroughness and diversity of measurement techniques heretofore unachieved. The GTMS is designed around the Incoherent Scatter Radar Chain in the western hemisphere. The European incoherent scatter radars and the worldwide communities of Fabry-Perot interferometers, meteor wind radars, partial reflection drifts radars, MST radars, and satellite probes are included to extend the spatial coverage and types of measurements available. Theoretical and modeling support in the areas of thermospheric and ionospheric structure, tides, and electric fields are included to aid in program planning and data interpretation. Solar activity was low on the three observation days (F10.7 = 97, 98, 96) and magnetic conditions were unsettled to active (A = 10, 12, 20). All six incoherent scatter radar facilities collected data. Each collected F region data day and night while Saint Santin and Millstone Hill additionally collected E region data during daylight hours. Initial results from Sondrestrom and Millstone Hill are presented. Good quality Fabry Perot data were collected at Fritz Peak and San Jose dos Campos. Weather conditions produced poor results at Arequipa and Arecibo. Initial results from Fritz Peak are presented. Mesosphere/lower-thermosphere observations were conducted under the ATMAP organization. The magnetometer chains also were operational during this campaign. Initial thermospheric general circulation model predictions were made for assumed solar-geophysical conditions, and selected results are presented.

Diversity and productivity of hypogeous fungal sporocarps in a variably thinned Douglas-fir forest.

Treesearch

W.C. III Colgan; A.B. Carey; J.M. Trappe; R. Molina; D. Thysell

1999-01-01

Although ecosystem management techniques are designed to enhance species diversity in managed forests, no comprehensive study has been conducted to evaluate effects of such techniques on diversity and productivity of hypogeous fungi (truffles). During this study, truffles were collected in a 55- to 65-year-old Douglas-fir forest from March 1993 through December 1995 at...

Application of Statistical Downscaling Techniques to Predict Rainfall and Its Spatial Analysis Over Subansiri River Basin of Assam, India

NASA Astrophysics Data System (ADS)

Barman, S.; Bhattacharjya, R. K.

2017-12-01

The River Subansiri is the major north bank tributary of river Brahmaputra. It originates from the range of Himalayas beyond the Great Himalayan range at an altitude of approximately 5340m. Subansiri basin extends from tropical to temperate zones and hence exhibits a great diversity in rainfall characteristics. In the Northern and Central Himalayan tracts, precipitation is scarce on account of high altitudes. On the other hand, Southeast part of the Subansiri basin comprising the sub-Himalayan and the plain tract in Arunachal Pradesh and Assam, lies in the tropics. Due to Northeast as well as Southwest monsoon, precipitation occurs in this region in abundant quantities. Particularly, Southwest monsoon causes very heavy precipitation in the entire Subansiri basin during May to October. In this study, the rainfall over Subansiri basin has been studied at 24 different locations by multiple linear and non-linear regression based statistical downscaling techniques and by Artificial Neural Network based model. APHRODITE's gridded rainfall data of 0.25˚ x 0.25˚ resolutions and climatic parameters of HadCM3 GCM of resolution 2.5˚ x 3.75˚ (latitude by longitude) have been used in this study. It has been found that multiple non-linear regression based statistical downscaling technique outperformed the other techniques. Using this method, the future rainfall pattern over the Subansiri basin has been analyzed up to the year 2099 for four different time periods, viz., 2020-39, 2040-59, 2060-79, and 2080-99 at all the 24 locations. On the basis of historical rainfall, the months have been categorized as wet months, months with moderate rainfall and dry months. The spatial changes in rainfall patterns for all these three types of months have also been analyzed over the basin. Potential decrease of rainfall in the wet months and months with moderate rainfall and increase of rainfall in the dry months are observed for the future rainfall pattern of the Subansiri basin.

Complementarity of Rotating Video and Underwater Visual Census for Assessing Species Richness, Frequency and Density of Reef Fish on Coral Reef Slopes

PubMed Central

Mallet, Delphine; Wantiez, Laurent; Lemouellic, Soazig; Vigliola, Laurent; Pelletier, Dominique

2014-01-01

Estimating diversity and abundance of fish species is fundamental for understanding community structure and dynamics of coral reefs. When designing a sampling protocol, one crucial step is the choice of the most suitable sampling technique which is a compromise between the questions addressed, the available means and the precision required. The objective of this study is to compare the ability to sample reef fish communities at the same locations using two techniques based on the same stationary point count method: one using Underwater Visual Census (UVC) and the other rotating video (STAVIRO). UVC and STAVIRO observations were carried out on the exact same 26 points on the reef slope of an intermediate reef and the associated inner barrier reefs. STAVIRO systems were always deployed 30 min to 1 hour after UVC and set exactly at the same place. Our study shows that; (i) fish community observations by UVC and STAVIRO differed significantly; (ii) species richness and density of large species were not significantly different between techniques; (iii) species richness and density of small species were higher for UVC; (iv) density of fished species was higher for STAVIRO and (v) only UVC detected significant differences in fish assemblage structure across reef type at the spatial scale studied. We recommend that the two techniques should be used in a complementary way to survey a large area within a short period of time. UVC may census reef fish within complex habitats or in very shallow areas such as reef flat whereas STAVIRO would enable carrying out a large number of stations focused on large and diver-averse species, particularly in the areas not covered by UVC due to time and depth constraints. This methodology would considerably increase the spatial coverage and replication level of fish monitoring surveys. PMID:24392126

Predicting the genetic consequences of future climate change: The power of coupling spatial demography, the coalescent, and historical landscape changes.

PubMed

Brown, Jason L; Weber, Jennifer J; Alvarado-Serrano, Diego F; Hickerson, Michael J; Franks, Steven J; Carnaval, Ana C

2016-01-01

Climate change is a widely accepted threat to biodiversity. Species distribution models (SDMs) are used to forecast whether and how species distributions may track these changes. Yet, SDMs generally fail to account for genetic and demographic processes, limiting population-level inferences. We still do not understand how predicted environmental shifts will impact the spatial distribution of genetic diversity within taxa. We propose a novel method that predicts spatially explicit genetic and demographic landscapes of populations under future climatic conditions. We use carefully parameterized SDMs as estimates of the spatial distribution of suitable habitats and landscape dispersal permeability under present-day, past, and future conditions. We use empirical genetic data and approximate Bayesian computation to estimate unknown demographic parameters. Finally, we employ these parameters to simulate realistic and complex models of responses to future environmental shifts. We contrast parameterized models under current and future landscapes to quantify the expected magnitude of change. We implement this framework on neutral genetic data available from Penstemon deustus. Our results predict that future climate change will result in geographically widespread declines in genetic diversity in this species. The extent of reduction will heavily depend on the continuity of population networks and deme sizes. To our knowledge, this is the first study to provide spatially explicit predictions of within-species genetic diversity using climatic, demographic, and genetic data. Our approach accounts for climatic, geographic, and biological complexity. This framework is promising for understanding evolutionary consequences of climate change, and guiding conservation planning. © 2016 Botanical Society of America.

Spatial extent of analysis influences observed patterns of population genetic structure in a widespread darter species (Percidae)

USGS Publications Warehouse

Argentina, Jane E.; Angermeier, Paul L.; Hallerman, Eric M.; Welsh, Stuart A.

2018-01-01

Connectivity among stream fish populations allows for exchange of genetic material and helps maintain genetic diversity, adaptive potential and population stability over time. Changes in species demographics and population connectivity have the potential to permanently alter the genetic patterns of stream fish, although these changes through space and time are variable and understudied in small‐bodied freshwater fish.As a spatially widespread, common species of benthic freshwater fish, the variegate darter (Etheostoma variatum) is a model species for documenting how patterns of genetic structure and diversity respond to increasing isolation due to large dams and how scale of study may shape our understanding of these patterns. We sampled variegate darters from 34 sites across their range in the North American Ohio River basin and examined how patterns of genetic structure and diversity within and between populations responded to historical population changes and dams within and between populations.Spatial scale and configuration of genetic structure varied across the eight identified populations, from tributaries within a watershed, to a single watershed, to multiple watersheds that encompass Ohio River mainstem habitats. This multiwatershed pattern of population structuring suggests genetic dispersal across large distances was and may continue to be common, although some populations remain isolated despite no apparent structural dispersal barriers. Populations with low effective population sizes and evidence of past population bottlenecks showed low allelic richness, but diversity patterns were not related to watershed size, a surrogate for habitat availability. Pairwise genetic differentiation (FST) increased with fluvial distance and was related to both historic and contemporary processes. Genetic diversity changes were influenced by underlying population size and stability, and while instream barriers were not strong determinants of genetic structuring or loss of genetic diversity, they reduce population connectivity and may impact long‐term population persistence.The broad spatial scale of this study demonstrated the large spatial extent of some variegate darter populations and indicated that dispersal is more extensive than expected given the movement patterns typically observed for small‐bodied, benthic fish. Dam impacts depended on underlying population size and stability, with larger populations more resilient to genetic drift and allelic richness loss than smaller populations.Other darters that inhabit large river habitats may show similar patterns in landscape‐scale studies, and large river barriers may impact populations of small‐bodied fish more than previously expected. Estimation of dispersal rates and behaviours is critical to conservation of imperilled riverine species such as darters.

Subtle Ecological Gradient in the Tropics Triggers High Species-Turnover in a Local Geographical Scale

PubMed Central

Nguyen, Dinh T.

2016-01-01

Our perception of diversity, including both alpha- and beta-diversity components, depends on spatial scale. Studies of spatial variation of the latter are just starting, with a paucity of research on beta-diversity patterns at smaller scales. Understanding these patterns and the processes shaping the distribution of diversity is critical to describe this diversity, but it is paramount in conservation too. Here, we investigate the diversity and structure of a tropical community of herbivorous beetles at a reduced local scale of some 10 km2, evaluating the effect of a small, gradual ecological change on this structure. We sampled leaf beetles in the Núi Chúa National Park (S Vietnam), studying changes in alpha- and beta-diversity across an elevation gradient up to 500 m, encompassing the ecotone between critically endangered lowland dry deciduous forest and mixed evergreen forest at higher elevations. Leaf beetle diversity was assessed using several molecular tree-based species delimitation approaches (with mtDNA cox1 data), species richness using rarefaction and incidence-based diversity indexes, and beta-diversity was investigated decomposing the contribution of species turnover and nestedness. We documented 155 species in the area explored and species-richness estimates 1.5–2.0x higher. Species diversity was similar in both forest types and changes in alpha-diversity along the elevation gradient showed an expected local increase of diversity in the ecotone. Beta-diversity was high among forest paths (average Sørensen's dissimilarity = 0.694) and, tentatively fixing at 300 m the boundary between otherwise continuous biomes, demonstrated similarly high beta-diversity (Sørensen's dissimilarity = 0.581), with samples clustering according to biome/elevation. Highly relevant considering the local scale of the study, beta-diversity had a high contribution of species replacement among locales (54.8%) and between biomes (79.6%), suggesting environmental heterogeneity as the dominant force shaping diversity at such small scale, directly and indirectly on the plant communities. Protection actions in the Park, especially these addressed at the imperative conservation of dry forest, must ponder the small scale at which processes shape species diversity and community structure for inconspicuous, yet extraordinarily diverse organisms such as the leaf beetles. PMID:27276228

Demonstration of polarization-insensitive spatial light modulation using a single polarization-sensitive spatial light modulator.

PubMed

Liu, Jun; Wang, Jian

2015-07-06

We present a simple configuration incorporating a single polarization-sensitive phase-only liquid crystal spatial light modulator (LC-SLM) to facilitate polarization-insensitive spatial light modulation. The polarization-insensitive configuration is formed by a polarization beam splitter (PBS), a polarization-sensitive phase-only LC-SLM, a half-wave plate (HWP), and a mirror in a loop structure. We experimentally demonstrate polarization-insensitive spatial light modulations for incident linearly polarized beams with different polarization states and polarization-multiplexed beams. Polarization-insensitive spatial light modulations generating orbital angular momentum (OAM) beams are demonstrated in the experiment. The designed polarization-insensitive configuration may find promising applications in spatial light modulations accommodating diverse incident polarizations.

Habitat predictors of genetic diversity for two sympatric wetland-breeding amphibian species.

PubMed

McKee, Anna M; Maerz, John C; Smith, Lora L; Glenn, Travis C

2017-08-01

Population genetic diversity is widely accepted as important to the conservation and management of wildlife. However, habitat features may differentially affect evolutionary processes that facilitate population genetic diversity among sympatric species. We measured genetic diversity for two pond-breeding amphibian species (Dwarf salamanders, Eurycea quadridigitata ; and Southern Leopard frogs, Lithobates sphenocephalus ) to understand how habitat characteristics and spatial scale affect genetic diversity across a landscape. Samples were collected from wetlands on a longleaf pine reserve in Georgia. We genotyped microsatellite loci for both species to assess population structures and determine which habitat features were most closely associated with observed heterozygosity and rarefied allelic richness. Both species exhibited significant population genetic structure; however, structure in Southern Leopard frogs was driven primarily by one outlier site. Dwarf salamander allelic richness was greater at sites with less surrounding road area within 0.5 km and more wetland area within 1.0 and 2.5 km, and heterozygosity was greater at sites with more wetland area within 0.5 km. In contrast, neither measure of Southern Leopard frog genetic diversity was associated with any habitat features at any scale we evaluated. Genetic diversity in the Dwarf salamander was strongly associated with land cover variables up to 2.5 km away from breeding wetlands, and/or results suggest that minimizing roads in wetland buffers may be beneficial to the maintenance of population genetic diversity. This study suggests that patterns of genetic differentiation and genetic diversity have associations with different habitat features across different spatial scales for two syntopic pond-breeding amphibian species.

Distribution, abundance, and diversity of stream fishes under variable environmental conditions

Treesearch

Christopher M. Taylor; Thomas L. Holder; Richard A. Fiorillo; Lance R. Williams; R. Brent Thomas; Melvin L. Warren

2006-01-01

The effects of stream size and flow regime on spatial and temporal variability of stream fish distribution, abundance, and diversity patterns were investigated. Assemblage variability and species richness were each significantly associated with a complex environmental gradient contrasting smaller, hydrologically variable stream localities with larger localities...

Envisioning, quantifying, and managing thermal regimes on river networks

Treesearch

E. Ashley Steel; Timothy J. Beechie; Christian E. Torgersen; Aimee H. Fullerton

2017-01-01

Water temperatures fluctuate in time and space, creating diverse thermal regimes on river networks. Temporal variability in these thermal landscapes has important biological and ecological consequences because of nonlinearities in physiological reactions; spatial diversity in thermal landscapes provides aquatic organisms with options to maximize growth and survival....

A reverberation-time-aware DNN approach leveraging spatial information for microphone array dereverberation

NASA Astrophysics Data System (ADS)

Wu, Bo; Yang, Minglei; Li, Kehuang; Huang, Zhen; Siniscalchi, Sabato Marco; Wang, Tong; Lee, Chin-Hui

2017-12-01

A reverberation-time-aware deep-neural-network (DNN)-based multi-channel speech dereverberation framework is proposed to handle a wide range of reverberation times (RT60s). There are three key steps in designing a robust system. First, to accomplish simultaneous speech dereverberation and beamforming, we propose a framework, namely DNNSpatial, by selectively concatenating log-power spectral (LPS) input features of reverberant speech from multiple microphones in an array and map them into the expected output LPS features of anechoic reference speech based on a single deep neural network (DNN). Next, the temporal auto-correlation function of received signals at different RT60s is investigated to show that RT60-dependent temporal-spatial contexts in feature selection are needed in the DNNSpatial training stage in order to optimize the system performance in diverse reverberant environments. Finally, the RT60 is estimated to select the proper temporal and spatial contexts before feeding the log-power spectrum features to the trained DNNs for speech dereverberation. The experimental evidence gathered in this study indicates that the proposed framework outperforms the state-of-the-art signal processing dereverberation algorithm weighted prediction error (WPE) and conventional DNNSpatial systems without taking the reverberation time into account, even for extremely weak and severe reverberant conditions. The proposed technique generalizes well to unseen room size, array geometry and loudspeaker position, and is robust to reverberation time estimation error.

Expansion Under Climate Change: The Genetic Consequences.

PubMed

Garnier, Jimmy; Lewis, Mark A

2016-11-01

Range expansion and range shifts are crucial population responses to climate change. Genetic consequences are not well understood but are clearly coupled to ecological dynamics that, in turn, are driven by shifting climate conditions. We model a population with a deterministic reaction-diffusion model coupled to a heterogeneous environment that develops in time due to climate change. We decompose the resulting travelling wave solution into neutral genetic components to analyse the spatio-temporal dynamics of its genetic structure. Our analysis shows that range expansions and range shifts under slow climate change preserve genetic diversity. This is because slow climate change creates range boundaries that promote spatial mixing of genetic components. Mathematically, the mixing leads to so-called pushed travelling wave solutions. This mixing phenomenon is not seen in spatially homogeneous environments, where range expansion reduces genetic diversity through gene surfing arising from pulled travelling wave solutions. However, the preservation of diversity is diminished when climate change occurs too quickly. Using diversity indices, we show that fast expansions and range shifts erode genetic diversity more than slow range expansions and range shifts. Our study provides analytical insight into the dynamics of travelling wave solutions in heterogeneous environments.

Performance of Orbital Neutron Instruments for Spatially Resolved Hydrogen Measurements of Airless Planetary Bodies

PubMed Central

Elphic, Richard C.; Feldman, William C.; Funsten, Herbert O.; Prettyman, Thomas H.

2010-01-01

Abstract Orbital neutron spectroscopy has become a standard technique for measuring planetary surface compositions from orbit. While this technique has led to important discoveries, such as the deposits of hydrogen at the Moon and Mars, a limitation is its poor spatial resolution. For omni-directional neutron sensors, spatial resolutions are 1–1.5 times the spacecraft's altitude above the planetary surface (or 40–600 km for typical orbital altitudes). Neutron sensors with enhanced spatial resolution have been proposed, and one with a collimated field of view is scheduled to fly on a mission to measure lunar polar hydrogen. No quantitative studies or analyses have been published that evaluate in detail the detection and sensitivity limits of spatially resolved neutron measurements. Here, we describe two complementary techniques for evaluating the hydrogen sensitivity of spatially resolved neutron sensors: an analytic, closed-form expression that has been validated with Lunar Prospector neutron data, and a three-dimensional modeling technique. The analytic technique, called the Spatially resolved Neutron Analytic Sensitivity Approximation (SNASA), provides a straightforward method to evaluate spatially resolved neutron data from existing instruments as well as to plan for future mission scenarios. We conclude that the existing detector—the Lunar Exploration Neutron Detector (LEND)—scheduled to launch on the Lunar Reconnaissance Orbiter will have hydrogen sensitivities that are over an order of magnitude poorer than previously estimated. We further conclude that a sensor with a geometric factor of ∼ 100 cm2 Sr (compared to the LEND geometric factor of ∼ 10.9 cm2 Sr) could make substantially improved measurements of the lunar polar hydrogen spatial distribution. Key Words: Planetary instrumentation—Planetary science—Moon—Spacecraft experiments—Hydrogen. Astrobiology 10, 183–200. PMID:20298147

Combined point and distributed techniques for multidimensional estimation of spatial groundwater-stream water exchange in a heterogeneous sand bed-stream.

NASA Astrophysics Data System (ADS)

Gaona Garcia, J.; Lewandowski, J.; Bellin, A.

2017-12-01

Groundwater-stream water interactions in rivers determine water balances, but also chemical and biological processes in the streambed at different spatial and temporal scales. Due to the difficult identification and quantification of gaining, neutral and losing conditions, it is necessary to combine techniques with complementary capabilities and scale ranges. We applied this concept to a study site at the River Schlaube, East Brandenburg-Germany, a sand bed stream with intense sediment heterogeneity and complex environmental conditions. In our approach, point techniques such as temperature profiles of the streambed together with vertical hydraulic gradients provide data for the estimation of fluxes between groundwater and surface water with the numerical model 1DTempPro. On behalf of distributed techniques, fiber optic distributed temperature sensing identifies the spatial patterns of neutral, down- and up-welling areas by analysis of the changes in the thermal patterns at the streambed interface under certain flow. The study finally links point and surface temperatures to provide a method for upscaling of fluxes. Point techniques provide point flux estimates with essential depth detail to infer streambed structures while the results hardly represent the spatial distribution of fluxes caused by the heterogeneity of streambed properties. Fiber optics proved capable of providing spatial thermal patterns with enough resolution to observe distinct hyporheic thermal footprints at multiple scales. The relation of thermal footprint patterns and temporal behavior with flux results from point techniques enabled the use of methods for spatial flux estimates. The lack of detailed information of the physical driver's spatial distribution restricts the spatial flux estimation to the application of the T-proxy method, whose highly uncertain results mainly provide coarse spatial flux estimates. The study concludes that the upscaling of groundwater-stream water interactions using thermal measurements with combined point and distributed techniques requires the integration of physical drivers because of the heterogeneity of the flux patterns. Combined experimental and modeling approaches may help to obtain more reliable understanding of groundwater-surface water interactions at multiple scales.

Optimization of spatial frequency domain imaging technique for estimating optical properties of food and biological materials

USDA-ARS?s Scientific Manuscript database

Spatial frequency domain imaging technique has recently been developed for determination of the optical properties of food and biological materials. However, accurate estimation of the optical property parameters by the technique is challenging due to measurement errors associated with signal acquis...

CHARACTERIZING SPATIAL AND TEMPORAL DYNAMICS: DEVELOPMENT OF A GRID-BASED WATERSHED MERCURY LOADING MODEL

EPA Science Inventory

A distributed grid-based watershed mercury loading model has been developed to characterize spatial and temporal dynamics of mercury from both point and non-point sources. The model simulates flow, sediment transport, and mercury dynamics on a daily time step across a diverse lan...

Shrub expansion in northern Chihuahuan Desert grasslands: Spatial patterns of transition and biophysical constraints

USDA-ARS?s Scientific Manuscript database

Among the greatest contemporary threats to the structure, function and biological diversity of desert grassland and shrub savanna ecosystems of the southwestern United States is the displacement of mesophytic grasses by xerophytic woody plants. Through a combination of field sampling and spatial mod...

Multi-scale soil salinity mapping and monitoring with proximal and remote sensing

USDA-ARS?s Scientific Manuscript database

This talk is part of a technical short course on “Soil mapping and process modelling at diverse scales”. In the talk, guidelines, special considerations, protocols, and strengths and limitations are presented for characterizing spatial and temporal variation in soil salinity at several spatial scale...

Large-scale diversity of slope fishes: pattern inconsistency between multiple diversity indices.

PubMed

Gaertner, Jean-Claude; Maiorano, Porzia; Mérigot, Bastien; Colloca, Francesco; Politou, Chrissi-Yianna; Gil De Sola, Luis; Bertrand, Jacques A; Murenu, Matteo; Durbec, Jean-Pierre; Kallianiotis, Argyris; Mannini, Alessandro

2013-01-01

Large-scale studies focused on the diversity of continental slope ecosystems are still rare, usually restricted to a limited number of diversity indices and mainly based on the empirical comparison of heterogeneous local data sets. In contrast, we investigate large-scale fish diversity on the basis of multiple diversity indices and using 1454 standardized trawl hauls collected throughout the upper and middle slope of the whole northern Mediterranean Sea (36°3'- 45°7' N; 5°3'W - 28°E). We have analyzed (1) the empirical relationships between a set of 11 diversity indices in order to assess their degree of complementarity/redundancy and (2) the consistency of spatial patterns exhibited by each of the complementary groups of indices. Regarding species richness, our results contrasted both the traditional view based on the hump-shaped theory for bathymetric pattern and the commonly-admitted hypothesis of a large-scale decreasing trend correlated with a similar gradient of primary production in the Mediterranean Sea. More generally, we found that the components of slope fish diversity we analyzed did not always show a consistent pattern of distribution according either to depth or to spatial areas, suggesting that they are not driven by the same factors. These results, which stress the need to extend the number of indices traditionally considered in diversity monitoring networks, could provide a basis for rethinking not only the methodological approach used in monitoring systems, but also the definition of priority zones for protection. Finally, our results call into question the feasibility of properly investigating large-scale diversity patterns using a widespread approach in ecology, which is based on the compilation of pre-existing heterogeneous and disparate data sets, in particular when focusing on indices that are very sensitive to sampling design standardization, such as species richness.

Altitudinal Patterns of Species Diversity and Phylogenetic Diversity across Temperate Mountain Forests of Northern China.

PubMed

Zhang, Wenxin; Huang, Dizhou; Wang, Renqing; Liu, Jian; Du, Ning

2016-01-01

The spatial patterns of biodiversity and their underlying mechanisms have been an active area of research for a long time. In this study, a total of 63 samples (20m × 30m) were systematically established along elevation gradients on Mount Tai and Mount Lao, China. We explored altitudinal patterns of plant diversity in the two mountain systems. In order to understand the mechanisms driving current diversity patterns, we used phylogenetic approaches to detect the spatial patterns of phylogenetic diversity and phylogenetic structure along two elevation gradients. We found that total species richness had a monotonically decreasing pattern and tree richness had a unimodal pattern along the elevation gradients in the two study areas. However, altitudinal patterns in shrub richness and herbs richness were not consistent on the two mountains. At low elevation, anthropogenic disturbances contributed to the increase of plant diversity, especially for shrubs and herbs in understory layers, which are more sensitive to changes in microenvironment. The phylogenetic structure of plant communities exhibited an inverted hump-shaped pattern along the elevation gradient on Mount Tai, which demonstrates that environmental filtering is the main driver of plant community assembly at high and low elevations and inter-specific competition may be the main driver of plant community assembly in the middle elevations. However, the phylogenetic structure of plant communities did not display a clear pattern on Mount Lao where the climate is milder. Phylogenetic beta diversity and species beta diversity consistently increased with increasing altitudinal divergence in the two study areas. However, the altitudinal patterns of species richness did not completely mirror phylogenetic diversity patterns. Conservation areas should be selected taking into consideration the preservation of high species richness, while maximizing phylogenetic diversity to improve the potential for diversification in the future.

Satellite Remote Sensing Detection of Wastewater Plumes in Southern California

NASA Astrophysics Data System (ADS)

Trinh, R. C.; Holt, B.; Pan, B. J.; Rains, C.; Gierach, M. M.

2014-12-01

Wastewater discharged through ocean outfalls can surface near coastlines and beaches, posing a threat to the marine environment and human health. Coastal waters of the Southern California Bight (SCB) are an ecologically important marine habitat and a valuable resource in terms of commercial fishing and recreation. Two of the largest wastewater treatment plants along the U.S. West Coast discharge into the SCB, including the Hyperion Wastewater Treatment Plant (HWTP) and the Orange County Sanitation District (OCSD). In 2006, HWTP conducted an internal inspection of its primary 8 km outfall pipe (60 m depth), diverting treated effluent to a shorter 1.2 km pipe (18 m depth) from Nov. 28 to Nov. 30. From Sep. 11 - Oct. 4, 2012, OCSD conducted a similar diversion, diverting effluent from their 7 km outfall pipe to a shallower 2.2 km pipe, both with similar depths to HWTP. Prevailing oceanographic conditions in the SCB, such as temporally reduced stratification and surface circulation patterns, increased the risk of effluent being discharged from these shorter and shallower pipes surfacing and moving onshore. The aim of this study was to evaluate the capabilities of satellite remote sensing data (i.e., sea surface roughness from SAR, sea surface temperature from MODIS-Aqua and ASTER-Terra, chlorophyll-a and water leaving radiance from MODIS-Aqua) in the identification and tracking of wastewater plumes during the 2006 HWTP and 2012 OCSD diversion events. Satellite observations were combined with in situ, wind, and current data taken during the diversion events, to validate remote sensing techniques and gain surface to subsurface context of the nearshore diversion events. Overall, it was found that satellite remote sensing data were able to detect surfaced wastewater plumes along the coast, providing key spatial information that could inform in situ field sampling during future diversion events, such as the planned 2015 HWTP diversion, and thereby constrain costs.

Evolution and enabling capabilities of spatially resolved techniques for the characterization of heterogeneously catalyzed reactions

DOE PAGES

Morgan, Kevin; Touitou, Jamal; Choi, Jae -Soon; ...

2016-01-15

The development and optimization of catalysts and catalytic processes requires knowledge of reaction kinetics and mechanisms. In traditional catalyst kinetic characterization, the gas composition is known at the inlet, and the exit flow is measured to determine changes in concentration. As such, the progression of the chemistry within the catalyst is not known. Technological advances in electromagnetic and physical probes have made visualizing the evolution of the chemistry within catalyst samples a reality, as part of a methodology commonly known as spatial resolution. Herein, we discuss and evaluate the development of spatially resolved techniques, including the evolutions and achievements ofmore » this growing area of catalytic research. The impact of such techniques is discussed in terms of the invasiveness of physical probes on catalytic systems, as well as how experimentally obtained spatial profiles can be used in conjunction with kinetic modeling. Moreover, some aims and aspirations for further evolution of spatially resolved techniques are considered.« less

[The role of the floodplain gradient in structuring of testate amoebae communities in the Ilych River].

PubMed

Mazeĭ, Iu A; Malysheva, E A; Lapteva, E M; Komarov, A A; Taskaeva, A A

2012-01-01

Forty-two testate amoebae taxa were identified in alluvial soils of floodplain islands in the Ilych River. Among the pedo- and eurybionts, there were aquatic rhizopods. Along the floodplain transect (willow --> meadow --> deciduous forest --> coniferous forest), the testate amoebae community changed directly. There are spatially homogeneous (low beta-diversity) testacean communities but species rich on the local level (high alpha-diversity) within forests. Within willows and meadows, communities are characterized by low alpha-diversity and high heterogeneity that leads to high gamma-diversity.

Application of Unmanned Aircraft System Instrumentation to Study Coastal Geochemistry

NASA Astrophysics Data System (ADS)

Coffin, R. B.; Osburn, C. L.; Smith, J. P.

2016-02-01

Coastal evaluation of key geochemical cycles is in strong need for thorough spatial data to address diverse topics. In many field studies we find that fixed station data taken from ship operations does not provide complete understanding of key research questions. In complicated systems where there is a need to integrate physical, chemical and biological parameters data taken from research vessels needs to be interpreted across large spatial areas. New technology in Unmanned Aircraft System (UAS) instrumentation coupled with ship board data can provide the thorough spatial data needed for a thorough evaluation of coastal sciences. This presentation will provide field data related to UAS application in two diverse environments. One study focuses on the flux of carbon dioxide and methane from Alaskan Arctic tundra and shallow Beaufort Sea coastal region to the atmosphere. In this study gas chemistry from samples is used to predict the relative fluxes to the atmosphere. A second study applies bio-optical analyses to differentiate between Gulf of Mexico coastal water column DOC and Lignin. This wide range of parameters in diverse ecosystems is selected to show current capability for application of UAS and the potential for understanding large scale questions about climate change and carbon cycling in coastal waters.

The Emerging Spatial Organization of the Metropolis: Zones of Diversity and Minority Enclaves in Chicago

PubMed Central

Zhang, Wenquan; Logan, John R.

2018-01-01

The rapid growth of Asian and Hispanic populations in urban areas is superceding traditional classifications of neighborhoods (for example as white, transitional, or minority). The “global neighborhood” that includes all groups (white, black, Hispanic and Asian) is one important new category. We examine the emerging spatial pattern of racial/ethnic composition in the Chicago metropolis, documenting an expansion of all-minority neighborhoods in the city and just beyond its borders, a shrinking set of all-white neighborhoods in the outer suburbs, and more diverse neighborhoods including whites mainly in between. The most novel element of this pattern is how large the zone of diversity has become and how far it extends into suburbia, upending the old dichotomy of “chocolate city” and “vanilla suburbs.” In addition to comparing the distance of different kinds of neighborhoods from the urban core, we also analyze their adjacency to neighborhoods of the same type or other types. There is a strong tendency toward spatial clustering of each neighborhood type and also for transitions on the boundaries of clusters either to expand or to contract their territory. PMID:29430517

Melanopsin-expressing retinal ganglion-cell photoreceptors: cellular diversity and role in pattern vision

PubMed Central

Ecker, Jennifer L.; Dumitrescu, Olivia N.; Wong, Kwoon Y.; Alam, Nazia M.; Chen, Shih-Kuo; LeGates, Tara; Renna, Jordan M.; Prusky, Glen T.; Berson, David M.; Hattar, Samer

2010-01-01

Using the photopigment melanopsin, intrinsically photosensitive retinal ganglion cells (ipRGCs) respond directly to light to drive circadian clock resetting and pupillary constriction. We now report that ipRGCs are more abundant and diverse than previously appreciated, project more widely within the brain, and can support spatial visual perception. A Cre-based melanopsin reporter mouse line revealed at least five subtypes of ipRGCs with distinct morphological and physiological characteristics. Collectively, these cells project beyond the known brain targets of ipRGCs to heavily innervate the superior colliculus and dorsal lateral geniculate nucleus, retinotopically-organized nuclei mediating object localization and discrimination. Mice lacking classical rod-cone photoreception, and thus entirely dependent on melanopsin for light detection, were able to discriminate grating stimuli from equiluminant gray, and had measurable visual acuity. Thus, non-classical retinal photoreception occurs within diverse cell types, and influences circuits and functions encompassing luminance as well as spatial information. PMID:20624591

Exocrine drainage in vascularized pancreas transplantation in the new millennium

PubMed Central

El-Hennawy, Hany; Stratta, Robert J; Smith, Fowler

2016-01-01

The history of vascularized pancreas transplantation largely parallels developments in immunosuppression and technical refinements in transplant surgery. From the late-1980s to 1995, most pancreas transplants were whole organ pancreatic grafts with insulin delivery to the iliac vein and diversion of the pancreatic ductal secretions to the urinary bladder (systemic-bladder technique). The advent of bladder drainage revolutionized the safety and improved the success of pancreas transplantation. However, starting in 1995, a seismic change occurred from bladder to bowel exocrine drainage coincident with improvements in immunosuppression, preservation techniques, diagnostic monitoring, general medical care, and the success and frequency of enteric conversion. In the new millennium, pancreas transplants are performed predominantly as pancreatico-duodenal grafts with enteric diversion of the pancreatic ductal secretions coupled with iliac vein provision of insulin (systemic-enteric technique) although the systemic-bladder technique endures as a preferred alternative in selected cases. In the early 1990s, a novel technique of venous drainage into the superior mesenteric vein combined with bowel exocrine diversion (portal-enteric technique) was designed and subsequently refined over the next ≥ 20 years to re-create the natural physiology of the pancreas with first-pass hepatic processing of insulin. Enteric drainage usually refers to jejunal or ileal diversion of the exocrine secretions either with a primary enteric anastomosis or with an additional Roux limb. The portal-enteric technique has spawned a number of newer and revisited techniques of enteric exocrine drainage including duodenal or gastric diversion. Reports in the literature suggest no differences in pancreas transplant outcomes irrespective of type of either venous or exocrine diversion. The purpose of this review is to examine the literature on exocrine drainage in the new millennium (the purported “enteric drainage” era) with special attention to technical variations and nuances in vascularized pancreas transplantation that have been proposed and studied in this time period. PMID:27358771

Ergodic channel capacity of spatial correlated multiple-input multiple-output free space optical links using multipulse pulse-position modulation

NASA Astrophysics Data System (ADS)

Wang, Huiqin; Wang, Xue; Cao, Minghua

2017-02-01

The spatial correlation extensively exists in the multiple-input multiple-output (MIMO) free space optical (FSO) communication systems due to the channel fading and the antenna space limitation. Wilkinson's method was utilized to investigate the impact of spatial correlation on the MIMO FSO communication system employing multipulse pulse-position modulation. Simulation results show that the existence of spatial correlation reduces the ergodic channel capacity, and the reception diversity is more competent to resist this kind of performance degradation.

Safety becomes danger: dilemmas of drug-use in public space.

PubMed

Dovey, K; Fitzgerald, J; Choi, Y

2001-12-01

This paper provides a socio-spatial analysis of injecting drug-use in public space. It focuses on one urban district in Melbourne, Australia, which has become strongly identified with heroin sale and use in public space. Selling activities are camouflaged within a diverse street life while injecting sites are dispersed through a broad diversity of laneways, car parks and toilets. These injecting zones occupy liminal places which slide between categories of private and public, and which mediate complex and paradoxical relations between safety and danger. Those who inject in public space are caught in a dilemma--needing both privacy and exposure in the event of an overdose, safety from police becomes danger from an overdose. This empirical work, based on interview and spatial analysis, is presented as a basis for theorizing the socio-spatial construction of heroin use and for assessing the prospects for safe injecting.

Universal scaling of the distribution of land in urban areas

NASA Astrophysics Data System (ADS)

Riascos, A. P.

2017-09-01

In this work, we explore the spatial structure of built zones and green areas in diverse western cities by analyzing the probability distribution of areas and a coefficient that characterize their respective shapes. From the analysis of diverse datasets describing land lots in urban areas, we found that the distribution of built-up areas and natural zones in cities obey inverse power laws with a similar scaling for the cities explored. On the other hand, by studying the distribution of shapes of lots in urban regions, we are able to detect global differences in the spatial structure of the distribution of land. Our findings introduce information about spatial patterns that emerge in the structure of urban settlements; this knowledge is useful for the understanding of urban growth, to improve existing models of cities, in the context of sustainability, in studies about human mobility in urban areas, among other applications.

Contribution of geodiversity, climate and spatial variables for biodiversity across a gradient of human influence

NASA Astrophysics Data System (ADS)

Tukiainen, Helena; Alahuhta, Janne; Ala-Hulkko, Terhi; Field, Richard; Lampinen, Raino; Hjort, Jan

2016-04-01

Implementation of geodiversity may provide new perspectives for nature conservation. The relation between geodiversity and biodiversity has been established in recent studies but remains underexplored in environments with high human pressure. In this study, we explored the effect of geodiversity (i.e. geological, hydrological and geomorphological diversity), climate and spatial variables on biodiversity (vascular plant species richness) in environments with different human impact. The study area ranged trough the boreal vegetation zone in Finland and included altogether 1401 1-km2 grid cells from urban, rural and natural environments. The contribution of environmental variable groups for species diversity in different environments was statistically analyzed with variation partitioning method. According to the results, the contribution of geodiversity decreased and the contribution of climate and spatial variables increased as the land use became more human-induced. Hence, the connection between geodiversity and species richness was most pronounced in natural state environments.

Spatial patterns of phylogenetic diversity.

PubMed

Morlon, Hélène; Schwilk, Dylan W; Bryant, Jessica A; Marquet, Pablo A; Rebelo, Anthony G; Tauss, Catherine; Bohannan, Brendan J M; Green, Jessica L

2011-02-01

Ecologists and conservation biologists have historically used species-area and distance-decay relationships as tools to predict the spatial distribution of biodiversity and the impact of habitat loss on biodiversity. These tools treat each species as evolutionarily equivalent, yet the importance of species' evolutionary history in their ecology and conservation is becoming increasingly evident. Here, we provide theoretical predictions for phylogenetic analogues of the species-area and distance-decay relationships. We use a random model of community assembly and a spatially explicit flora dataset collected in four Mediterranean-type regions to provide theoretical predictions for the increase in phylogenetic diversity - the total phylogenetic branch-length separating a set of species - with increasing area and the decay in phylogenetic similarity with geographic separation. These developments may ultimately provide insights into the evolution and assembly of biological communities, and guide the selection of protected areas. © 2010 Blackwell Publishing Ltd/CNRS.

Capturing the genetic makeup of the active microbiome in situ

DOE PAGES

Singer, Esther; Wagner, Michael; Woyke, Tanja

2017-06-02

More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and thatmore » have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.« less

From classical to quantum and back: Hamiltonian adaptive resolution path integral, ring polymer, and centroid molecular dynamics

NASA Astrophysics Data System (ADS)

Kreis, Karsten; Kremer, Kurt; Potestio, Raffaello; Tuckerman, Mark E.

2017-12-01

Path integral-based methodologies play a crucial role for the investigation of nuclear quantum effects by means of computer simulations. However, these techniques are significantly more demanding than corresponding classical simulations. To reduce this numerical effort, we recently proposed a method, based on a rigorous Hamiltonian formulation, which restricts the quantum modeling to a small but relevant spatial region within a larger reservoir where particles are treated classically. In this work, we extend this idea and show how it can be implemented along with state-of-the-art path integral simulation techniques, including path-integral molecular dynamics, which allows for the calculation of quantum statistical properties, and ring-polymer and centroid molecular dynamics, which allow the calculation of approximate quantum dynamical properties. To this end, we derive a new integration algorithm that also makes use of multiple time-stepping. The scheme is validated via adaptive classical-path-integral simulations of liquid water. Potential applications of the proposed multiresolution method are diverse and include efficient quantum simulations of interfaces as well as complex biomolecular systems such as membranes and proteins.

Mass Spectrometry Imaging, an Emerging Technology in Neuropsychopharmacology

PubMed Central

Shariatgorji, Mohammadreza; Svenningsson, Per; Andrén, Per E

2014-01-01

Mass spectrometry imaging is a powerful tool for directly determining the distribution of proteins, peptides, lipids, neurotransmitters, metabolites and drugs in neural tissue sections in situ. Molecule-specific imaging can be achieved using various ionization techniques that are suited to different applications but which all yield data with high mass accuracies and spatial resolutions. The ability to simultaneously obtain images showing the distributions of chemical species ranging from metal ions to macromolecules makes it possible to explore the chemical organization of a sample and to correlate the results obtained with specific anatomical features. The imaging of biomolecules has provided new insights into multiple neurological diseases, including Parkinson's and Alzheimer's disease. Mass spectrometry imaging can also be used in conjunction with other imaging techniques in order to identify correlations between changes in the distribution of important chemical species and other changes in the properties of the tissue. Here we review the applications of mass spectrometry imaging in neuroscience research and discuss its potential. The results presented demonstrate that mass spectrometry imaging is a useful experimental method with diverse applications in neuroscience. PMID:23966069

Capturing the genetic makeup of the active microbiome in situ

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singer, Esther; Wagner, Michael; Woyke, Tanja

More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and thatmore » have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koniges, A.E.; Craddock, G.G.; Schnack, D.D.

The purpose of the workshop was to assemble workers, both within and outside of the fusion-related computations areas, for discussion regarding the issues of dynamically adaptive gridding. There were three invited talks related to adaptive gridding application experiences in various related fields of computational fluid dynamics (CFD), and nine short talks reporting on the progress of adaptive techniques in the specific areas of scrape-off-layer (SOL) modeling and magnetohydrodynamic (MHD) stability. Adaptive mesh methods have been successful in a number of diverse fields of CFD for over a decade. The method involves dynamic refinement of computed field profiles in a waymore » that disperses uniformly the numerical errors associated with discrete approximations. Because the process optimizes computational effort, adaptive mesh methods can be used to study otherwise the intractable physical problems that involve complex boundary shapes or multiple spatial/temporal scales. Recent results indicate that these adaptive techniques will be required for tokamak fluid-based simulations involving the diverted tokamak SOL modeling and MHD simulations problems related to the highest priority ITER relevant issues.Individual papers are indexed separately on the energy data bases.« less

A Review of Mid-Infrared and Near-Infrared Imaging: Principles, Concepts and Applications in Plant Tissue Analysis.

PubMed

Türker-Kaya, Sevgi; Huck, Christian W

2017-01-20

Plant cells, tissues and organs are composed of various biomolecules arranged as structurally diverse units, which represent heterogeneity at microscopic levels. Molecular knowledge about those constituents with their localization in such complexity is very crucial for both basic and applied plant sciences. In this context, infrared imaging techniques have advantages over conventional methods to investigate heterogeneous plant structures in providing quantitative and qualitative analyses with spatial distribution of the components. Thus, particularly, with the use of proper analytical approaches and sampling methods, these technologies offer significant information for the studies on plant classification, physiology, ecology, genetics, pathology and other related disciplines. This review aims to present a general perspective about near-infrared and mid-infrared imaging/microspectroscopy in plant research. It is addressed to compare potentialities of these methodologies with their advantages and limitations. With regard to the organization of the document, the first section will introduce the respective underlying principles followed by instrumentation, sampling techniques, sample preparations, measurement, and an overview of spectral pre-processing and multivariate analysis. The last section will review selected applications in the literature.

Mass spectrometry imaging, an emerging technology in neuropsychopharmacology.

PubMed

Shariatgorji, Mohammadreza; Svenningsson, Per; Andrén, Per E

2014-01-01

Mass spectrometry imaging is a powerful tool for directly determining the distribution of proteins, peptides, lipids, neurotransmitters, metabolites and drugs in neural tissue sections in situ. Molecule-specific imaging can be achieved using various ionization techniques that are suited to different applications but which all yield data with high mass accuracies and spatial resolutions. The ability to simultaneously obtain images showing the distributions of chemical species ranging from metal ions to macromolecules makes it possible to explore the chemical organization of a sample and to correlate the results obtained with specific anatomical features. The imaging of biomolecules has provided new insights into multiple neurological diseases, including Parkinson's and Alzheimer's disease. Mass spectrometry imaging can also be used in conjunction with other imaging techniques in order to identify correlations between changes in the distribution of important chemical species and other changes in the properties of the tissue. Here we review the applications of mass spectrometry imaging in neuroscience research and discuss its potential. The results presented demonstrate that mass spectrometry imaging is a useful experimental method with diverse applications in neuroscience.

Multiplex, quantitative cellular analysis in large tissue volumes with clearing-enhanced 3D microscopy (Ce3D)

PubMed Central

Li, Weizhe; Germain, Ronald N.

2017-01-01

Organ homeostasis, cellular differentiation, signal relay, and in situ function all depend on the spatial organization of cells in complex tissues. For this reason, comprehensive, high-resolution mapping of cell positioning, phenotypic identity, and functional state in the context of macroscale tissue structure is critical to a deeper understanding of diverse biological processes. Here we report an easy to use method, clearing-enhanced 3D (Ce3D), which generates excellent tissue transparency for most organs, preserves cellular morphology and protein fluorescence, and is robustly compatible with antibody-based immunolabeling. This enhanced signal quality and capacity for extensive probe multiplexing permits quantitative analysis of distinct, highly intermixed cell populations in intact Ce3D-treated tissues via 3D histo-cytometry. We use this technology to demonstrate large-volume, high-resolution microscopy of diverse cell types in lymphoid and nonlymphoid organs, as well as to perform quantitative analysis of the composition and tissue distribution of multiple cell populations in lymphoid tissues. Combined with histo-cytometry, Ce3D provides a comprehensive strategy for volumetric quantitative imaging and analysis that bridges the gap between conventional section imaging and disassociation-based techniques. PMID:28808033

Performance analysis of optimal power allocation in wireless cooperative communication systems

NASA Astrophysics Data System (ADS)

Babikir Adam, Edriss E.; Samb, Doudou; Yu, Li

2013-03-01

Cooperative communication has been recently proposed in wireless communication systems for exploring the inherent spatial diversity in relay channels.The Amplify-and-Forward (AF) cooperation protocols with multiple relays have not been sufficiently investigated even if it has a low complexity in term of implementation. We consider in this work a cooperative diversity system in which a source transmits some information to a destination with the help of multiple relay nodes with AF protocols and investigate the optimality of allocating powers both at the source and the relays system by optimizing the symbol error rate (SER) performance in an efficient way. Firstly we derive a closedform SER formulation for MPSK signal using the concept of moment generating function and some statistical approximations in high signal to noise ratio (SNR) for the system under studied. We then find a tight corresponding lower bound which converges to the same limit as the theoretical upper bound and develop an optimal power allocation (OPA) technique with mean channel gains to minimize the SER. Simulation results show that our scheme outperforms the equal power allocation (EPA) scheme and is tight to the theoretical approximation based on the SER upper bound in high SNR for different number of relays.

Lentinula edodes-derived polysaccharide alters the spatial structure of gut microbiota in mice.

PubMed

Xu, Xiaofei; Zhang, Xuewu

2015-01-01

Lentinula edodes-derived polysaccharides possess many therapeutic characteristics, including anti-tumor and immuno-modulation. The gut microbes play a critical role in modulation of immune function. However, the impact of Lentinula edodes-derived polysaccharides on the gut microbes have not yet been explored. In this study, high-throughput pyrosequencing technique was employed to investigate the effects of a new heteropolysaccharide L2 from Lentinula edodes on microbiota diversity and composition of small intestine, cecum, colon and distal end of colon (feces) in mice. The results demonstrated that along mouse intestine the microbiota exhibit distinctly different space distribution. L2 treatment reduced the diversity and evenness of gut microbiota along the intestine, especially in the cecum and colon. In the fecal microbial communities, the decrease of Bacteroidetes by significantly increasing Proteobacteria were observed, which were characterized by the increased Helicobacteraceae and reduced S24-7 at family level. Some OTUs, corresponding to Bacteroides acidifaciens, Alistipes and Helicobacter suncus, were found to be significantly increased in L2 treated-mice. In particular, 4 phyla Chloroflexi, Gemmatimonadetes, Nitrospirae and Planctomycetes are exclusively present in L2-treated mice. This is helpful for further demonstrating healthy action mechanism of Lentinula edodes-derived polysaccharide L2.

ENVIRONMENTAL FACTORS INFLUENCING THE SPATIAL DISTRIBUTION OF DINOFLAGELLATE CYST ASSEMBLAGES IN SHALLOW LAGOONS IN SOUTHERN NEW ENGLAND (USA)

EPA Science Inventory

Surface sediment samples from 24 sites within eleven back-barrier lagoons of Rhode Island and Massachusetts (USA) contain abundant (200-6000 cysts cm-3) and diverse (up to 40 taxa) dinoflagellate cyst assemblages. The lowest cyst concentrations and diversity are observed in lagoo...

The assembly of ecological communities inferred from taxonomic and functional composition

Treesearch

Eric R. Sokol; E.F. Benfield; Lisa K. Belden; H. Maurice. Valett

2011-01-01

Among-site variation in metacommunities (beta diversity) is typically correlated with the distance separating the sites (spatial lag). This distance decay in similarity pattern has been linked to both niche-based and dispersal-based community assembly hypotheses. Here we show that beta diversity patterns in community composition, when supplemented with functional-trait...

Monitoring biological diversity: strategies, tools, limitations, and challenges.

Treesearch

Erik A. Beever

2006-01-01

Monitoring is an assessment of the spatial and temporal variability in one or more ecosystem properties, and is an essential component of adaptive management. Monitoring can help determine whether mandated environmental standards are being met and can provide an early-warning system of ecological change. Development of a strategy for monitoring biological diversity...

Hyperspectral remote sensing of canopy biodiversity in Hawaiian lowland rainforests

Treesearch

Kimberly M. Carlson; Gregory P. Asner; R. Flint Hughes; Rebecca Ostertag; Roberta E. Martin

2007-01-01

Mapping biological diversity is a high priority for conservation research, management and policy development, but few studies have provided diversity data at high spatial resolution from remote sensing. We used airborne imaging spectroscopy to map woody vascular plant species richness in lowland tropical forest ecosystems in Hawaii. Hyperspectral signatures spanning...

Diverse applications of advanced man-telerobot interfaces

NASA Technical Reports Server (NTRS)

Mcaffee, Douglas A.

1991-01-01

Advancements in man-machine interfaces and control technologies used in space telerobotics and teleoperators have potential application wherever human operators need to manipulate multi-dimensional spatial relationships. Bilateral six degree-of-freedom position and force cues exchanged between the user and a complex system can broaden and improve the effectiveness of several diverse man-machine interfaces.

Biotic homogenization can decrease landscape-scale forest multifunctionality.

PubMed

van der Plas, Fons; Manning, Pete; Soliveres, Santiago; Allan, Eric; Scherer-Lorenzen, Michael; Verheyen, Kris; Wirth, Christian; Zavala, Miguel A; Ampoorter, Evy; Baeten, Lander; Barbaro, Luc; Bauhus, Jürgen; Benavides, Raquel; Benneter, Adam; Bonal, Damien; Bouriaud, Olivier; Bruelheide, Helge; Bussotti, Filippo; Carnol, Monique; Castagneyrol, Bastien; Charbonnier, Yohan; Coomes, David Anthony; Coppi, Andrea; Bastias, Cristina C; Dawud, Seid Muhie; De Wandeler, Hans; Domisch, Timo; Finér, Leena; Gessler, Arthur; Granier, André; Grossiord, Charlotte; Guyot, Virginie; Hättenschwiler, Stephan; Jactel, Hervé; Jaroszewicz, Bogdan; Joly, François-Xavier; Jucker, Tommaso; Koricheva, Julia; Milligan, Harriet; Mueller, Sandra; Muys, Bart; Nguyen, Diem; Pollastrini, Martina; Ratcliffe, Sophia; Raulund-Rasmussen, Karsten; Selvi, Federico; Stenlid, Jan; Valladares, Fernando; Vesterdal, Lars; Zielínski, Dawid; Fischer, Markus

2016-03-29

Many experiments have shown that local biodiversity loss impairs the ability of ecosystems to maintain multiple ecosystem functions at high levels (multifunctionality). In contrast, the role of biodiversity in driving ecosystem multifunctionality at landscape scales remains unresolved. We used a comprehensive pan-European dataset, including 16 ecosystem functions measured in 209 forest plots across six European countries, and performed simulations to investigate how local plot-scale richness of tree species (α-diversity) and their turnover between plots (β-diversity) are related to landscape-scale multifunctionality. After accounting for variation in environmental conditions, we found that relationships between α-diversity and landscape-scale multifunctionality varied from positive to negative depending on the multifunctionality metric used. In contrast, when significant, relationships between β-diversity and landscape-scale multifunctionality were always positive, because a high spatial turnover in species composition was closely related to a high spatial turnover in functions that were supported at high levels. Our findings have major implications for forest management and indicate that biotic homogenization can have previously unrecognized and negative consequences for large-scale ecosystem multifunctionality.

Biotic homogenization can decrease landscape-scale forest multifunctionality

PubMed Central

van der Plas, Fons; Manning, Pete; Soliveres, Santiago; Allan, Eric; Scherer-Lorenzen, Michael; Verheyen, Kris; Wirth, Christian; Zavala, Miguel A.; Ampoorter, Evy; Baeten, Lander; Barbaro, Luc; Bauhus, Jürgen; Benavides, Raquel; Benneter, Adam; Bonal, Damien; Bouriaud, Olivier; Bruelheide, Helge; Bussotti, Filippo; Carnol, Monique; Castagneyrol, Bastien; Charbonnier, Yohan; Coppi, Andrea; Bastias, Cristina C.; Dawud, Seid Muhie; De Wandeler, Hans; Domisch, Timo; Finér, Leena; Granier, André; Grossiord, Charlotte; Guyot, Virginie; Hättenschwiler, Stephan; Jactel, Hervé; Jaroszewicz, Bogdan; Joly, François-xavier; Jucker, Tommaso; Koricheva, Julia; Milligan, Harriet; Mueller, Sandra; Muys, Bart; Nguyen, Diem; Pollastrini, Martina; Ratcliffe, Sophia; Raulund-Rasmussen, Karsten; Selvi, Federico; Stenlid, Jan; Valladares, Fernando; Vesterdal, Lars; Zielínski, Dawid; Fischer, Markus

2016-01-01

Many experiments have shown that local biodiversity loss impairs the ability of ecosystems to maintain multiple ecosystem functions at high levels (multifunctionality). In contrast, the role of biodiversity in driving ecosystem multifunctionality at landscape scales remains unresolved. We used a comprehensive pan-European dataset, including 16 ecosystem functions measured in 209 forest plots across six European countries, and performed simulations to investigate how local plot-scale richness of tree species (α-diversity) and their turnover between plots (β-diversity) are related to landscape-scale multifunctionality. After accounting for variation in environmental conditions, we found that relationships between α-diversity and landscape-scale multifunctionality varied from positive to negative depending on the multifunctionality metric used. In contrast, when significant, relationships between β-diversity and landscape-scale multifunctionality were always positive, because a high spatial turnover in species composition was closely related to a high spatial turnover in functions that were supported at high levels. Our findings have major implications for forest management and indicate that biotic homogenization can have previously unrecognized and negative consequences for large-scale ecosystem multifunctionality. PMID:26979952

Demonstration of polarization-insensitive spatial light modulation using a single polarization-sensitive spatial light modulator

PubMed Central

Liu, Jun; Wang, Jian

2015-01-01

We present a simple configuration incorporating a single polarization-sensitive phase-only liquid crystal spatial light modulator (LC-SLM) to facilitate polarization-insensitive spatial light modulation. The polarization-insensitive configuration is formed by a polarization beam splitter (PBS), a polarization-sensitive phase-only LC-SLM, a half-wave plate (HWP), and a mirror in a loop structure. We experimentally demonstrate polarization-insensitive spatial light modulations for incident linearly polarized beams with different polarization states and polarization-multiplexed beams. Polarization-insensitive spatial light modulations generating orbital angular momentum (OAM) beams are demonstrated in the experiment. The designed polarization-insensitive configuration may find promising applications in spatial light modulations accommodating diverse incident polarizations. PMID:26146032

Regional Management Units for Marine Turtles: A Novel Framework for Prioritizing Conservation and Research across Multiple Scales

PubMed Central

Wallace, Bryan P.; DiMatteo, Andrew D.; Hurley, Brendan J.; Finkbeiner, Elena M.; Bolten, Alan B.; Chaloupka, Milani Y.; Hutchinson, Brian J.; Abreu-Grobois, F. Alberto; Amorocho, Diego; Bjorndal, Karen A.; Bourjea, Jerome; Bowen, Brian W.; Dueñas, Raquel Briseño; Casale, Paolo; Choudhury, B. C.; Costa, Alice; Dutton, Peter H.; Fallabrino, Alejandro; Girard, Alexandre; Girondot, Marc; Godfrey, Matthew H.; Hamann, Mark; López-Mendilaharsu, Milagros; Marcovaldi, Maria Angela; Mortimer, Jeanne A.; Musick, John A.; Nel, Ronel; Pilcher, Nicolas J.; Seminoff, Jeffrey A.; Troëng, Sebastian; Witherington, Blair; Mast, Roderic B.

2010-01-01

Background Resolving threats to widely distributed marine megafauna requires definition of the geographic distributions of both the threats as well as the population unit(s) of interest. In turn, because individual threats can operate on varying spatial scales, their impacts can affect different segments of a population of the same species. Therefore, integration of multiple tools and techniques — including site-based monitoring, genetic analyses, mark-recapture studies and telemetry — can facilitate robust definitions of population segments at multiple biological and spatial scales to address different management and research challenges. Methodology/Principal Findings To address these issues for marine turtles, we collated all available studies on marine turtle biogeography, including nesting sites, population abundances and trends, population genetics, and satellite telemetry. We georeferenced this information to generate separate layers for nesting sites, genetic stocks, and core distributions of population segments of all marine turtle species. We then spatially integrated this information from fine- to coarse-spatial scales to develop nested envelope models, or Regional Management Units (RMUs), for marine turtles globally. Conclusions/Significance The RMU framework is a solution to the challenge of how to organize marine turtles into units of protection above the level of nesting populations, but below the level of species, within regional entities that might be on independent evolutionary trajectories. Among many potential applications, RMUs provide a framework for identifying data gaps, assessing high diversity areas for multiple species and genetic stocks, and evaluating conservation status of marine turtles. Furthermore, RMUs allow for identification of geographic barriers to gene flow, and can provide valuable guidance to marine spatial planning initiatives that integrate spatial distributions of protected species and human activities. In addition, the RMU framework — including maps and supporting metadata — will be an iterative, user-driven tool made publicly available in an online application for comments, improvements, download and analysis. PMID:21253007

MOSAIC - A space-multiplexing technique for optical processing of large images

NASA Technical Reports Server (NTRS)

Athale, Ravindra A.; Astor, Michael E.; Yu, Jeffrey

1993-01-01

A technique for Fourier processing of images larger than the space-bandwidth products of conventional or smart spatial light modulators and two-dimensional detector arrays is described. The technique involves a spatial combination of subimages displayed on individual spatial light modulators to form a phase-coherent image, which is subsequently processed with Fourier optical techniques. Because of the technique's similarity with the mosaic technique used in art, the processor used is termed an optical MOSAIC processor. The phase accuracy requirements of this system were studied by computer simulation. It was found that phase errors of less than lambda/8 did not degrade the performance of the system and that the system was relatively insensitive to amplitude nonuniformities. Several schemes for implementing the subimage combination are described. Initial experimental results demonstrating the validity of the mosaic concept are also presented.

Population genetics of sporophytic self-incompatibility in Senecio squalidus L. (Asteraceae) II: a spatial autocorrelation approach to determining mating behaviour in the presence of low S allele diversity.

PubMed

Brennan, A C; Harris, S A; Hiscock, S J

2003-11-01

We recently estimated that as few as six S alleles represent the extent of S locus diversity in a British population of the self-incompatible (SI) coloniser Senecio squalidus (Oxford Ragwort). Despite the predicted constraints to mating imposed by such a low number of S alleles, S. squalidus maintains a strong sporophytic self-incompatibility (SSI) system and there is no evidence for a breakdown of SSI or any obvious negative reproductive consequences for this highly successful coloniser. The present paper assesses mating behaviour in an Oxford S. squalidus population through observations of its effect on spatial patterns of genetic diversity and thus the extent to which it is responsible for ameliorating the potentially detrimental reproductive consequences of low S allele diversity in British S. squalidus. A spatial autocorrelation (SA) treatment of S locus and allozyme polymorphism data for four loci indicates that mating events regularly occur at all the distance classes examined from 60 to 480 m throughout the entire sample population. Less SA is observed for S locus data than for allozyme data in accordance with the hypothesis that SSI and low diversity at the S locus are driving these large-scale mating events. The limited population structure at small distances of 60 m and less observed for SA analysis of the Me-2 locus and by F-statistics for all the allozyme data, is evidence of some local relatedness due to limited seed and pollen dispersal in S. squalidus. However, the overall impression of mating dynamics in this S. squalidus population is that of ample potential mating opportunities with many individuals at large population scales, indicating that reproductive success is not seriously affected by few S alleles available for mating interactions.

Global direct pressures on biodiversity by large-scale metal mining: Spatial distribution and implications for conservation.

PubMed

Murguía, Diego I; Bringezu, Stefan; Schaldach, Rüdiger

2016-09-15

Biodiversity loss is widely recognized as a serious global environmental change process. While large-scale metal mining activities do not belong to the top drivers of such change, these operations exert or may intensify pressures on biodiversity by adversely changing habitats, directly and indirectly, at local and regional scales. So far, analyses of global spatial dynamics of mining and its burden on biodiversity focused on the overlap between mines and protected areas or areas of high value for conservation. However, it is less clear how operating metal mines are globally exerting pressure on zones of different biodiversity richness; a similar gap exists for unmined but known mineral deposits. By using vascular plants' diversity as a proxy to quantify overall biodiversity, this study provides a first examination of the global spatial distribution of mines and deposits for five key metals across different biodiversity zones. The results indicate that mines and deposits are not randomly distributed, but concentrated within intermediate and high diversity zones, especially bauxite and silver. In contrast, iron, gold, and copper mines and deposits are closer to a more proportional distribution while showing a high concentration in the intermediate biodiversity zone. Considering the five metals together, 63% and 61% of available mines and deposits, respectively, are located in intermediate diversity zones, comprising 52% of the global land terrestrial surface. 23% of mines and 20% of ore deposits are located in areas of high plant diversity, covering 17% of the land. 13% of mines and 19% of deposits are in areas of low plant diversity, comprising 31% of the land surface. Thus, there seems to be potential for opening new mines in areas of low biodiversity in the future. Copyright © 2016 Elsevier Ltd. All rights reserved.

Shaping the Latitudinal Diversity Gradient: New Perspectives from a Synthesis of Paleobiology and Biogeography.

PubMed

Jablonski, David; Huang, Shan; Roy, Kaustuv; Valentine, James W

2017-01-01

An impediment to understanding the origin and dynamics of the latitudinal diversity gradient (LDG)-the most pervasive large-scale biotic pattern on Earth-has been the tendency to focus narrowly on a single causal factor when a more synthetic, integrative approach is needed. Using marine bivalves as a model system and drawing on other systems where possible, we review paleobiologic and biogeographic support for two supposedly opposing views, that the LDG is shaped primarily by (a) local environmental factors that determine the number of species and higher taxa at a given latitude (in situ hypotheses) or (b) the entry of lineages arising elsewhere into a focal region (spatial dynamics hypotheses). Support for in situ hypotheses includes the fit of present-day diversity trends in many clades to such environmental factors as temperature and the correlation of extinction intensities in Pliocene bivalve faunas with net regional temperature changes. Support for spatial dynamics hypotheses includes the age-frequency distribution of bivalve genera across latitudes, which is consistent with an out-of-the-tropics dynamic, as are the higher species diversities in temperate southeastern Australia and southeastern Japan than in the tropical Caribbean. Thus, both in situ and spatial dynamics processes must shape the bivalve LDG and are likely to operate in other groups as well. The relative strengths of the two processes may differ among groups showing similar LDGs, but dissecting their effects will require improved methods of integrating fossil data with molecular phylogenies. We highlight several potential research directions and argue that many of the most dramatic biotic patterns, past and present, are likely to have been generated by diverse, mutually reinforcing drivers.

Spatial genetic structure in Beta vulgaris subsp. maritima and Beta macrocarpa reveals the effect of contrasting mating system, influence of marine currents, and footprints of postglacial recolonization routes.

PubMed

Leys, Marie; Petit, Eric J; El-Bahloul, Yasmina; Liso, Camille; Fournet, Sylvain; Arnaud, Jean-François

2014-05-01

Understanding the factors that contribute to population genetic divergence across a species' range is a long-standing goal in evolutionary biology and ecological genetics. We examined the relative importance of historical and ecological features in shaping the present-day spatial patterns of genetic structure in two related plant species, Beta vulgaris subsp. maritima and Beta macrocarpa. Using nuclear and mitochondrial markers, we surveyed 93 populations from Brittany (France) to Morocco - the southern limit of their species' range distribution. Whereas B. macrocarpa showed a genotypic structure and a high level of genetic differentiation indicative of selfing, the population genetic structure of B. vulgaris subsp. maritima was consistent with an outcrossing mating system. We further showed (1) a strong geographic clustering in coastal B. vulgaris subsp. maritima populations that highlighted the influence of marine currents in shaping different lineages and (2) a peculiar genetic structure of inland B. vulgaris subsp. maritima populations that could indicate the admixture of distinct evolutionary lineages and recent expansions associated with anthropogenic disturbances. Spatial patterns of nuclear diversity and differentiation also supported a stepwise recolonization of Europe from Atlantic-Mediterranean refugia after the last glacial period, with leading-edge expansions. However, cytoplasmic diversity was not impacted by postglacial recolonization: stochastic long-distance seed dispersal mediated by major oceanic currents may mitigate the common patterns of reduced cytoplasmic diversity observed for edge populations. Overall, the patterns we documented here challenge the general view of reduced genetic diversity at the edge of a species' range distribution and provide clues for understanding how life-history and major geographic features interact to shape the distribution of genetic diversity.

Spatial genetic structure in Beta vulgaris subsp. maritima and Beta macrocarpa reveals the effect of contrasting mating system, influence of marine currents, and footprints of postglacial recolonization routes

PubMed Central

Leys, Marie; Petit, Eric J; El-Bahloul, Yasmina; Liso, Camille; Fournet, Sylvain; Arnaud, Jean-François

2014-01-01

Understanding the factors that contribute to population genetic divergence across a species' range is a long-standing goal in evolutionary biology and ecological genetics. We examined the relative importance of historical and ecological features in shaping the present-day spatial patterns of genetic structure in two related plant species, Beta vulgaris subsp. maritima and Beta macrocarpa. Using nuclear and mitochondrial markers, we surveyed 93 populations from Brittany (France) to Morocco – the southern limit of their species' range distribution. Whereas B. macrocarpa showed a genotypic structure and a high level of genetic differentiation indicative of selfing, the population genetic structure of B. vulgaris subsp. maritima was consistent with an outcrossing mating system. We further showed (1) a strong geographic clustering in coastal B. vulgaris subsp. maritima populations that highlighted the influence of marine currents in shaping different lineages and (2) a peculiar genetic structure of inland B. vulgaris subsp. maritima populations that could indicate the admixture of distinct evolutionary lineages and recent expansions associated with anthropogenic disturbances. Spatial patterns of nuclear diversity and differentiation also supported a stepwise recolonization of Europe from Atlantic-Mediterranean refugia after the last glacial period, with leading-edge expansions. However, cytoplasmic diversity was not impacted by postglacial recolonization: stochastic long-distance seed dispersal mediated by major oceanic currents may mitigate the common patterns of reduced cytoplasmic diversity observed for edge populations. Overall, the patterns we documented here challenge the general view of reduced genetic diversity at the edge of a species' range distribution and provide clues for understanding how life-history and major geographic features interact to shape the distribution of genetic diversity. PMID:24963380

High-Throughput Ligand Discovery Reveals a Sitewise Gradient of Diversity in Broadly Evolved Hydrophilic Fibronectin Domains

PubMed Central

Woldring, Daniel R.; Holec, Patrick V.; Zhou, Hong; Hackel, Benjamin J.

2015-01-01

Discovering new binding function via a combinatorial library in small protein scaffolds requires balance between appropriate mutations to introduce favorable intermolecular interactions while maintaining intramolecular integrity. Sitewise constraints exist in a non-spatial gradient from diverse to conserved in evolved antibody repertoires; yet non-antibody scaffolds generally do not implement this strategy in combinatorial libraries. Despite the fact that biased amino acid distributions, typically elevated in tyrosine, serine, and glycine, have gained wider use in synthetic scaffolds, these distributions are still predominantly applied uniformly to diversified sites. While select sites in fibronectin domains and DARPins have shown benefit from sitewise designs, they have not been deeply evaluated. Inspired by this disparity between diversity distributions in natural libraries and synthetic scaffold libraries, we hypothesized that binders resulting from discovery and evolution would exhibit a non-spatial, sitewise gradient of amino acid diversity. To identify sitewise diversities consistent with efficient evolution in the context of a hydrophilic fibronectin domain, >105 binders to six targets were evolved and sequenced. Evolutionarily favorable amino acid distributions at 25 sites reveal Shannon entropies (range: 0.3–3.9; median: 2.1; standard deviation: 1.1) supporting the diversity gradient hypothesis. Sitewise constraints in evolved sequences are consistent with complementarity, stability, and consensus biases. Implementation of sitewise constrained diversity enables direct selection of nanomolar affinity binders validating an efficient strategy to balance inter- and intra-molecular interaction demands at each site. PMID:26383268

The road to higher permanence and biodiversity in exurban wetlands.

PubMed

Urban, Mark C; Roehm, Robert

2018-01-01

Exurban areas are expanding throughout the world, yet their effects on local biodiversity remain poorly understood. Wetlands, in particular, face ongoing and substantial threats from exurban development. We predicted that exurbanization would reduce the diversity of wetland amphibian and invertebrate communities and that more spatially aggregated residential development would leave more undisturbed natural land, thereby promoting greater local diversity. Using structural equation models, we tested a series of predictions about the direct and indirect pathways by which exurbanization extent, spatial pattern, and wetland characteristics might affect diversity patterns in 38 wetlands recorded during a growing season. We used redundancy, indicator species, and nested community analyses to evaluate how exurbanization affected species composition. In contrast to expectations, we found higher diversity in exurban wetlands. We also found that housing aggregation did not significantly affect diversity. Exurbanization affected biodiversity indirectly by increasing roads and development, which promoted permanent wetlands with less canopy cover and more aquatic vegetation. These pond characteristics supported greater diversity. However, exurbanization was associated with fewer temporary wetlands and fewer of the species that depend on these habitats. Moreover, the best indicator species for an exurban wetland was the ram's head snail, a common disease vector in disturbed ponds. Overall, results suggest that exurbanization is homogenizing wetlands into more permanent water bodies. These more permanent, exurban ponds support higher overall animal diversity, but exclude temporary wetland specialists. Conserving the full assemblage of wetland species in expanding exurban regions throughout the world will require protecting and creating temporary wetlands.

Grassland management regimens reduce small-scale heterogeneity and species diversity of beta-proteobacterial ammonia pxidizer populations.

PubMed

Webster, Gordon; Embley, T Martin; Prosser, James I

2002-01-01

The impact of soil management practices on ammonia oxidizer diversity and spatial heterogeneity was determined in improved (addition of N fertilizer), unimproved (no additions), and semi-improved (intermediate management) grassland pastures at the Sourhope Research Station in Scotland. Ammonia oxidizer diversity within each grassland soil was assessed by PCR amplification of microbial community DNA with both ammonia oxidizer-specific, 16S rRNA gene (rDNA) and functional, amoA, gene primers. PCR products were analysed by denaturing gradient gel electrophoresis, phylogenetic analysis of partial 16S rDNA and amoA sequences, and hybridization with ammonia oxidizer-specific oligonucleotide probes. Ammonia oxidizer populations in unimproved soils were more diverse than those in improved soils and were dominated by organisms representing Nitrosospira clusters 1 and 3 and Nitrosomonas cluster 7 (closely related phylogenetically to Nitrosomonas europaea). Improved soils were only dominated by Nitrosospira cluster 3 and Nitrosomonas cluster 7. These differences were also reflected in functional gene (amoA) diversity, with amoA gene sequences of both Nitrosomonas and Nitrosospira species detected. Replicate 0.5-g samples of unimproved soil demonstrated significant spatial heterogeneity in 16S rDNA-defined ammonia oxidizer clusters, which was reflected in heterogeneity in ammonium concentration and pH. Heterogeneity in soil characteristics and ammonia oxidizer diversity were lower in improved soils. The results therefore demonstrate significant effects of soil management on diversity and heterogeneity of ammonia oxidizer populations that are related to similar changes in relevant soil characteristics.

A technique to calibrate spatial light modulator for varying phase response over its spatial regions

NASA Astrophysics Data System (ADS)

Gupta, Deepak K.; Tata, B. V. R.; Ravindran, T. R.

2018-05-01

Holographic Optical Tweezers (HOTs) employ the technique of beam shaping and holography in an optical manipulation system to create a multitude of focal spots for simultaneous trapping and manipulation of sub-microscopic particles. The beam shaping is accomplished by the use of a phase only liquid crystal spatial light modulator (SLM). The efficiency and the uniformity in the generated traps greatly depend on the phase response behavior of SLMs. In addition the SLMs are found to show different phase response over its different spatial regions, due to non-flat structure of SLMs. Also the phase responses are found to vary over different spatial regions due to non-uniform illumination (Gaussian profile of incident laser). There are various techniques to calibrate for the varying phase response by characterizing the phase modulation at various sub-sections. We present a simple and fast technique to calibrate the SLM suffering with spatially varying phase response. We divide the SLM into many sub-sections and optimize the brightness and gamma of each sub-section for maximum diffraction efficiency. This correction is incorporated in the Weighted Gerchberg Saxton (WGS) algorithm for generation of holograms.

Genetic and epigenetic diversity and structure of Phragmites australis from local habitats of the Songnen Prairie using amplified fragment length polymorphism markers.

PubMed

Qiu, T; Jiang, L L; Yang, Y F

2016-08-19

The genetic and epigenetic diversity and structure of naturally occurring Phragmites australis populations occupying two different habitats on a small spatial scale in the Songnen Prairie in northeastern China were investigated by assessing amplified fragment length polymorphisms (AFLPs) and methylation-sensitive amplified polymorphisms (MSAPs) through fluorescent capillary detection. The two groups of P. australis were located in a seasonal waterlogged low-lying and alkalized meadow with a pH of 8-8.5 and in an alkaline patch without accumulated rainwater and with a pH greater than 10. These groups showed high levels of genetic diversity at the habitat level based on the percentage of polymorphic bands (90.32, 82.56%), Nei's gene diversity index (0.262, 0.248), and the Shannon diversity index (0.407, 0.383). Although little is known about the between-habitat genetic differentiation of P. australis on a small spatial scale, our results implied significant genetic differentiation between habitats. Extensive epigenetic diversity within habitats, along with clear differentiation, was found. Specifically, the former habitat (Habitat 1, designated H1) harbored higher levels of genetic and epigenetic diversity than the latter (Habitat 2, designated H2), and population-level diversity was also high. This study represents one of few attempts to predict habitat-based genetic differentiation of reeds on a small scale. These assessments of genetic and epigenetic variation are integral aspects of molecular ecological studies on P. australis. Possible causes for within- and between-habitat genetic and epigenetic variations are discussed.

Spectral-spatial hyperspectral image classification using super-pixel-based spatial pyramid representation

NASA Astrophysics Data System (ADS)

Fan, Jiayuan; Tan, Hui Li; Toomik, Maria; Lu, Shijian

2016-10-01

Spatial pyramid matching has demonstrated its power for image recognition task by pooling features from spatially increasingly fine sub-regions. Motivated by the concept of feature pooling at multiple pyramid levels, we propose a novel spectral-spatial hyperspectral image classification approach using superpixel-based spatial pyramid representation. This technique first generates multiple superpixel maps by decreasing the superpixel number gradually along with the increased spatial regions for labelled samples. By using every superpixel map, sparse representation of pixels within every spatial region is then computed through local max pooling. Finally, features learned from training samples are aggregated and trained by a support vector machine (SVM) classifier. The proposed spectral-spatial hyperspectral image classification technique has been evaluated on two public hyperspectral datasets, including the Indian Pines image containing 16 different agricultural scene categories with a 20m resolution acquired by AVIRIS and the University of Pavia image containing 9 land-use categories with a 1.3m spatial resolution acquired by the ROSIS-03 sensor. Experimental results show significantly improved performance compared with the state-of-the-art works. The major contributions of this proposed technique include (1) a new spectral-spatial classification approach to generate feature representation for hyperspectral image, (2) a complementary yet effective feature pooling approach, i.e. the superpixel-based spatial pyramid representation that is used for the spatial correlation study, (3) evaluation on two public hyperspectral image datasets with superior image classification performance.

Multifractal analyis of soil invertebrates along a transect under different land uses

NASA Astrophysics Data System (ADS)

Machado Siqueira, Glécio; Alves Silva, Raimunda; Vidal-Vázquez, Eva; Paz-González, Antonio

2017-04-01

Soil fauna play a central role in many essential ecosystem processes. Land use and management can have a dramatic effect upon soil invertebrate community. Indices based on soil invertebrates abundance and diversity are fundamental for soil quality assessment. Many soil properties and attributes have been shown to exhibit spatial variabilityThe aim of this study was to analyze the scaling heterogeneity of the soil invertebrate community sampled using pitfall traps across a transect. The field study was conducted at Mata Roma municipality, Maranhão State, Brazil. Transects were marked under seven different agricultural/forestry land uses (millet, soybean, maize, eucalyptus, pasture, secondary savannah and native savannah). Native vegetation was considered as a reference, whereas the agricultural fields showed a range of soil use intensities. Along these transects 130 pitfall per land use were installed. First, differences in community assemblages and composition under different land use systems were evaluated using classical indices. Then, the spatial distribution of soil fauna trapped by pitfall techniques, characterized through generalized dimension, Dq, and singularity spectra, f(α) - α, showed a well-defined multifractal structure. Differences in scaling heterogeneity and other multifractal characteristics were examined in relation to land use intensification.

Quantifying the metabolic activities of human-associated microbial communities across multiple ecological scales

PubMed Central

Maurice, Corinne Ferrier; Turnbaugh, Peter James

2013-01-01

Humans are home to complex microbial communities, whose aggregate genomes and their encoded metabolic activities are referred to as the human microbiome. Recently, researchers have begun to appreciate that different human body habitats and the activities of their resident microorganisms can be better understood in ecological terms, as a range of spatial scales encompassing single cells, guilds of microorganisms responsive to a similar substrate, microbial communities, body habitats, and host populations. However, the bulk of the work to date has focused on studies of culturable microorganisms in isolation or on DNA sequencing-based surveys of microbial diversity in small to moderately sized cohorts of individuals. Here, we discuss recent work that highlights the potential for assessing the human microbiome at a range of spatial scales, and for developing novel techniques that bridge multiple levels: for example, through the combination of single cell methods and metagenomic sequencing. These studies promise to not only provide a much-needed epidemiological and ecological context for mechanistic studies of culturable and genetically tractable microorganisms, but may also lead to the discovery of fundamental rules that govern the assembly and function of host-associated microbial communities. PMID:23550823

Population genetics of Ceratitis capitata in South Africa: implications for dispersal and pest management.

PubMed

Karsten, Minette; van Vuuren, Bettine Jansen; Barnaud, Adeline; Terblanche, John S

2013-01-01

The invasive Mediterranean fruit fly (medfly), Ceratitis capitata, is one of the major agricultural and economical pests globally. Understanding invasion risk and mitigation of medfly in agricultural landscapes requires knowledge of its population structure and dispersal patterns. Here, estimates of dispersal ability are provided in medfly from South Africa at three spatial scales using molecular approaches. Individuals were genotyped at 11 polymorphic microsatellite loci and a subset of individuals were also sequenced for the mitochondrial cytochrome oxidase subunit I gene. Our results show that South African medfly populations are generally characterized by high levels of genetic diversity and limited population differentiation at all spatial scales. This suggests high levels of gene flow among sampling locations. However, natural dispersal in C. capitata has been shown to rarely exceed 10 km. Therefore, documented levels of high gene flow in the present study, even between distant populations (>1600 km), are likely the result of human-mediated dispersal or at least some form of long-distance jump dispersal. These findings may have broad applicability to other global fruit production areas and have significant implications for ongoing pest management practices, such as the sterile insect technique.

Decoding auditory spatial and emotional information encoding using multivariate versus univariate techniques.

PubMed

Kryklywy, James H; Macpherson, Ewan A; Mitchell, Derek G V

2018-04-01

Emotion can have diverse effects on behaviour and perception, modulating function in some circumstances, and sometimes having little effect. Recently, it was identified that part of the heterogeneity of emotional effects could be due to a dissociable representation of emotion in dual pathway models of sensory processing. Our previous fMRI experiment using traditional univariate analyses showed that emotion modulated processing in the auditory 'what' but not 'where' processing pathway. The current study aims to further investigate this dissociation using a more recently emerging multi-voxel pattern analysis searchlight approach. While undergoing fMRI, participants localized sounds of varying emotional content. A searchlight multi-voxel pattern analysis was conducted to identify activity patterns predictive of sound location and/or emotion. Relative to the prior univariate analysis, MVPA indicated larger overlapping spatial and emotional representations of sound within early secondary regions associated with auditory localization. However, consistent with the univariate analysis, these two dimensions were increasingly segregated in late secondary and tertiary regions of the auditory processing streams. These results, while complimentary to our original univariate analyses, highlight the utility of multiple analytic approaches for neuroimaging, particularly for neural processes with known representations dependent on population coding.

Forest Ecosystem Analysis Using a GIS

Treesearch

S.G. McNulty; W.T. Swank

1996-01-01

Forest ecosystem studies have expanded spatially in recent years to address large scale environmental issues. We are using a geographic information system (GIS) to understand and integrate forest processes at landscape to regional spatial scales. This paper presents three diverse research studies using a GIS. First, we used a GIS to develop a landscape scale model to...

Implementing a High School Level Geospatial Technologies and Spatial Thinking Course

ERIC Educational Resources Information Center

Nielsen, Curtis P.; Oberle, Alex; Sugumaran, Ramanathan

2011-01-01

Understanding geospatial technologies (GSTs) and spatial thinking is increasingly vital to contemporary life including common activities and hobbies; learning in science, mathematics, and social science; and employment within fields as diverse as engineering, health, business, and planning. As such, there is a need for a stand-alone K-12…

Use of inverse spatial conservation prioritization to avoid biological diversity loss outside protected areas.

PubMed

Kareksela, Santtu; Moilanen, Atte; Tuominen, Seppo; Kotiaho, Janne S

2013-12-01

Globally expanding human land use sets constantly increasing pressure for maintenance of biological diversity and functioning ecosystems. To fight the decline of biological diversity, conservation science has broken ground with methods such as the operational model of systematic conservation planning (SCP), which focuses on design and on-the-ground implementation of conservation areas. The most commonly used method in SCP is reserve selection that focuses on the spatial design of reserve networks and their expansion. We expanded these methods by introducing another form of spatial allocation of conservation effort relevant for land-use zoning at the landscape scale that avoids negative ecological effects of human land use outside protected areas. We call our method inverse spatial conservation prioritization. It can be used to identify areas suitable for economic development while simultaneously limiting total ecological and environmental effects of that development at the landscape level by identifying areas with highest economic but lowest ecological value. Our method is not based on a priori targets, and as such it is applicable to cases where the effects of land use on, for example, individual species or ecosystem types are relatively small and would not lead to violation of regional or national conservation targets. We applied our method to land-use allocation to peat mining. Our method identified a combination of profitable production areas that provides the needed area for peat production while retaining most of the landscape-level ecological value of the ecosystem. The results of this inverse spatial conservation prioritization are being used in land-use zoning in the province of Central Finland. © 2013 Society for Conservation Biology.

Over 150 years of long-term fertilization alters spatial scaling of microbial biodiversity

DOE PAGES

Liang, Yuting; Wu, Liyou; Clark, Ian M.; ...

2015-04-07

Spatial scaling is a critical issue in ecology, but how anthropogenic activities like fertilization affect spatial scaling is poorly understood, especially for microbial communities. Here, we determined the effects of long-term fertilization on the spatial scaling of microbial functional diversity and its relationships to plant diversity in the 150-year-old Park Grass Experiment, the oldest continuous grassland experiment in the world. Nested samples were taken from plots with contrasting inorganic fertilization regimes, and community DNAs were analyzed using the GeoChip-based functional gene array. The slopes of microbial gene-area relationships (GARs) and plant species-area relationships (SARs) were estimated in a plot receivingmore » nitrogen (N), phosphorus (P), and potassium (K) and a control plot without fertilization. Our results indicated that long-term inorganic fertilization significantly increased both microbial GARs and plant SARs. Microbial spatial turnover rates (i.e., z values) were less than 0.1 and were significantly higher in the fertilized plot (0.0583) than in the control plot (0.0449) (P < 0.0001). The z values also varied significantly with different functional genes involved in carbon (C), N, P, and sulfur (S) cycling and with various phylogenetic groups (archaea, bacteria, and fungi). Similarly, the plant SARs increased significantly (P < 0.0001), from 0.225 in the control plot to 0.419 in the fertilized plot. Soil fertilization, plant diversity, and spatial distance had roughly equal contributions in shaping the microbial functional community structure, while soil geochemical variables contributed less. These results indicated that long-term agricultural practice could alter the spatial scaling of microbial biodiversity. Determining the spatial scaling of microbial biodiversity and its response to human activities is important but challenging in microbial ecology. Most studies to date are based on different sites that may not be truly comparable or on short-term perturbations, and hence, the results observed could represent transient responses. This study examined the spatial patterns of microbial communities in response to different fertilization regimes at the Rothamsted Research Experimental Station, which has become an invaluable resource for ecologists, environmentalists, and soil scientists. The current study is the first showing that long-term fertilization has dramatic impacts on the spatial scaling of microbial communities. By identifying the spatial patterns in response to long-term fertilization and their underlying mechanisms, this study makes fundamental contributions to predictive understanding of microbial biogeography.« less